HEADER TRANSFERASE 11-JUL-16 5KT7 TITLE TERANRY COMPLEX OF HUMAN DNA POLYMERASE IOTA(1-445) INSERTING DCMPNPP TITLE 2 OPPOSITE TEMPLATE G IN THE PRESENCE OF MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'); COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE IOTA; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: ETA2,RAD30 HOMOLOG B; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: POLI, RAD30B; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, POLI, MANGANESE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.CHOI,A.PATRA,M.YEOM,Y.S.LEE,Q.ZHANG,M.EGLI,F.P.GUENGERICH REVDAT 6 06-MAR-24 5KT7 1 LINK REVDAT 5 18-DEC-19 5KT7 1 REMARK REVDAT 4 13-SEP-17 5KT7 1 JRNL REMARK REVDAT 3 19-OCT-16 5KT7 1 JRNL REVDAT 2 07-SEP-16 5KT7 1 JRNL REVDAT 1 31-AUG-16 5KT7 0 JRNL AUTH J.Y.CHOI,A.PATRA,M.YEOM,Y.S.LEE,Q.ZHANG,M.EGLI, JRNL AUTH 2 F.P.GUENGERICH JRNL TITL KINETIC AND STRUCTURAL IMPACT OF METAL IONS AND GENETIC JRNL TITL 2 VARIATIONS ON HUMAN DNA POLYMERASE IOTA. JRNL REF J.BIOL.CHEM. V. 291 21063 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27555320 JRNL DOI 10.1074/JBC.M116.748285 REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10450 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.520 REMARK 3 FREE R VALUE TEST SET COUNT : 577 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 48.8759 - 5.0005 1.00 2636 141 0.2110 0.2166 REMARK 3 2 5.0005 - 3.9696 1.00 2470 136 0.1817 0.2143 REMARK 3 3 3.9696 - 3.4680 1.00 2396 153 0.2026 0.2371 REMARK 3 4 3.4680 - 3.1510 1.00 2371 147 0.2212 0.3096 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.37 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 : 0.004 3382 REMARK 3 ANGLE : 0.676 4652 REMARK 3 CHIRALITY : 0.043 549 REMARK 3 PLANARITY : 0.005 538 REMARK 3 DIHEDRAL : 17.467 2016 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 5KT7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10495 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 20.80 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 21.10 REMARK 200 R MERGE FOR SHELL (I) : 0.81100 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG MME 5000, 0.1M MES BUFFER, REMARK 280 0.3M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 134.67533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.33767 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.00650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.66883 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 168.34417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 134.67533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.33767 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.66883 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.00650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 168.34417 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, A 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 -24 REMARK 465 GLU A -23 REMARK 465 LYS A -22 REMARK 465 LEU A -21 REMARK 465 GLY A -20 REMARK 465 VAL A -19 REMARK 465 GLU A -18 REMARK 465 PRO A -17 REMARK 465 GLU A -16 REMARK 465 GLU A -15 REMARK 465 GLU A -14 REMARK 465 GLY A -13 REMARK 465 GLY A -12 REMARK 465 GLY A -11 REMARK 465 ASP A -10 REMARK 465 ASP A -9 REMARK 465 ASP A -8 REMARK 465 GLU A -7 REMARK 465 GLU A -6 REMARK 465 ASP A -5 REMARK 465 ALA A -4 REMARK 465 GLU A -3 REMARK 465 ALA A -2 REMARK 465 TRP A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 GLY A 14 REMARK 465 VAL A 15 REMARK 465 HIS A 16 REMARK 465 ASP A 17 REMARK 465 GLN A 18 REMARK 465 VAL A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 THR A 22 REMARK 465 PRO A 23 REMARK 465 ASN A 24 REMARK 465 ALA A 25 REMARK 465 SER A 350 REMARK 465 SER A 351 REMARK 465 GLU A 352 REMARK 465 LYS A 353 REMARK 465 HIS A 354 REMARK 465 TYR A 355 REMARK 465 GLY A 373 REMARK 465 THR A 374 REMARK 465 GLY A 375 REMARK 465 ASN A 376 REMARK 465 ALA A 415 REMARK 465 LEU A 416 REMARK 465 ASN A 417 REMARK 465 THR A 418 REMARK 465 ALA A 419 REMARK 465 LYS A 420 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 ARG A 101 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 138 CD CE NZ REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 LYS A 338 CG CD CE NZ REMARK 470 TYR A 349 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 370 CG CD OE1 NE2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 TYR A 377 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 385 CG OD1 OD2 REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 LYS A 398 CG CD CE NZ REMARK 470 MET A 399 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 161 OG SER A 225 2.12 REMARK 500 OP1 DC P 873 NZ LYS A 207 2.18 REMARK 500 NE2 GLN A 161 OE1 GLU A 224 2.18 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 CYS A 37 59.75 32.91 REMARK 500 LYS A 60 -121.81 57.92 REMARK 500 MET A 380 -71.58 -47.40 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 MN P 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 873 O3' REMARK 620 2 ASP A 34 OD1 132.8 REMARK 620 3 ASP A 126 OD1 110.3 90.0 REMARK 620 4 GLU A 127 OE2 74.3 64.3 87.4 REMARK 620 5 0KX A 501 O2A 117.9 93.4 107.6 153.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD2 REMARK 620 2 LEU A 35 O 85.0 REMARK 620 3 ASP A 126 OD2 96.7 99.6 REMARK 620 4 0KX A 501 O1G 79.2 101.9 157.7 REMARK 620 5 0KX A 501 O2B 156.0 91.2 107.3 78.5 REMARK 620 6 0KX A 501 O2A 107.7 167.2 80.6 79.8 76.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0KX A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KT2 RELATED DB: PDB REMARK 900 RELATED ID: 5KT3 RELATED DB: PDB REMARK 900 RELATED ID: 5KT4 RELATED DB: PDB REMARK 900 RELATED ID: 5KT5 RELATED DB: PDB REMARK 900 RELATED ID: 5KT6 RELATED DB: PDB DBREF 5KT7 T 838 847 PDB 5KT7 5KT7 838 847 DBREF 5KT7 P 867 873 PDB 5KT7 5KT7 867 873 DBREF 5KT7 A -24 420 UNP Q9UNA4 POLI_HUMAN 1 445 SEQRES 1 T 10 DC DT DG DG DG DG DT DC DC DT SEQRES 1 P 7 DA DG DG DA DC DC DC SEQRES 1 A 445 MET GLU LYS LEU GLY VAL GLU PRO GLU GLU GLU GLY GLY SEQRES 2 A 445 GLY ASP ASP ASP GLU GLU ASP ALA GLU ALA TRP ALA MET SEQRES 3 A 445 GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN GLY SEQRES 4 A 445 VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER SER SEQRES 5 A 445 ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR ALA SEQRES 6 A 445 GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP LYS SEQRES 7 A 445 PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR CYS SEQRES 8 A 445 ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU MET SEQRES 9 A 445 ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU VAL SEQRES 10 A 445 LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU MET SEQRES 11 A 445 SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER PRO SEQRES 12 A 445 VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL ASP SEQRES 13 A 445 LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU GLN SEQRES 14 A 445 SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS VAL SEQRES 15 A 445 TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU HIS SEQRES 16 A 445 ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU MET SEQRES 17 A 445 ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY CYS SEQRES 18 A 445 ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU VAL SEQRES 19 A 445 SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU LEU SEQRES 20 A 445 PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN HIS SEQRES 21 A 445 ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA LYS SEQRES 22 A 445 CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP LEU SEQRES 23 A 445 GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU GLY SEQRES 24 A 445 ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE GLY SEQRES 25 A 445 GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO GLN SEQRES 26 A 445 SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SER SEQRES 27 A 445 GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU ALA SEQRES 28 A 445 SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS PRO SEQRES 29 A 445 HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER GLU SEQRES 30 A 445 LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE PRO SEQRES 31 A 445 SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR ASP SEQRES 32 A 445 VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU PHE SEQRES 33 A 445 ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU THR SEQRES 34 A 445 LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU ASN SEQRES 35 A 445 THR ALA LYS HET MN P 901 1 HET 0KX A 501 28 HET MN A 502 1 HETNAM MN MANGANESE (II) ION HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE FORMUL 4 MN 2(MN 2+) FORMUL 5 0KX C9 H17 N4 O12 P3 HELIX 1 AA1 CYS A 37 ASN A 47 1 11 HELIX 2 AA2 PRO A 48 LYS A 51 5 4 HELIX 3 AA3 ASN A 67 LEU A 73 1 7 HELIX 4 AA4 VAL A 81 CYS A 88 1 8 HELIX 5 AA5 LEU A 99 SER A 117 1 19 HELIX 6 AA6 LEU A 132 LEU A 143 1 12 HELIX 7 AA7 GLN A 144 SER A 149 1 6 HELIX 8 AA8 ASN A 159 GLN A 161 5 3 HELIX 9 AA9 ASP A 167 GLY A 192 1 26 HELIX 10 AB1 ASN A 202 GLY A 211 1 10 HELIX 11 AB2 LEU A 222 GLU A 224 5 3 HELIX 12 AB3 SER A 225 SER A 232 1 8 HELIX 13 AB4 HIS A 235 ILE A 239 5 5 HELIX 14 AB5 GLY A 243 ALA A 252 1 10 HELIX 15 AB6 SER A 257 PHE A 264 1 8 HELIX 16 AB7 SER A 265 GLY A 274 1 10 HELIX 17 AB8 GLY A 274 PHE A 286 1 13 HELIX 18 AB9 SER A 313 GLY A 336 1 24 HELIX 19 AC1 PRO A 365 LEU A 372 1 8 HELIX 20 AC2 VAL A 379 VAL A 395 1 17 SHEET 1 AA1 6 VAL A 120 LEU A 123 0 SHEET 2 AA1 6 GLU A 127 ASP A 131 -1 O PHE A 129 N GLU A 121 SHEET 3 AA1 6 ILE A 30 LEU A 35 -1 N VAL A 33 O ASN A 128 SHEET 4 AA1 6 GLY A 195 ALA A 200 -1 O ALA A 200 N ILE A 30 SHEET 5 AA1 6 GLN A 218 VAL A 220 1 O THR A 219 N ALA A 197 SHEET 6 AA1 6 HIS A 156 VAL A 157 1 N HIS A 156 O GLN A 218 SHEET 1 AA2 4 MET A 79 ASN A 80 0 SHEET 2 AA2 4 LEU A 62 CYS A 66 -1 N VAL A 63 O MET A 79 SHEET 3 AA2 4 LEU A 55 GLN A 59 -1 N VAL A 57 O THR A 65 SHEET 4 AA2 4 VAL A 92 ASN A 95 1 O VAL A 92 N GLY A 56 SHEET 1 AA3 4 SER A 301 SER A 307 0 SHEET 2 AA3 4 LEU A 403 LYS A 414 -1 O PHE A 410 N PHE A 302 SHEET 3 AA3 4 LYS A 338 ARG A 348 -1 N ARG A 347 O THR A 404 SHEET 4 AA3 4 ARG A 357 CYS A 362 -1 O CYS A 362 N VAL A 342 LINK O3' DC P 873 MN MN P 901 1555 1555 1.85 LINK MN MN P 901 OD1 ASP A 34 1555 1555 2.48 LINK MN MN P 901 OD1 ASP A 126 1555 1555 2.50 LINK MN MN P 901 OE2 GLU A 127 1555 1555 2.53 LINK MN MN P 901 O2A 0KX A 501 1555 1555 1.73 LINK OD2 ASP A 34 MN MN A 502 1555 1555 2.02 LINK O LEU A 35 MN MN A 502 1555 1555 2.12 LINK OD2 ASP A 126 MN MN A 502 1555 1555 1.99 LINK O1G 0KX A 501 MN MN A 502 1555 1555 2.31 LINK O2B 0KX A 501 MN MN A 502 1555 1555 1.87 LINK O2A 0KX A 501 MN MN A 502 1555 1555 2.27 CISPEP 1 LYS A 214 PRO A 215 0 -5.75 SITE 1 AC1 6 ASP A 34 ASP A 126 GLU A 127 0KX A 501 SITE 2 AC1 6 MN A 502 DC P 873 SITE 1 AC2 18 ASP A 34 LEU A 35 ASP A 36 CYS A 37 SITE 2 AC2 18 PHE A 38 TYR A 39 VAL A 64 THR A 65 SITE 3 AC2 18 TYR A 68 ARG A 71 LYS A 77 ASP A 126 SITE 4 AC2 18 LYS A 214 MN A 502 DC P 873 MN P 901 SITE 5 AC2 18 DG T 840 DG T 841 SITE 1 AC3 5 ASP A 34 LEU A 35 ASP A 126 0KX A 501 SITE 2 AC3 5 MN P 901 CRYST1 97.740 97.740 202.013 90.00 90.00 120.00 P 65 2 2 12 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 0.010231 0.005907 0.000000 0.00000 SCALE2 0.000000 0.011814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004950 0.00000