PDB Short entry for 3PMN HEADER LYASE,TRANSFERASE/DNA 17-NOV-10 3PMN TITLE TERNARY CRYSTAL STRUCTURE OF POLYMERASE LAMBDA VARIANT WITH A GT TITLE 2 MISPAIR AT THE PRIMER TERMINUS WITH MN2+ IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 242-575; COMPND 5 SYNONYM: POL LAMBDA, DNA POLYMERASE BETA-2, POL BETA2, DNA POLYMERASE COMPND 6 KAPPA; COMPND 7 EC: 2.7.7.7, 4.2.99.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: TEMPLATE DNA; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*CP*AP*GP*TP*AP*G)-3'; COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: PRIMER DNA; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: 5'-D(*GP*CP*CP*G)-3'; COMPND 21 CHAIN: D; COMPND 22 ENGINEERED: YES; COMPND 23 OTHER_DETAILS: DOWNSTREAM DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, LYASE, TRANSFERASE, DNA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BEBENEK,L.C.PEDERSEN,T.A.KUNKEL REVDAT 3 21-FEB-24 3PMN 1 REMARK LINK REVDAT 2 16-FEB-11 3PMN 1 JRNL REVDAT 1 02-FEB-11 3PMN 0 JRNL AUTH K.BEBENEK,L.C.PEDERSEN,T.A.KUNKEL JRNL TITL REPLICATION INFIDELITY VIA A MISMATCH WITH WATSON-CRICK JRNL TITL 2 GEOMETRY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 1862 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21233421 JRNL DOI 10.1073/PNAS.1012825108 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 558756.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 22799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1148 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2934 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 169 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2427 REMARK 3 NUCLEIC ACID ATOMS : 421 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 202 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 42.64 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : ALL.PAR REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NUCLEIC_COMPOUNDS.TO REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 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 : NA REMARK 200 OPTICS : VARIMAX-HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 98923.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M FORMATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 28.19500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.94050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.20850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.94050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.19500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.20850 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 THR A 250 OG1 CG2 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 422 N REMARK 480 DG D 1 O5' 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 ASN A 253 39.83 -143.64 REMARK 500 ILE A 256 -60.38 -94.76 REMARK 500 GLU A 330 0.53 -68.06 REMARK 500 CYS A 415 -131.20 -102.31 REMARK 500 ARG A 438 -19.64 -146.93 REMARK 500 ILE A 443 -54.13 -125.18 REMARK 500 PHE A 444 -70.58 -18.46 REMARK 500 ALA A 535 159.61 -46.68 REMARK 500 ARG A 573 55.20 -109.60 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 A 2 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 1GC A 1 O2A REMARK 620 2 ASP A 427 OD1 90.6 REMARK 620 3 ASP A 429 OD2 86.1 100.4 REMARK 620 4 ASP A 490 OD2 172.6 95.4 97.0 REMARK 620 5 HOH A 577 O 83.7 84.3 168.8 92.6 REMARK 620 6 DG C 6 O3' 95.7 170.3 87.4 77.8 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 576 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 1GC A 1 O2A REMARK 620 2 1GC A 1 O1G 102.1 REMARK 620 3 1GC A 1 O2B 87.7 86.2 REMARK 620 4 ASP A 427 OD2 107.6 92.2 164.6 REMARK 620 5 ASP A 429 OD1 88.6 166.9 86.6 91.8 REMARK 620 6 HOH A 578 O 166.6 85.9 82.1 82.5 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 5 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 94.6 REMARK 620 3 ALA A 344 O 91.4 86.6 REMARK 620 4 HOH A 580 O 87.1 98.4 174.9 REMARK 620 5 DA C 5 OP1 166.8 98.3 92.1 88.3 REMARK 620 6 HOH C 10 O 79.4 171.9 88.1 86.8 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 6 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 382 OD1 REMARK 620 2 HIS A 486 ND1 96.3 REMARK 620 3 HOH A 588 O 71.1 91.2 REMARK 620 4 HOH A 589 O 85.1 175.9 92.9 REMARK 620 5 HOH A 590 O 126.3 88.8 162.5 87.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 7 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 30 O REMARK 620 2 HIS A 530 NE2 86.4 REMARK 620 3 HOH A 602 O 98.0 166.8 REMARK 620 4 DA B 8 OP1 101.7 98.2 93.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 10 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 305 O 76.0 REMARK 620 3 HOH A 632 O 86.4 146.4 REMARK 620 4 DC D 3 OP1 139.4 90.2 84.8 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 1GC A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MGI RELATED DB: PDB REMARK 900 RELATED ID: 3MGH RELATED DB: PDB REMARK 900 RELATED ID: 3PML RELATED DB: PDB REMARK 900 RELATED ID: 3PNC RELATED DB: PDB REMARK 999 REMARK 999 AUTHOR STATES THAT POLYMERASE LAMBDA LOOP RESIDUES FROM 463 TO REMARK 999 471 (SQEENGQQQ) ARE REPLACED BY RESIDUES "KGET" DBREF 3PMN A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 3PMN B 1 11 PDB 3PMN 3PMN 1 11 DBREF 3PMN C 1 6 PDB 3PMN 3PMN 1 6 DBREF 3PMN D 1 4 PDB 3PMN 3PMN 1 4 SEQADV 3PMN LYS A 463 UNP Q9UGP5 SER 463 SEE REMARK 999 SEQADV 3PMN GLY A 464 UNP Q9UGP5 GLN 464 SEE REMARK 999 SEQADV 3PMN A UNP Q9UGP5 GLU 465 SEE REMARK 999 SEQADV 3PMN A UNP Q9UGP5 GLU 466 SEE REMARK 999 SEQADV 3PMN A UNP Q9UGP5 ASN 467 SEE REMARK 999 SEQADV 3PMN A UNP Q9UGP5 GLY 468 SEE REMARK 999 SEQADV 3PMN A UNP Q9UGP5 GLN 469 SEE REMARK 999 SEQADV 3PMN GLU A 470 UNP Q9UGP5 GLN 470 SEE REMARK 999 SEQADV 3PMN THR A 471 UNP Q9UGP5 GLN 471 SEE REMARK 999 SEQRES 1 A 329 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 329 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 329 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 329 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 329 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 329 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 329 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 329 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 329 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 329 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 329 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 329 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 329 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 329 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 329 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 329 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 329 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 329 LYS GLY GLU THR LYS TYR LEU GLY VAL CYS ARG LEU PRO SEQRES 19 A 329 GLY PRO GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL SEQRES 20 A 329 VAL PRO TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE SEQRES 21 A 329 THR GLY SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU SEQRES 22 A 329 ALA LYS THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SEQRES 23 A 329 SER THR ALA VAL VAL ARG ASN THR HIS GLY CYS LYS VAL SEQRES 24 A 329 GLY PRO GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP SEQRES 25 A 329 VAL PHE ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA SEQRES 26 A 329 GLU ARG ASP TRP SEQRES 1 B 11 DC DG DG DC DC DT DT DA DC DT DG SEQRES 1 C 6 DC DA DG DT DA DG SEQRES 1 D 4 DG DC DC DG HET 1GC A 1 31 HET MG A 576 1 HET MN A 2 1 HET NA A 5 1 HET MN A 6 1 HET MN A 7 1 HET CL A 8 1 HET CL A 9 1 HET NA A 10 1 HETNAM 1GC 2'-DEOXY-5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 1GC PHOSPHORYL]METHYL}PHOSPHORYL]GUANOSINE HETNAM MG MAGNESIUM ION HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 1GC C11 H18 N5 O12 P3 FORMUL 6 MG MG 2+ FORMUL 7 MN 3(MN 2+) FORMUL 8 NA 2(NA 1+) FORMUL 11 CL 2(CL 1-) FORMUL 14 HOH *202(H2 O) HELIX 1 1 ASN A 253 GLN A 270 1 18 HELIX 2 2 ASP A 272 SER A 288 1 17 HELIX 3 3 SER A 295 ILE A 302 1 8 HELIX 4 4 GLY A 306 GLY A 320 1 15 HELIX 5 5 LEU A 322 ILE A 328 5 7 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ALA A 405 1 17 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 ILE A 443 GLU A 454 1 12 HELIX 14 14 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 GLU A 569 ARG A 573 5 5 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 B 5 LEU A 457 LYS A 463 -1 N THR A 458 O VAL A 476 SHEET 1 C 3 MET A 525 LEU A 527 0 SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 C 3 VAL A 550 LEU A 551 -1 O LEU A 551 N LEU A 532 LINK O2A 1GC A 1 MN MN A 2 1555 1555 2.31 LINK O2A 1GC A 1 MG MG A 576 1555 1555 2.01 LINK O1G 1GC A 1 MG MG A 576 1555 1555 2.01 LINK O2B 1GC A 1 MG MG A 576 1555 1555 2.03 LINK MN MN A 2 OD1 ASP A 427 1555 1555 2.07 LINK MN MN A 2 OD2 ASP A 429 1555 1555 2.14 LINK MN MN A 2 OD2 ASP A 490 1555 1555 2.05 LINK MN MN A 2 O HOH A 577 1555 1555 2.39 LINK MN MN A 2 O3' DG C 6 1555 1555 2.46 LINK NA NA A 5 O SER A 339 1555 1555 2.37 LINK NA NA A 5 O ILE A 341 1555 1555 2.54 LINK NA NA A 5 O ALA A 344 1555 1555 2.30 LINK NA NA A 5 O HOH A 580 1555 1555 2.27 LINK NA NA A 5 OP1 DA C 5 1555 1555 2.42 LINK NA NA A 5 O HOH C 10 1555 1555 2.42 LINK MN MN A 6 OD1 ASP A 382 1555 1555 2.10 LINK MN MN A 6 ND1 HIS A 486 1555 1555 2.56 LINK MN MN A 6 O HOH A 588 1555 1555 2.60 LINK MN MN A 6 O HOH A 589 1555 1555 2.70 LINK MN MN A 6 O HOH A 590 1555 1555 2.53 LINK MN MN A 7 O HOH A 30 1555 1555 2.51 LINK MN MN A 7 NE2 HIS A 530 1555 1555 2.16 LINK MN MN A 7 O HOH A 602 1555 1555 2.73 LINK MN MN A 7 OP1 DA B 8 1555 1555 2.44 LINK NA NA A 10 O CYS A 300 1555 1555 2.56 LINK NA NA A 10 O ILE A 305 1555 1555 2.58 LINK NA NA A 10 O HOH A 632 1555 1555 2.35 LINK NA NA A 10 OP1 DC D 3 1555 1555 3.12 LINK OD2 ASP A 427 MG MG A 576 1555 1555 1.93 LINK OD1 ASP A 429 MG MG A 576 1555 1555 2.18 LINK MG MG A 576 O HOH A 578 1555 1555 2.13 CISPEP 1 GLY A 508 SER A 509 0 1.69 SITE 1 AC1 25 MN A 2 HOH A 3 HOH A 27 HOH A 53 SITE 2 AC1 25 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 3 AC1 25 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 4 AC1 25 PHE A 506 THR A 507 GLY A 508 ALA A 510 SITE 5 AC1 25 ASN A 513 ARG A 517 MG A 576 HOH A 577 SITE 6 AC1 25 HOH A 578 HOH A 629 DC B 5 DG C 6 SITE 7 AC1 25 HOH C 72 SITE 1 AC2 5 1GC A 1 MN A 2 ASP A 427 ASP A 429 SITE 2 AC2 5 HOH A 578 SITE 1 AC3 7 1GC A 1 ASP A 427 ASP A 429 ASP A 490 SITE 2 AC3 7 MG A 576 HOH A 577 DG C 6 SITE 1 AC4 6 SER A 339 ILE A 341 ALA A 344 HOH A 580 SITE 2 AC4 6 DA C 5 HOH C 10 SITE 1 AC5 6 CL A 8 ASP A 382 HIS A 486 HOH A 588 SITE 2 AC5 6 HOH A 589 HOH A 590 SITE 1 AC6 4 HOH A 30 HIS A 530 HOH A 602 DA B 8 SITE 1 AC7 2 MN A 6 HOH A 588 SITE 1 AC8 1 ARG A 514 SITE 1 AC9 5 CYS A 300 ILE A 302 ILE A 305 HOH A 632 SITE 2 AC9 5 DC D 3 CRYST1 56.390 62.417 139.881 90.00 90.00 90.00 P 21 21 21 4 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 0.017734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016021 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007149 0.00000