HEADER DNA BINDING PROTEIN/DNA 15-JUL-18 6E3X TITLE STRUCTURE OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 8OA IN THE TITLE 2 TEMPLATE BASE PAIRED WITH INCOMING NON-HYDROLYZABLE ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*(A38) COMPND 8 P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606 KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX, DNA BINDING PROTEIN, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.-C.KOAG,S.LEE REVDAT 3 11-OCT-23 6E3X 1 LINK REVDAT 2 18-DEC-19 6E3X 1 REMARK REVDAT 1 03-APR-19 6E3X 0 JRNL AUTH M.-C.KOAG,S.LEE JRNL TITL STRUCTURE OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 8OA IN JRNL TITL 2 THE TEMPLATE BASE PAIRED WITH INCOMING NON-HYDROLYZABLE ATP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 12817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.7376 - 4.1484 0.99 3259 156 0.1591 0.1968 REMARK 3 2 4.1484 - 3.2977 0.99 3201 150 0.1841 0.2683 REMARK 3 3 3.2977 - 2.8823 0.96 3042 178 0.2388 0.3376 REMARK 3 4 2.8823 - 2.6194 0.84 2689 142 0.2511 0.3452 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 3381 REMARK 3 ANGLE : 1.170 4691 REMARK 3 CHIRALITY : 0.074 517 REMARK 3 PLANARITY : 0.004 491 REMARK 3 DIHEDRAL : 21.763 1326 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6E3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12915 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, PHASER REMARK 200 STARTING MODEL: 3ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% TO 23% PEG3400, AND 350 MM SODIUM REMARK 280 ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.47400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.126 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 10 21.02 -75.81 REMARK 500 PRO A 50 31.62 -81.04 REMARK 500 ASN A 128 50.03 -114.40 REMARK 500 ASP A 170 112.73 -164.64 REMARK 500 CYS A 178 -136.56 -97.77 REMARK 500 PRO A 198 5.70 -68.37 REMARK 500 ASN A 245 -122.72 47.49 REMARK 500 ALA A 286 -60.92 85.51 REMARK 500 GLN A 324 52.41 35.09 REMARK 500 ARG A 333 35.16 -85.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 79.5 REMARK 620 3 VAL A 65 O 74.6 74.1 REMARK 620 4 DC D 3 OP1 153.6 78.6 85.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 99.5 REMARK 620 3 ILE A 106 O 89.9 80.7 REMARK 620 4 HOH A 555 O 88.1 99.6 178.0 REMARK 620 5 DG P 9 OP1 159.4 100.4 88.0 93.9 REMARK 620 6 HOH P 102 O 76.5 150.8 70.5 109.1 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 91.2 REMARK 620 3 DZ4 A 405 O1G 85.1 172.2 REMARK 620 4 DZ4 A 405 O2A 98.3 87.3 86.4 REMARK 620 5 DZ4 A 405 O2B 166.9 100.6 82.5 76.9 REMARK 620 6 HOH A 507 O 100.0 96.0 91.4 161.3 84.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 93.3 REMARK 620 3 DZ4 A 405 O2A 80.6 90.0 REMARK 620 4 DA P 10 O3' 99.6 166.8 94.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DZ4 A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XK3 RELATED DB: PDB REMARK 900 RELATED ID: 4XK5 RELATED DB: PDB REMARK 900 RELATED ID: 4XK6 RELATED DB: PDB DBREF 6E3X A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 6E3X T 1 16 PDB 6E3X 6E3X 1 16 DBREF 6E3X P 1 10 PDB 6E3X 6E3X 1 10 DBREF 6E3X D 1 5 PDB 6E3X 6E3X 1 5 SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC A38 DT DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA SEQRES 1 D 5 DG DT DC DG DG HET A38 T 6 22 HET NA A 401 1 HET NA A 402 1 HET MG A 403 1 HET MG A 404 1 HET DZ4 A 405 30 HETNAM A38 8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE FORMUL 2 A38 C10 H14 N5 O7 P FORMUL 5 NA 2(NA 1+) FORMUL 7 MG 2(MG 2+) FORMUL 9 DZ4 C10 H17 N6 O11 P3 FORMUL 10 HOH *81(H2 O) HELIX 1 AA1 GLN A 8 LEU A 11 5 4 HELIX 2 AA2 ASN A 12 VAL A 29 1 18 HELIX 3 AA3 ALA A 32 LYS A 48 1 17 HELIX 4 AA4 SER A 55 LYS A 60 1 6 HELIX 5 AA5 GLY A 66 GLY A 80 1 15 HELIX 6 AA6 LEU A 82 ASP A 91 1 10 HELIX 7 AA7 ASP A 91 THR A 101 1 11 HELIX 8 AA8 GLY A 107 GLU A 117 1 11 HELIX 9 AA9 THR A 121 ASN A 128 1 8 HELIX 10 AB1 GLU A 129 LEU A 132 5 4 HELIX 11 AB2 ASN A 133 TYR A 142 1 10 HELIX 12 AB3 TYR A 142 GLU A 147 1 6 HELIX 13 AB4 ARG A 152 ASP A 170 1 19 HELIX 14 AB5 CYS A 178 ARG A 183 1 6 HELIX 15 AB6 PRO A 208 VAL A 221 1 14 HELIX 16 AB7 PRO A 261 ASP A 263 5 3 HELIX 17 AB8 GLN A 264 GLY A 274 1 11 HELIX 18 AB9 SER A 275 HIS A 285 1 11 HELIX 19 AC1 SER A 315 ILE A 323 1 9 HELIX 20 AC2 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 AA3 2 PHE A 291 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P A38 T 6 1555 1555 1.61 LINK O3' A38 T 6 P DT T 7 1555 1555 1.61 LINK O LYS A 60 NA NA A 401 1555 1555 2.50 LINK O LEU A 62 NA NA A 401 1555 1555 3.18 LINK O VAL A 65 NA NA A 401 1555 1555 2.77 LINK O THR A 101 NA NA A 402 1555 1555 2.30 LINK O VAL A 103 NA NA A 402 1555 1555 2.42 LINK O ILE A 106 NA NA A 402 1555 1555 2.52 LINK OD1 ASP A 190 MG MG A 403 1555 1555 1.99 LINK OD2 ASP A 190 MG MG A 404 1555 1555 2.45 LINK OD2 ASP A 192 MG MG A 403 1555 1555 2.10 LINK OD1 ASP A 192 MG MG A 404 1555 1555 2.13 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.59 LINK NA NA A 402 O HOH A 555 1555 1555 2.68 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.29 LINK NA NA A 402 O HOH P 102 1555 1555 2.57 LINK MG MG A 403 O1G DZ4 A 405 1555 1555 2.02 LINK MG MG A 403 O2A DZ4 A 405 1555 1555 2.01 LINK MG MG A 403 O2B DZ4 A 405 1555 1555 1.99 LINK MG MG A 403 O HOH A 507 1555 1555 1.94 LINK MG MG A 404 O2A DZ4 A 405 1555 1555 2.62 LINK MG MG A 404 O3' DA P 10 1555 1555 2.36 CISPEP 1 GLY A 274 SER A 275 0 -0.70 CISPEP 2 HIS A 285 ALA A 286 0 24.05 CISPEP 3 LEU A 301 GLY A 302 0 13.97 SITE 1 AC1 4 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 1 AC2 7 THR A 101 VAL A 103 SER A 104 ILE A 106 SITE 2 AC2 7 HOH A 555 DG P 9 HOH P 102 SITE 1 AC3 4 ASP A 190 ASP A 192 DZ4 A 405 HOH A 507 SITE 1 AC4 4 ASP A 190 ASP A 192 DZ4 A 405 DA P 10 SITE 1 AC5 18 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC5 18 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AC5 18 TYR A 271 PHE A 272 GLY A 274 ASP A 276 SITE 4 AC5 18 ASN A 279 MG A 403 MG A 404 HOH A 507 SITE 5 AC5 18 DA P 10 A38 T 6 CRYST1 54.964 78.948 54.823 90.00 106.53 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018194 0.000000 0.005401 0.00000 SCALE2 0.000000 0.012667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019027 0.00000 TER 2594 GLU A 335 HETATM 2692 P A38 T 6 21.137 1.234 0.109 1.00 53.61 P HETATM 2693 O1P A38 T 6 21.204 1.245 -1.400 1.00 35.73 O HETATM 2694 O2P A38 T 6 20.808 -0.050 0.834 1.00 57.19 O HETATM 2695 O5' A38 T 6 20.087 2.358 0.572 1.00 45.26 O HETATM 2696 C5' A38 T 6 19.222 2.129 1.678 1.00 40.92 C HETATM 2697 C4' A38 T 6 17.922 2.866 1.408 1.00 45.71 C HETATM 2698 O4' A38 T 6 17.003 2.646 2.473 1.00 54.01 O HETATM 2699 C3' A38 T 6 18.149 4.363 1.352 1.00 47.83 C HETATM 2700 O3' A38 T 6 17.168 4.865 0.441 1.00 44.86 O HETATM 2701 C2' A38 T 6 17.860 4.859 2.756 1.00 46.66 C HETATM 2702 C1' A38 T 6 16.926 3.796 3.320 1.00 49.47 C HETATM 2703 N9 A38 T 6 17.214 3.366 4.713 1.00 46.89 N HETATM 2704 C8 A38 T 6 18.360 3.134 5.371 1.00 48.34 C HETATM 2705 N7 A38 T 6 18.239 2.734 6.648 1.00 45.10 N HETATM 2706 C5 A38 T 6 16.912 2.690 6.853 1.00 48.47 C HETATM 2707 C6 A38 T 6 16.013 2.347 7.982 1.00 38.02 C HETATM 2708 N6 A38 T 6 16.510 1.959 9.180 1.00 36.40 N HETATM 2709 N1 A38 T 6 14.678 2.432 7.782 1.00 37.76 N HETATM 2710 C2 A38 T 6 14.156 2.812 6.603 1.00 43.20 C HETATM 2711 N3 A38 T 6 14.903 3.137 5.536 1.00 41.31 N HETATM 2712 C4 A38 T 6 16.254 3.100 5.595 1.00 44.85 C HETATM 2713 O A38 T 6 19.520 3.285 4.836 1.00 50.47 O TER 2916 DC T 16 TER 3122 DA P 10 TER 3229 DG D 5 HETATM 3230 NA NA A 401 32.070 -10.501 -3.491 1.00 35.10 NA HETATM 3231 NA NA A 402 19.427 2.103 22.237 1.00 17.25 NA HETATM 3232 MG MG A 403 7.082 -4.725 13.750 1.00 8.12 MG HETATM 3233 MG MG A 404 8.063 -1.013 13.951 1.00 28.30 MG HETATM 3234 N1 DZ4 A 405 13.636 -0.882 4.536 1.00 37.30 N HETATM 3235 C2 DZ4 A 405 12.362 -1.143 3.996 1.00 36.52 C HETATM 3236 N3 DZ4 A 405 11.310 -1.274 4.900 1.00 36.77 N HETATM 3237 C4 DZ4 A 405 11.542 -1.145 6.226 1.00 37.70 C HETATM 3238 C5 DZ4 A 405 12.778 -0.899 6.708 1.00 36.72 C HETATM 3239 C6 DZ4 A 405 13.811 -0.774 5.857 1.00 35.16 C HETATM 3240 N6 DZ4 A 405 15.015 -0.531 6.360 1.00 33.09 N HETATM 3241 N7 DZ4 A 405 12.685 -0.819 8.041 1.00 35.28 N HETATM 3242 C8 DZ4 A 405 11.410 -1.015 8.384 1.00 36.73 C HETATM 3243 N9 DZ4 A 405 10.699 -1.209 7.264 1.00 37.41 N HETATM 3244 PA DZ4 A 405 9.454 -3.355 11.888 1.00 33.21 P HETATM 3245 PB DZ4 A 405 8.707 -6.097 11.336 1.00 28.21 P HETATM 3246 PG DZ4 A 405 9.224 -7.149 13.877 1.00 29.73 P HETATM 3247 C1' DZ4 A 405 9.226 -1.502 7.109 1.00 34.24 C HETATM 3248 O1A DZ4 A 405 10.817 -2.661 12.370 1.00 32.60 O HETATM 3249 O1B DZ4 A 405 8.468 -6.768 9.821 1.00 25.50 O HETATM 3250 O1G DZ4 A 405 8.679 -5.832 14.315 1.00 28.27 O HETATM 3251 C2' DZ4 A 405 9.047 -2.964 6.728 1.00 33.00 C HETATM 3252 O2A DZ4 A 405 8.413 -3.425 12.982 1.00 32.06 O HETATM 3253 O2B DZ4 A 405 7.500 -5.505 11.972 1.00 27.24 O HETATM 3254 O2G DZ4 A 405 8.451 -8.419 14.498 1.00 31.05 O HETATM 3255 C3' DZ4 A 405 8.836 -3.619 8.049 1.00 31.14 C HETATM 3256 O3' DZ4 A 405 8.236 -4.908 7.874 1.00 28.88 O HETATM 3257 N3A DZ4 A 405 9.958 -4.906 11.197 1.00 28.60 N HETATM 3258 O3B DZ4 A 405 9.174 -7.337 12.265 1.00 27.90 O HETATM 3259 O3G DZ4 A 405 10.708 -7.454 14.402 1.00 29.48 O HETATM 3260 C4' DZ4 A 405 7.838 -2.637 8.594 1.00 31.88 C HETATM 3261 O4' DZ4 A 405 8.468 -1.365 8.338 1.00 33.47 O HETATM 3262 C5' DZ4 A 405 7.705 -2.784 10.111 1.00 31.37 C HETATM 3263 O5' DZ4 A 405 8.946 -2.426 10.725 1.00 31.49 O HETATM 3264 O HOH A 501 20.158 -0.473 20.379 1.00 24.72 O HETATM 3265 O HOH A 502 -5.837 18.022 7.027 1.00 36.91 O HETATM 3266 O HOH A 503 -18.228 2.588 16.915 1.00 24.98 O HETATM 3267 O HOH A 504 4.666 1.504 -0.480 1.00 27.50 O HETATM 3268 O HOH A 505 -7.807 -3.328 -7.082 1.00 55.76 O HETATM 3269 O HOH A 506 37.402 2.968 8.581 1.00 19.92 O HETATM 3270 O HOH A 507 5.901 -6.250 13.931 1.00 22.42 O HETATM 3271 O HOH A 508 2.726 -4.956 13.717 1.00 22.83 O HETATM 3272 O HOH A 509 3.077 -12.030 15.460 1.00 27.82 O HETATM 3273 O HOH A 510 10.334 11.727 24.973 1.00 17.94 O HETATM 3274 O HOH A 511 5.643 1.212 12.876 1.00 30.65 O HETATM 3275 O HOH A 512 0.962 -6.860 27.059 1.00 32.13 O HETATM 3276 O HOH A 513 13.627 4.466 34.514 1.00 22.07 O HETATM 3277 O HOH A 514 -5.289 -12.218 28.783 1.00 27.87 O HETATM 3278 O HOH A 515 22.762 -16.334 -0.222 1.00 27.54 O HETATM 3279 O HOH A 516 -5.739 -4.660 11.894 1.00 24.30 O HETATM 3280 O HOH A 517 -14.988 11.941 15.686 1.00 27.56 O HETATM 3281 O HOH A 518 13.388 6.831 -17.367 1.00 38.18 O HETATM 3282 O HOH A 519 7.151 9.568 16.813 1.00 32.54 O HETATM 3283 O HOH A 520 -5.123 -10.360 40.877 1.00 57.09 O HETATM 3284 O HOH A 521 -9.293 -10.603 23.309 1.00 29.98 O HETATM 3285 O HOH A 522 40.143 -18.112 1.649 1.00 25.73 O HETATM 3286 O HOH A 523 30.403 5.691 20.623 1.00 22.58 O HETATM 3287 O HOH A 524 16.554 9.360 -14.844 1.00 59.07 O HETATM 3288 O HOH A 525 -0.069 -17.594 10.582 1.00 25.63 O HETATM 3289 O HOH A 526 -16.141 -1.531 11.273 1.00 18.05 O HETATM 3290 O HOH A 527 -9.914 10.978 22.878 1.00 28.45 O HETATM 3291 O HOH A 528 15.563 -1.558 -4.281 1.00 49.67 O HETATM 3292 O HOH A 529 15.174 -0.434 26.365 1.00 21.54 O HETATM 3293 O HOH A 530 -3.771 -15.842 13.763 1.00 25.23 O HETATM 3294 O HOH A 531 33.326 -28.946 -1.070 1.00 27.54 O HETATM 3295 O HOH A 532 22.238 -9.344 9.279 1.00 22.93 O HETATM 3296 O HOH A 533 36.069 -14.395 18.199 1.00 30.28 O HETATM 3297 O HOH A 534 -8.497 -1.926 0.545 1.00 35.16 O HETATM 3298 O HOH A 535 30.366 4.391 8.060 1.00 17.93 O HETATM 3299 O HOH A 536 43.329 -14.323 7.942 1.00 25.47 O HETATM 3300 O HOH A 537 35.688 9.684 34.347 1.00 33.50 O HETATM 3301 O HOH A 538 7.757 -5.256 22.870 1.00 30.27 O HETATM 3302 O HOH A 539 8.940 0.700 -7.712 1.00 60.34 O HETATM 3303 O HOH A 540 39.131 0.092 28.338 1.00 33.56 O HETATM 3304 O HOH A 541 21.279 -19.714 10.128 1.00 46.76 O HETATM 3305 O HOH A 542 40.873 -8.607 10.698 1.00 23.87 O HETATM 3306 O HOH A 543 4.230 -13.290 28.584 1.00 21.35 O HETATM 3307 O HOH A 544 -2.936 -13.572 32.893 1.00 53.56 O HETATM 3308 O HOH A 545 8.548 -17.387 16.361 1.00 32.28 O HETATM 3309 O HOH A 546 33.557 -7.011 29.305 1.00 28.66 O HETATM 3310 O HOH A 547 9.553 6.852 1.639 1.00 40.73 O HETATM 3311 O HOH A 548 38.046 -24.218 13.959 1.00 28.53 O HETATM 3312 O HOH A 549 -4.438 0.990 -10.800 1.00 34.20 O HETATM 3313 O HOH A 550 -19.155 6.445 15.903 1.00 31.16 O HETATM 3314 O HOH A 551 2.667 -13.967 31.364 1.00 42.06 O HETATM 3315 O HOH A 552 18.253 14.738 30.214 1.00 32.67 O HETATM 3316 O HOH A 553 25.556 -6.273 24.827 1.00 26.49 O HETATM 3317 O HOH A 554 3.509 -8.269 38.279 1.00 45.20 O HETATM 3318 O HOH A 555 17.676 0.148 21.688 1.00 22.12 O HETATM 3319 O HOH A 556 5.239 16.464 -9.889 1.00 41.57 O HETATM 3320 O HOH A 557 -3.688 -17.114 5.335 1.00 49.82 O HETATM 3321 O HOH A 558 17.446 -2.935 2.610 1.00 35.91 O HETATM 3322 O HOH T 101 12.875 12.031 25.422 1.00 22.92 O HETATM 3323 O HOH T 102 13.494 14.527 28.994 1.00 17.47 O HETATM 3324 O HOH T 103 15.077 20.926 26.783 1.00 42.12 O HETATM 3325 O HOH T 104 17.108 25.056 23.363 1.00 28.56 O HETATM 3326 O HOH T 105 16.162 14.044 21.463 1.00 30.85 O HETATM 3327 O HOH T 106 17.679 8.562 3.024 1.00 50.33 O HETATM 3328 O HOH T 107 20.697 27.884 23.979 1.00 30.58 O HETATM 3329 O HOH T 108 16.876 -0.273 3.439 1.00 41.36 O HETATM 3330 O HOH T 109 7.489 13.887 24.337 1.00 22.98 O HETATM 3331 O HOH T 110 9.150 16.183 9.684 1.00 31.91 O HETATM 3332 O HOH T 111 26.200 -0.349 -0.678 1.00 21.72 O HETATM 3333 O HOH T 112 18.879 -2.481 0.061 1.00 33.98 O HETATM 3334 O HOH T 113 5.122 17.917 21.203 1.00 34.66 O HETATM 3335 O HOH P 101 19.014 28.273 13.148 1.00 31.72 O HETATM 3336 O HOH P 102 20.973 2.435 20.216 1.00 17.66 O HETATM 3337 O HOH P 103 12.466 0.910 21.621 1.00 20.42 O HETATM 3338 O HOH P 104 20.384 13.529 11.914 1.00 19.37 O HETATM 3339 O HOH P 105 21.750 11.247 23.339 1.00 27.50 O HETATM 3340 O HOH P 106 27.571 14.601 12.978 1.00 29.05 O HETATM 3341 O HOH D 101 36.090 -3.407 10.525 1.00 22.36 O HETATM 3342 O HOH D 102 29.799 2.933 -8.100 1.00 29.26 O HETATM 3343 O HOH D 103 28.123 0.824 -5.944 1.00 25.35 O HETATM 3344 O HOH D 104 30.559 5.702 -16.416 1.00 40.63 O CONECT 405 3230 CONECT 423 3230 CONECT 442 3230 CONECT 727 3231 CONECT 745 3231 CONECT 762 3231 CONECT 1441 3232 CONECT 1442 3233 CONECT 1457 3233 CONECT 1458 3232 CONECT 2681 2692 CONECT 2692 2681 2693 2694 2695 CONECT 2693 2692 CONECT 2694 2692 CONECT 2695 2692 2696 CONECT 2696 2695 2697 CONECT 2697 2696 2698 2699 CONECT 2698 2697 2702 CONECT 2699 2697 2700 2701 CONECT 2700 2699 2714 CONECT 2701 2699 2702 CONECT 2702 2698 2701 2703 CONECT 2703 2702 2704 2712 CONECT 2704 2703 2705 2713 CONECT 2705 2704 2706 CONECT 2706 2705 2707 2712 CONECT 2707 2706 2708 2709 CONECT 2708 2707 CONECT 2709 2707 2710 CONECT 2710 2709 2711 CONECT 2711 2710 2712 CONECT 2712 2703 2706 2711 CONECT 2713 2704 CONECT 2714 2700 CONECT 3080 3231 CONECT 3109 3233 CONECT 3167 3230 CONECT 3230 405 423 442 3167 CONECT 3231 727 745 762 3080 CONECT 3231 3318 3336 CONECT 3232 1441 1458 3250 3252 CONECT 3232 3253 3270 CONECT 3233 1442 1457 3109 3252 CONECT 3234 3235 3239 CONECT 3235 3234 3236 CONECT 3236 3235 3237 CONECT 3237 3236 3238 3243 CONECT 3238 3237 3239 3241 CONECT 3239 3234 3238 3240 CONECT 3240 3239 CONECT 3241 3238 3242 CONECT 3242 3241 3243 CONECT 3243 3237 3242 3247 CONECT 3244 3248 3252 3257 3263 CONECT 3245 3249 3253 3257 3258 CONECT 3246 3250 3254 3258 3259 CONECT 3247 3243 3251 3261 CONECT 3248 3244 CONECT 3249 3245 CONECT 3250 3232 3246 CONECT 3251 3247 3255 CONECT 3252 3232 3233 3244 CONECT 3253 3232 3245 CONECT 3254 3246 CONECT 3255 3251 3256 3260 CONECT 3256 3255 CONECT 3257 3244 3245 CONECT 3258 3245 3246 CONECT 3259 3246 CONECT 3260 3255 3261 3262 CONECT 3261 3247 3260 CONECT 3262 3260 3263 CONECT 3263 3244 3262 CONECT 3270 3232 CONECT 3318 3231 CONECT 3336 3231 MASTER 333 0 6 20 9 0 10 6 3340 4 76 30 END