HEADER HYDROLASE/DNA 26-JAN-16 5HT2 TITLE MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MG2+ COMPLEX WITH TITLE 2 1-N6-ETHENO-ADENINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA COMPND 5 PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- COMPND 6 ASSOCIATED PROTEIN; COMPND 7 EC: 3.1.4.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TDP2, TTRAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG9; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PMCSG9 KEYWDS HYDROLASE, DNA REPAIR, ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE (EEP) KEYWDS 2 DOMAIN, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,C.K.VILAS,R.S.WILLIAMS REVDAT 7 13-MAR-24 5HT2 1 SOURCE REVDAT 6 18-OCT-23 5HT2 1 REMARK REVDAT 5 26-OCT-22 5HT2 1 COMPND SOURCE SEQRES LINK REVDAT 4 18-DEC-19 5HT2 1 REMARK REVDAT 3 20-SEP-17 5HT2 1 JRNL REMARK REVDAT 2 18-MAY-16 5HT2 1 JRNL REVDAT 1 27-APR-16 5HT2 0 JRNL AUTH M.J.SCHELLENBERG,L.PERERA,C.N.STROM,C.A.WATERS,B.MONIAN, JRNL AUTH 2 C.D.APPEL,C.K.VILAS,J.G.WILLIAMS,D.A.RAMSDEN,R.S.WILLIAMS JRNL TITL REVERSAL OF DNA DAMAGE INDUCED TOPOISOMERASE 2 DNA-PROTEIN JRNL TITL 2 CROSSLINKS BY TDP2. JRNL REF NUCLEIC ACIDS RES. V. 44 3829 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27060144 JRNL DOI 10.1093/NAR/GKW228 REMARK 2 REMARK 2 RESOLUTION. 1.43 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 212129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.116 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 10580 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 29.9346 - 4.4401 0.90 6406 337 0.1583 0.1732 REMARK 3 2 4.4401 - 3.5260 0.96 6856 365 0.1066 0.1344 REMARK 3 3 3.5260 - 3.0808 0.97 6853 392 0.1108 0.1334 REMARK 3 4 3.0808 - 2.7994 0.97 6964 345 0.1183 0.1503 REMARK 3 5 2.7994 - 2.5988 0.97 6874 357 0.1088 0.1468 REMARK 3 6 2.5988 - 2.4457 0.97 6939 357 0.1045 0.1452 REMARK 3 7 2.4457 - 2.3233 0.97 6927 380 0.1012 0.1458 REMARK 3 8 2.3233 - 2.2222 0.97 6927 337 0.0987 0.1441 REMARK 3 9 2.2222 - 2.1366 0.97 6932 345 0.0936 0.1335 REMARK 3 10 2.1366 - 2.0629 0.96 6879 361 0.0942 0.1154 REMARK 3 11 2.0629 - 1.9984 0.96 6802 332 0.0898 0.1224 REMARK 3 12 1.9984 - 1.9413 0.95 6769 368 0.0869 0.1340 REMARK 3 13 1.9413 - 1.8902 0.96 6809 374 0.0951 0.1475 REMARK 3 14 1.8902 - 1.8441 0.95 6816 381 0.0953 0.1488 REMARK 3 15 1.8441 - 1.8022 0.96 6809 349 0.0998 0.1347 REMARK 3 16 1.8022 - 1.7639 0.96 6901 344 0.1003 0.1613 REMARK 3 17 1.7639 - 1.7286 0.96 6842 381 0.1026 0.1371 REMARK 3 18 1.7286 - 1.6960 0.96 6821 409 0.1044 0.1353 REMARK 3 19 1.6960 - 1.6657 0.96 6836 343 0.1121 0.1633 REMARK 3 20 1.6657 - 1.6374 0.96 6951 332 0.1198 0.1725 REMARK 3 21 1.6374 - 1.6110 0.97 6906 362 0.1239 0.1704 REMARK 3 22 1.6110 - 1.5862 0.96 6861 342 0.1256 0.1724 REMARK 3 23 1.5862 - 1.5629 0.97 6856 417 0.1380 0.1858 REMARK 3 24 1.5629 - 1.5409 0.96 6914 371 0.1493 0.1887 REMARK 3 25 1.5409 - 1.5201 0.97 6853 367 0.1637 0.2261 REMARK 3 26 1.5201 - 1.5003 0.95 6858 341 0.1736 0.1901 REMARK 3 27 1.5003 - 1.4816 0.92 6531 333 0.1941 0.2552 REMARK 3 28 1.4816 - 1.4637 0.85 6126 280 0.2202 0.2373 REMARK 3 29 1.4637 - 1.4467 0.79 5618 312 0.2368 0.2868 REMARK 3 30 1.4467 - 1.4305 0.72 5113 266 0.2634 0.3016 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.53 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 : 0.007 4738 REMARK 3 ANGLE : 1.180 6543 REMARK 3 CHIRALITY : 0.073 725 REMARK 3 PLANARITY : 0.006 782 REMARK 3 DIHEDRAL : 15.420 1840 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 5HT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000217679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114190 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.59900 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: PHENIX REMARK 200 STARTING MODEL: 4GZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, 200MM NAOAC, 20 MM MGOAC, 100 REMARK 280 MM HEPES, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 27.44200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.62350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.30200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.62350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.44200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.30200 REMARK 290 SMTRY3 4 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: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 GLU A 333 REMARK 465 SER B 115 REMARK 465 LYS B 116 REMARK 465 GLY B 117 REMARK 465 LEU B 118 REMARK 465 GLU B 119 REMARK 465 ASP B 120 REMARK 465 SER B 121 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 O HOH A 581 O HOH A 809 2.05 REMARK 500 O HOH B 507 O HOH B 512 2.10 REMARK 500 O HOH B 534 O HOH B 658 2.11 REMARK 500 O HOH B 767 O HOH B 771 2.17 REMARK 500 O HOH B 711 O HOH C 132 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 851 O HOH B 692 1565 2.11 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 240 151.63 83.68 REMARK 500 GLU B 238 131.51 -39.52 REMARK 500 THR B 240 154.73 84.46 REMARK 500 GLU B 334 111.32 -33.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 857 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 858 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 859 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 860 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 861 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 862 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH B 771 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B 772 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 773 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH B 774 DISTANCE = 6.51 ANGSTROMS 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 162 OE2 REMARK 620 2 HOH A 522 O 87.9 REMARK 620 3 HOH A 551 O 84.7 92.3 REMARK 620 4 HOH A 553 O 173.4 88.9 89.6 REMARK 620 5 EDA D 1 OP1 93.2 175.7 91.9 90.4 REMARK 620 6 HOH D 116 O 90.7 90.6 174.4 95.2 85.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 502 O REMARK 620 2 GLN B 340 O 78.2 REMARK 620 3 HOH B 506 O 152.6 129.1 REMARK 620 4 HOH B 661 O 98.2 79.3 87.0 REMARK 620 5 HOH B 710 O 90.4 102.7 85.3 171.4 REMARK 620 6 HOH B 765 O 92.4 170.2 60.5 104.9 74.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 162 OE2 REMARK 620 2 HOH B 526 O 88.8 REMARK 620 3 HOH B 538 O 174.4 90.2 REMARK 620 4 HOH B 557 O 84.6 93.5 89.9 REMARK 620 5 EDA C 1 OP3 92.1 175.7 89.3 90.7 REMARK 620 6 HOH C 117 O 90.5 89.5 95.0 174.2 86.3 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GZ1 RELATED DB: PDB REMARK 900 4GZ1 CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT DNA REMARK 900 MOLECULE REMARK 900 RELATED ID: 5INK RELATED DB: PDB REMARK 900 RELATED ID: 5INL RELATED DB: PDB REMARK 900 RELATED ID: 5INM RELATED DB: PDB REMARK 900 RELATED ID: 5INN RELATED DB: PDB REMARK 900 RELATED ID: 5INO RELATED DB: PDB REMARK 900 RELATED ID: 5INP RELATED DB: PDB REMARK 900 RELATED ID: 5INQ RELATED DB: PDB DBREF 5HT2 A 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5HT2 B 118 370 UNP Q9JJX7 TYDP2_MOUSE 118 370 DBREF 5HT2 C 1 9 PDB 5HT2 5HT2 1 9 DBREF 5HT2 D 1 9 PDB 5HT2 5HT2 1 9 SEQADV 5HT2 SER A 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5HT2 LYS A 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5HT2 GLY A 117 UNP Q9JJX7 EXPRESSION TAG SEQADV 5HT2 SER B 115 UNP Q9JJX7 EXPRESSION TAG SEQADV 5HT2 LYS B 116 UNP Q9JJX7 EXPRESSION TAG SEQADV 5HT2 GLY B 117 UNP Q9JJX7 EXPRESSION TAG SEQRES 1 A 256 SER LYS GLY LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 A 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 A 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 A 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 A 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 A 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 A 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 A 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 A 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 A 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLU HIS SER SEQRES 11 A 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 A 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 A 256 GLY ASP THR ASN LEU ARG ASP GLN GLU VAL ILE LYS CYS SEQRES 14 A 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 A 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 A 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA TYR LYS SEQRES 17 A 256 HIS ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 A 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 A 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 A 256 LEU LEU CYS THR LEU ASN VAL VAL LEU SEQRES 1 B 256 SER LYS GLY LEU GLU ASP SER SER THR ILE SER PHE ILE SEQRES 2 B 256 THR TRP ASN ILE ASP GLY LEU ASP GLY CYS ASN LEU PRO SEQRES 3 B 256 GLU ARG ALA ARG GLY VAL CYS SER CYS LEU ALA LEU TYR SEQRES 4 B 256 SER PRO ASP VAL VAL PHE LEU GLN GLU VAL ILE PRO PRO SEQRES 5 B 256 TYR CYS ALA TYR LEU LYS LYS ARG ALA ALA SER TYR THR SEQRES 6 B 256 ILE ILE THR GLY ASN GLU GLU GLY TYR PHE THR ALA ILE SEQRES 7 B 256 LEU LEU LYS LYS GLY ARG VAL LYS PHE LYS SER GLN GLU SEQRES 8 B 256 ILE ILE PRO PHE PRO ASN THR LYS MET MET ARG ASN LEU SEQRES 9 B 256 LEU CYS VAL ASN VAL SER LEU GLY GLY ASN GLU PHE CYS SEQRES 10 B 256 LEU MET THR SER HIS LEU GLU SER THR ARG GLU HIS SER SEQRES 11 B 256 ALA GLU ARG ILE ARG GLN LEU LYS THR VAL LEU GLY LYS SEQRES 12 B 256 MET GLN GLU ALA PRO ASP SER THR THR VAL ILE PHE ALA SEQRES 13 B 256 GLY ASP THR ASN LEU ARG ASP GLN GLU VAL ILE LYS CYS SEQRES 14 B 256 GLY GLY LEU PRO ASP ASN VAL PHE ASP ALA TRP GLU PHE SEQRES 15 B 256 LEU GLY LYS PRO LYS HIS CYS GLN TYR THR TRP ASP THR SEQRES 16 B 256 LYS ALA ASN ASN ASN LEU ARG ILE PRO ALA ALA TYR LYS SEQRES 17 B 256 HIS ARG PHE ASP ARG ILE PHE PHE ARG ALA GLU GLU GLY SEQRES 18 B 256 HIS LEU ILE PRO GLN SER LEU ASP LEU VAL GLY LEU GLU SEQRES 19 B 256 LYS LEU ASP CYS GLY ARG PHE PRO SER ASP HIS TRP GLY SEQRES 20 B 256 LEU LEU CYS THR LEU ASN VAL VAL LEU SEQRES 1 C 9 EDA DC DG DA DA DT DT DC DG SEQRES 1 D 9 EDA DC DG DA DA DT DT DC DG HET EDA C 1 24 HET EDA D 1 24 HET MG A 401 1 HET MG B 401 1 HET EPE B 402 32 HET PEG B 403 7 HET MG B 404 1 HETNAM EDA 3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS- HETNAM 2 EDA INDACENE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EPE HEPES FORMUL 3 EDA 2(C12 H14 N5 O6 P) FORMUL 5 MG 3(MG 2+) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 8 PEG C4 H10 O3 FORMUL 10 HOH *702(H2 O) HELIX 1 AA1 ASN A 138 SER A 154 1 17 HELIX 2 AA2 ILE A 164 ALA A 175 1 12 HELIX 3 AA3 THR A 240 GLU A 242 5 3 HELIX 4 AA4 HIS A 243 ALA A 261 1 19 HELIX 5 AA5 ARG A 276 CYS A 283 1 8 HELIX 6 AA6 ALA A 293 LEU A 297 1 5 HELIX 7 AA7 PRO A 300 GLN A 304 5 5 HELIX 8 AA8 ASN B 138 SER B 154 1 17 HELIX 9 AA9 ILE B 164 ALA B 175 1 12 HELIX 10 AB1 THR B 240 GLU B 242 5 3 HELIX 11 AB2 HIS B 243 GLN B 259 1 17 HELIX 12 AB3 ARG B 276 CYS B 283 1 8 HELIX 13 AB4 ALA B 293 LEU B 297 1 5 HELIX 14 AB5 PRO B 300 GLN B 304 5 5 SHEET 1 AA1 6 TYR A 178 THR A 182 0 SHEET 2 AA1 6 PHE A 189 LYS A 195 -1 O LEU A 194 N THR A 179 SHEET 3 AA1 6 VAL A 157 VAL A 163 -1 N LEU A 160 O ALA A 191 SHEET 4 AA1 6 THR A 123 ASN A 130 1 N ILE A 127 O PHE A 159 SHEET 5 AA1 6 GLY A 361 VAL A 368 -1 O CYS A 364 N PHE A 126 SHEET 6 AA1 6 LEU A 337 VAL A 345 -1 N ASP A 343 O LEU A 363 SHEET 1 AA2 6 VAL A 199 PRO A 208 0 SHEET 2 AA2 6 ASN A 217 LEU A 225 -1 O CYS A 220 N GLU A 205 SHEET 3 AA2 6 ASN A 228 SER A 235 -1 O LEU A 232 N VAL A 221 SHEET 4 AA2 6 THR A 266 ASP A 272 1 O ILE A 268 N MET A 233 SHEET 5 AA2 6 ASP A 326 ARG A 331 -1 O PHE A 329 N PHE A 269 SHEET 6 AA2 6 VAL A 290 ASP A 292 -1 N PHE A 291 O PHE A 330 SHEET 1 AA3 2 TRP A 307 ASP A 308 0 SHEET 2 AA3 2 LYS A 322 HIS A 323 -1 O HIS A 323 N TRP A 307 SHEET 1 AA4 6 TYR B 178 THR B 182 0 SHEET 2 AA4 6 PHE B 189 LYS B 195 -1 O LEU B 194 N THR B 179 SHEET 3 AA4 6 VAL B 157 VAL B 163 -1 N VAL B 158 O LEU B 193 SHEET 4 AA4 6 THR B 123 ASN B 130 1 N ILE B 127 O PHE B 159 SHEET 5 AA4 6 GLY B 361 ASN B 367 -1 O CYS B 364 N PHE B 126 SHEET 6 AA4 6 ILE B 338 VAL B 345 -1 N GLN B 340 O THR B 365 SHEET 1 AA5 6 LYS B 200 PRO B 208 0 SHEET 2 AA5 6 ASN B 217 LEU B 225 -1 O CYS B 220 N GLU B 205 SHEET 3 AA5 6 ASN B 228 SER B 235 -1 O LEU B 232 N VAL B 221 SHEET 4 AA5 6 THR B 266 ASP B 272 1 O ILE B 268 N MET B 233 SHEET 5 AA5 6 ASP B 326 ARG B 331 -1 O PHE B 329 N PHE B 269 SHEET 6 AA5 6 PHE B 291 ASP B 292 -1 N PHE B 291 O PHE B 330 SHEET 1 AA6 2 TRP B 307 ASP B 308 0 SHEET 2 AA6 2 LYS B 322 HIS B 323 -1 O HIS B 323 N TRP B 307 LINK O3' EDA C 1 P DC C 2 1555 1555 1.61 LINK O3' EDA D 1 P DC D 2 1555 1555 1.61 LINK OE2 GLU A 162 MG MG A 401 1555 1555 2.08 LINK MG MG A 401 O HOH A 522 1555 1555 2.06 LINK MG MG A 401 O HOH A 551 1555 1555 2.10 LINK MG MG A 401 O HOH A 553 1555 1555 2.09 LINK MG MG A 401 OP1 EDA D 1 1555 1555 2.07 LINK MG MG A 401 O HOH D 116 1555 1555 2.14 LINK O BHOH A 502 MG B MG B 404 3545 1555 2.57 LINK OE2 GLU B 162 MG MG B 401 1555 1555 2.10 LINK O GLN B 340 MG B MG B 404 1555 1555 2.12 LINK MG MG B 401 O HOH B 526 1555 1555 2.03 LINK MG MG B 401 O HOH B 538 1555 1555 2.08 LINK MG MG B 401 O HOH B 557 1555 1555 2.06 LINK MG MG B 401 OP3 EDA C 1 1555 1555 2.10 LINK MG MG B 401 O HOH C 117 1555 1555 2.14 LINK MG B MG B 404 O BHOH B 506 1555 1555 2.23 LINK MG B MG B 404 O BHOH B 661 1555 1555 2.04 LINK MG B MG B 404 O HOH B 710 1555 1555 2.32 LINK MG B MG B 404 O HOH B 765 1555 1555 2.65 SITE 1 AC1 5 GLU A 162 HOH A 522 HOH A 551 HOH A 553 SITE 2 AC1 5 HOH D 116 SITE 1 AC2 5 GLU B 162 HOH B 526 HOH B 538 HOH B 557 SITE 2 AC2 5 HOH C 117 SITE 1 AC3 8 CYS B 149 TYR B 153 VAL B 345 GLY B 346 SITE 2 AC3 8 LEU B 347 GLU B 348 HOH B 592 HOH B 681 SITE 1 AC4 5 HOH A 621 HOH A 645 HOH A 819 ILE B 180 SITE 2 AC4 5 ILE B 181 SITE 1 AC5 7 ASP A 288 HOH A 502 GLN B 340 HOH B 506 SITE 2 AC5 7 HOH B 661 HOH B 710 HOH B 765 CRYST1 54.884 68.604 167.247 90.00 90.00 90.00 P 21 21 21 8 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 0.018220 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005979 0.00000