HEADER TRANSFERASE/DNA 06-JAN-11 3Q8R TITLE HUMAN DNA POLYMERASE IOTA INCORPORATING DGTP OPPOSITE 8-OXO-GUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 1-420; COMPND 5 SYNONYM: ETA2, RAD30 HOMOLOG B; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 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: POLI, RAD30B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.N.KIROUAC,H.LING REVDAT 3 21-FEB-24 3Q8R 1 REMARK LINK REVDAT 2 30-MAR-11 3Q8R 1 JRNL REVDAT 1 23-FEB-11 3Q8R 0 JRNL AUTH K.N.KIROUAC,H.LING JRNL TITL UNIQUE ACTIVE SITE PROMOTES ERROR-FREE REPLICATION OPPOSITE JRNL TITL 2 AN 8-OXO-GUANINE LESION BY HUMAN DNA POLYMERASE IOTA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 3210 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21300901 JRNL DOI 10.1073/PNAS.1013909108 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 21842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 992 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 39.2428 - 4.6848 0.96 3109 144 0.1998 0.2424 REMARK 3 2 4.6848 - 3.7193 0.99 3014 146 0.1966 0.2334 REMARK 3 3 3.7193 - 3.2495 0.99 2982 136 0.2241 0.3110 REMARK 3 4 3.2495 - 2.9525 1.00 2964 137 0.2294 0.2672 REMARK 3 5 2.9525 - 2.7409 1.00 2937 143 0.2732 0.3470 REMARK 3 6 2.7409 - 2.5793 1.00 2929 146 0.3094 0.3750 REMARK 3 7 2.5793 - 2.4500 1.00 2915 140 0.3655 0.4542 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 54.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.860 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) : 1.34500 REMARK 3 B22 (A**2) : 1.34500 REMARK 3 B33 (A**2) : -2.69010 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 3323 REMARK 3 ANGLE : 1.256 4591 REMARK 3 CHIRALITY : 0.070 543 REMARK 3 PLANARITY : 0.004 532 REMARK 3 DIHEDRAL : 21.517 1245 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESID 27:133) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9622 -18.6493 -19.9894 REMARK 3 T TENSOR REMARK 3 T11: 0.1863 T22: 0.2042 REMARK 3 T33: 0.1951 T12: 0.0633 REMARK 3 T13: -0.0097 T23: -0.0594 REMARK 3 L TENSOR REMARK 3 L11: 0.6434 L22: 1.2207 REMARK 3 L33: 1.5461 L12: 0.2507 REMARK 3 L13: 0.9260 L23: 0.9440 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.0410 S13: 0.0023 REMARK 3 S21: -0.1180 S22: -0.2673 S23: 0.2351 REMARK 3 S31: -0.1463 S32: -0.0668 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 134:194) REMARK 3 ORIGIN FOR THE GROUP (A): 20.1846 -11.3181 -0.9879 REMARK 3 T TENSOR REMARK 3 T11: 0.2781 T22: 0.2754 REMARK 3 T33: 0.2212 T12: -0.0571 REMARK 3 T13: 0.0160 T23: -0.0275 REMARK 3 L TENSOR REMARK 3 L11: 0.7138 L22: 0.5930 REMARK 3 L33: 1.4443 L12: -0.7374 REMARK 3 L13: -0.2556 L23: 0.2441 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: -0.1098 S13: 0.1826 REMARK 3 S21: 0.0129 S22: -0.0019 S23: -0.1083 REMARK 3 S31: -0.0591 S32: 0.2304 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 195:299) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1836 -29.9068 0.5074 REMARK 3 T TENSOR REMARK 3 T11: 0.1960 T22: 0.1435 REMARK 3 T33: 0.2002 T12: 0.0088 REMARK 3 T13: 0.0666 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.2563 L22: -0.0194 REMARK 3 L33: 0.9220 L12: 0.1543 REMARK 3 L13: -0.8309 L23: -0.1973 REMARK 3 S TENSOR REMARK 3 S11: -0.1385 S12: -0.0096 S13: -0.3046 REMARK 3 S21: 0.0960 S22: -0.0838 S23: 0.0305 REMARK 3 S31: 0.0069 S32: 0.1107 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 300:414) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9860 -42.0339 -34.3531 REMARK 3 T TENSOR REMARK 3 T11: 0.5262 T22: 0.3332 REMARK 3 T33: 0.5206 T12: 0.1770 REMARK 3 T13: -0.2313 T23: -0.2312 REMARK 3 L TENSOR REMARK 3 L11: 0.8213 L22: 2.5620 REMARK 3 L33: 1.8210 L12: -1.1954 REMARK 3 L13: -0.1425 L23: 0.1294 REMARK 3 S TENSOR REMARK 3 S11: 0.3509 S12: 0.1652 S13: -0.2849 REMARK 3 S21: -0.7575 S22: -0.1706 S23: 0.4835 REMARK 3 S31: 0.1708 S32: 0.2164 S33: -0.0000 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 3Q8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 5000MME, 0.15M NH4SO4, 0.1M REMARK 280 MES 6.5, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K, PH 6.5 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 135.05467 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 67.52733 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 101.29100 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 33.76367 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 168.81833 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 135.05467 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 67.52733 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 33.76367 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 101.29100 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 168.81833 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: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, T, P 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 B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 3 REMARK 465 ALA B 4 REMARK 465 ASP B 5 REMARK 465 VAL B 6 REMARK 465 GLY B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 SER B 12 REMARK 465 GLN B 13 REMARK 465 GLY B 14 REMARK 465 VAL B 15 REMARK 465 HIS B 16 REMARK 465 ASP B 17 REMARK 465 GLN B 18 REMARK 465 VAL B 19 REMARK 465 LEU B 20 REMARK 465 PRO B 21 REMARK 465 THR B 22 REMARK 465 PRO B 23 REMARK 465 ASN B 24 REMARK 465 ALA B 25 REMARK 465 SER B 26 REMARK 465 SER B 351 REMARK 465 GLU B 352 REMARK 465 LYS B 353 REMARK 465 HIS B 354 REMARK 465 TYR B 355 REMARK 465 LYS B 371 REMARK 465 LEU B 372 REMARK 465 GLY B 373 REMARK 465 THR B 374 REMARK 465 GLY B 375 REMARK 465 ALA B 415 REMARK 465 LEU B 416 REMARK 465 ASN B 417 REMARK 465 THR B 418 REMARK 465 ALA B 419 REMARK 465 LYS B 420 REMARK 465 DT T 837 REMARK 465 DC T 838 REMARK 465 DA T 839 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 SER B 27 OG REMARK 470 ASN B 47 CG OD1 ND2 REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 LEU B 50 CG CD1 CD2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 ASP B 52 CG OD1 OD2 REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 TYR B 61 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 LEU B 78 CG CD1 CD2 REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 GLN B 90 CG CD OE1 NE2 REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 SER B 149 OG REMARK 470 LYS B 237 CG CD CE NZ REMARK 470 TYR B 244 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 245 CG CD CE NZ REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 LYS B 267 CG CD CE NZ REMARK 470 LYS B 271 CG CD CE NZ REMARK 470 LYS B 283 CG CD CE NZ REMARK 470 LYS B 309 CG CD CE NZ REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 GLU B 314 CG CD OE1 OE2 REMARK 470 GLN B 334 CG CD OE1 NE2 REMARK 470 ASP B 335 CG OD1 OD2 REMARK 470 LYS B 338 CG CD CE NZ REMARK 470 ARG B 348 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 349 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 370 CG CD OE1 NE2 REMARK 470 ASN B 376 CG OD1 ND2 REMARK 470 TYR B 377 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 389 CG CD CE NZ REMARK 470 LYS B 398 CG CD CE NZ REMARK 470 DC P 873 O3' 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 8OG T 840 O3' DG T 841 P -0.089 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 DG T 841 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC T 846 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT T 847 C3' - C2' - C1' ANGL. DEV. = -7.4 DEGREES REMARK 500 DA P 870 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES 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 B 37 63.57 30.67 REMARK 500 SER B 46 -71.79 -65.06 REMARK 500 LYS B 60 -116.09 47.96 REMARK 500 GLU B 69 -12.23 -45.82 REMARK 500 LEU B 73 40.25 -109.48 REMARK 500 LEU B 78 74.02 47.45 REMARK 500 ASN B 80 141.97 -38.32 REMARK 500 CYS B 88 84.17 -155.55 REMARK 500 ALA B 150 -47.99 125.29 REMARK 500 ASN B 160 26.29 45.29 REMARK 500 GLU B 224 2.26 -69.17 REMARK 500 LYS B 271 3.81 -59.45 REMARK 500 SER B 276 -71.60 -68.77 REMARK 500 ASP B 378 69.47 -118.65 REMARK 500 CYS B 411 -165.92 -117.38 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 MG B 423 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 34 OD1 REMARK 620 2 LEU B 35 O 75.5 REMARK 620 3 DGT B 421 O2G 155.5 128.9 REMARK 620 4 DGT B 421 O2A 71.0 105.5 96.6 REMARK 620 5 DGT B 421 O1B 101.7 57.8 92.1 67.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 422 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 237 O REMARK 620 2 ILE B 239 O 81.5 REMARK 620 3 ILE B 242 O 81.2 86.8 REMARK 620 4 HOH B 495 O 86.2 78.0 161.6 REMARK 620 5 HOH P 51 O 99.1 176.8 96.4 98.8 REMARK 620 6 DC P 872 OP1 174.4 94.7 94.6 97.0 85.0 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 DGT B 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 423 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q8P RELATED DB: PDB REMARK 900 RELATED ID: 3Q8Q RELATED DB: PDB REMARK 900 RELATED ID: 3Q8S RELATED DB: PDB DBREF 3Q8R B 1 420 UNP Q9UNA4 POLI_HUMAN 1 420 DBREF 3Q8R T 837 847 PDB 3Q8R 3Q8R 837 847 DBREF 3Q8R P 867 873 PDB 3Q8R 3Q8R 867 873 SEQRES 1 B 420 MET GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN SEQRES 2 B 420 GLY VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER SEQRES 3 B 420 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR SEQRES 4 B 420 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP SEQRES 5 B 420 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR SEQRES 6 B 420 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU SEQRES 7 B 420 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU SEQRES 8 B 420 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU SEQRES 9 B 420 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER SEQRES 10 B 420 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL SEQRES 11 B 420 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU SEQRES 12 B 420 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS SEQRES 13 B 420 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU SEQRES 14 B 420 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU SEQRES 15 B 420 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY SEQRES 16 B 420 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU SEQRES 17 B 420 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU SEQRES 18 B 420 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN SEQRES 19 B 420 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA SEQRES 20 B 420 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP SEQRES 21 B 420 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU SEQRES 22 B 420 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE SEQRES 23 B 420 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO SEQRES 24 B 420 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SEQRES 25 B 420 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU SEQRES 26 B 420 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS SEQRES 27 B 420 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER SEQRES 28 B 420 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE SEQRES 29 B 420 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR SEQRES 30 B 420 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU SEQRES 31 B 420 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU SEQRES 32 B 420 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU SEQRES 33 B 420 ASN THR ALA LYS SEQRES 1 T 11 DT DC DA 8OG DG DG DG DT DC DC DT SEQRES 1 P 7 DA DG DG DA DC DC DC MODRES 3Q8R 8OG T 840 DG HET 8OG T 840 46 HET DGT B 421 31 HET MG B 422 1 HET MG B 423 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 DGT C10 H16 N5 O13 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *151(H2 O) HELIX 1 1 CYS B 37 ASN B 47 1 11 HELIX 2 2 PRO B 48 LYS B 51 5 4 HELIX 3 3 ASN B 67 LYS B 72 1 6 HELIX 4 4 VAL B 81 CYS B 88 1 8 HELIX 5 5 LEU B 99 SER B 117 1 19 HELIX 6 6 LEU B 132 LEU B 143 1 12 HELIX 7 7 ASN B 159 GLN B 161 5 3 HELIX 8 8 ASP B 167 GLY B 192 1 26 HELIX 9 9 ASN B 202 GLY B 211 1 10 HELIX 10 10 LEU B 222 GLU B 224 5 3 HELIX 11 11 SER B 225 SER B 232 1 8 HELIX 12 12 HIS B 235 ILE B 239 5 5 HELIX 13 13 GLY B 243 ALA B 252 1 10 HELIX 14 14 SER B 257 PHE B 264 1 8 HELIX 15 15 SER B 265 PHE B 286 1 22 HELIX 16 16 SER B 313 GLN B 334 1 22 HELIX 17 17 VAL B 379 VAL B 395 1 17 SHEET 1 A 6 VAL B 120 LEU B 123 0 SHEET 2 A 6 GLU B 127 ASP B 131 -1 O PHE B 129 N GLU B 121 SHEET 3 A 6 ILE B 30 LEU B 35 -1 N VAL B 33 O ASN B 128 SHEET 4 A 6 GLY B 195 ALA B 200 -1 O CYS B 196 N ASP B 34 SHEET 5 A 6 GLN B 218 VAL B 220 1 O THR B 219 N VAL B 199 SHEET 6 A 6 HIS B 156 VAL B 157 1 N HIS B 156 O GLN B 218 SHEET 1 B 4 MET B 79 ASN B 80 0 SHEET 2 B 4 LEU B 62 CYS B 66 -1 N VAL B 63 O MET B 79 SHEET 3 B 4 LEU B 55 GLN B 59 -1 N GLN B 59 O LEU B 62 SHEET 4 B 4 VAL B 92 ASN B 95 1 O VAL B 94 N GLN B 58 SHEET 1 C 4 PHE B 302 CYS B 311 0 SHEET 2 C 4 LEU B 403 LEU B 413 -1 O LEU B 403 N CYS B 311 SHEET 3 C 4 PRO B 339 ARG B 348 -1 N ILE B 345 O SER B 407 SHEET 4 C 4 GLU B 358 PRO B 363 -1 O ARG B 360 N LEU B 344 LINK O3'A8OG T 840 P DG T 841 1555 1555 1.52 LINK O3'B8OG T 840 P DG T 841 1555 1555 1.61 LINK OD1 ASP B 34 MG MG B 423 1555 1555 2.52 LINK O LEU B 35 MG MG B 423 1555 1555 2.68 LINK O LYS B 237 MG MG B 422 1555 1555 2.46 LINK O ILE B 239 MG MG B 422 1555 1555 2.61 LINK O ILE B 242 MG MG B 422 1555 1555 2.46 LINK O2GADGT B 421 MG MG B 423 1555 1555 2.25 LINK O2AADGT B 421 MG MG B 423 1555 1555 2.77 LINK O1BADGT B 421 MG MG B 423 1555 1555 2.82 LINK MG MG B 422 O HOH B 495 1555 1555 2.79 LINK MG MG B 422 O HOH P 51 1555 1555 2.72 LINK MG MG B 422 OP1 DC P 872 1555 1555 2.56 CISPEP 1 SER B 149 ALA B 150 0 6.49 CISPEP 2 LYS B 214 PRO B 215 0 -3.63 SITE 1 AC1 19 ASP B 34 LEU B 35 ASP B 36 CYS B 37 SITE 2 AC1 19 PHE B 38 TYR B 39 THR B 65 TYR B 68 SITE 3 AC1 19 ARG B 71 ASP B 126 GLU B 127 LYS B 214 SITE 4 AC1 19 MG B 423 HOH B 488 HOH B 526 HOH B 537 SITE 5 AC1 19 DC P 873 8OG T 840 DG T 841 SITE 1 AC2 6 LYS B 237 ILE B 239 ILE B 242 HOH B 495 SITE 2 AC2 6 HOH P 51 DC P 872 SITE 1 AC3 3 ASP B 34 LEU B 35 DGT B 421 CRYST1 98.290 98.290 202.582 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 0.010174 0.005874 0.000000 0.00000 SCALE2 0.000000 0.011748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004936 0.00000