HEADER DNA/ANTIBIOTIC 03-JAN-24 8XP8 TITLE CRYSTAL STRUCTURE OF D(ACGMCCGT/ACGGCGT) IN COMPLEX WITH ECHINOMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ECHINOMYCIN; COMPND 11 CHAIN: D, E 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: STREPTOMYCES ECHINATUS.; SOURCE 11 ORGANISM_TAXID: 67293 KEYWDS DNA-LIGAND COMPLEX, DNA, ANTIBIOTIC, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,S.M.LIN,H.NEIDLE REVDAT 3 28-AUG-24 8XP8 1 JRNL REVDAT 2 14-AUG-24 8XP8 1 JRNL REVDAT 1 29-MAY-24 8XP8 0 JRNL AUTH S.M.LIN,H.T.HUANG,P.J.FANG,C.F.CHANG,R.SATANGE,C.K.CHANG, JRNL AUTH 2 S.H.CHOU,S.NEIDLE,M.H.HOU JRNL TITL STRUCTURAL BASIS OF WATER-MEDIATED CIS JRNL TITL 2 WATSON-CRICK/HOOGSTEEN BASE-PAIR FORMATION IN NON-CPG JRNL TITL 3 METHYLATION. JRNL REF NUCLEIC ACIDS RES. V. 52 8566 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38989613 JRNL DOI 10.1093/NAR/GKAE594 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 7240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 716 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 10.0000 - 2.8000 0.95 1295 145 0.1961 0.1961 REMARK 3 2 2.8000 - 2.2200 1.00 1314 143 0.2554 0.2702 REMARK 3 3 2.2200 - 1.9400 1.00 1322 148 0.3016 0.3490 REMARK 3 4 1.9400 - 1.7700 0.99 1308 135 0.2899 0.3143 REMARK 3 5 1.7700 - 1.6400 0.98 1285 145 0.2720 0.2942 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 NULL REMARK 3 ANGLE : 2.475 NULL REMARK 3 CHIRALITY : 0.151 86 REMARK 3 PLANARITY : 0.010 42 REMARK 3 DIHEDRAL : 32.400 186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' REMARK 3 ORIGIN FOR THE GROUP (A): 39.5321 11.9059 47.9784 REMARK 3 T TENSOR REMARK 3 T11: 0.2863 T22: 0.2565 REMARK 3 T33: 0.2958 T12: 0.0048 REMARK 3 T13: 0.0131 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 5.3321 L22: 5.2939 REMARK 3 L33: 5.9995 L12: 0.3096 REMARK 3 L13: -0.1349 L23: 0.0856 REMARK 3 S TENSOR REMARK 3 S11: 0.0376 S12: 0.4163 S13: -0.4250 REMARK 3 S21: 0.3952 S22: -0.2958 S23: -0.2908 REMARK 3 S31: 0.8966 S32: 0.4022 S33: 0.2415 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'A' AND (RESID 1 OR RESID 3 OR RESID 5 REMARK 3 THROUGH 7)) OR (CHAIN 'B' AND (RESID 1 OR RESID 3 OR REMARK 3 RESID 5 THROUGH 7)) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1949 14.0772 47.9596 REMARK 3 T TENSOR REMARK 3 T11: 0.2665 T22: 0.3266 REMARK 3 T33: 0.2821 T12: -0.0619 REMARK 3 T13: -0.0309 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 3.0557 L22: 2.8020 REMARK 3 L33: 2.4735 L12: 0.0682 REMARK 3 L13: -0.3622 L23: -0.3332 REMARK 3 S TENSOR REMARK 3 S11: 0.3730 S12: 0.5412 S13: -0.1725 REMARK 3 S21: 0.5667 S22: -0.2740 S23: -0.0795 REMARK 3 S31: 0.5640 S32: 0.3279 S33: 0.0571 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 2) REMARK 3 ORIGIN FOR THE GROUP (A): 36.0909 16.0748 59.9244 REMARK 3 T TENSOR REMARK 3 T11: 0.3074 T22: 0.0193 REMARK 3 T33: 0.1325 T12: -0.1752 REMARK 3 T13: -0.0516 T23: -0.0365 REMARK 3 L TENSOR REMARK 3 L11: 0.0441 L22: 0.0619 REMARK 3 L33: 0.0047 L12: -0.0198 REMARK 3 L13: 0.0106 L23: 0.0068 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.0121 S13: -0.0112 REMARK 3 S21: 0.0097 S22: -0.0078 S23: 0.0597 REMARK 3 S31: 0.0107 S32: -0.0113 S33: -0.0059 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 4) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7445 18.5751 50.7064 REMARK 3 T TENSOR REMARK 3 T11: 0.2289 T22: 0.3190 REMARK 3 T33: 0.1550 T12: -0.1155 REMARK 3 T13: -0.0226 T23: 0.0648 REMARK 3 L TENSOR REMARK 3 L11: 0.1169 L22: 0.0218 REMARK 3 L33: 0.1199 L12: 0.0093 REMARK 3 L13: 0.1043 L23: 0.0094 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: 0.0493 S13: -0.0050 REMARK 3 S21: -0.0176 S22: 0.0088 S23: 0.0374 REMARK 3 S31: 0.0096 S32: -0.0117 S33: -0.0020 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 8XP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-21 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 : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99984 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 : 7315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.11400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MES (PH 6), 5MM SPERMINE HCL, REMARK 280 1.2% PEG 200, 10MM MNCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -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 15.98467 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 31.96933 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 31.96933 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.98467 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 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 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 400 REMARK 400 COMPOUND REMARK 400 THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER REMARK 400 OF THE QUINOXALINE CLASS OF ANTIBIOTICS. REMARK 400 HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. REMARK 400 REMARK 400 THE ECHINOMYCIN IS CYCLIC DEPSIPEPTIDE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ECHINOMYCIN REMARK 400 CHAIN: D, E REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE QUI, 2 COPIES REMARK 400 DESCRIPTION: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. REMARK 400 BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE REMARK 400 C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 REMARK 400 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED REMARK 400 TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG A 3 O3' DG A 4 P -0.138 REMARK 500 DG A 3 O3' DG A 4 P -0.149 REMARK 500 ALA D 2 C N2C D 3 N 0.158 REMARK 500 N2C D 3 C MVA D 4 N 0.170 REMARK 500 ALA D 6 C NCY D 7 N 0.141 REMARK 500 NCY D 7 C MVA D 8 N 0.165 REMARK 500 ALA E 2 C N2C E 3 N 0.143 REMARK 500 N2C E 3 C MVA E 4 N 0.162 REMARK 500 NCY E 7 C MVA E 8 N 0.156 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 A 3 C3' - O3' - P ANGL. DEV. = 14.1 DEGREES REMARK 500 DG A 3 C3' - O3' - P ANGL. DEV. = 12.4 DEGREES REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 4 C8 - N9 - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 DG A 4 C4 - N9 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 DA B 1 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 3 O3' - P - OP2 ANGL. DEV. = 10.1 DEGREES REMARK 500 DG B 3 O3' - P - OP2 ANGL. DEV. = 12.3 DEGREES 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 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 N7 REMARK 620 2 HOH A 207 O 88.9 REMARK 620 3 HOH A 216 O 95.2 173.2 REMARK 620 4 DG B 3 N7 86.0 134.8 40.5 REMARK 620 5 HOH B 205 O 85.4 98.1 87.7 126.1 REMARK 620 6 HOH B 213 O 91.9 89.8 84.6 45.7 171.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 N7 REMARK 620 2 HOH A 208 O 92.7 REMARK 620 3 HOH A 212 O 94.1 118.2 REMARK 620 4 HOH A 215 O 83.5 62.2 57.8 REMARK 620 5 HOH A 217 O 93.2 162.3 77.9 135.0 REMARK 620 6 HOH A 224 O 143.5 93.7 114.0 130.7 71.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 6 N7 REMARK 620 2 HOH B 212 O 97.2 REMARK 620 3 HOH B 215 O 103.4 83.4 REMARK 620 4 HOH B 218 O 167.5 94.9 74.7 REMARK 620 N 1 2 3 DBREF 8XP8 A 1 7 PDB 8XP8 8XP8 1 7 DBREF 8XP8 B 1 7 PDB 8XP8 8XP8 1 7 DBREF 8XP8 D 1 8 PDB 8XP8 8XP8 1 8 DBREF 8XP8 E 1 8 PDB 8XP8 8XP8 1 8 SEQRES 1 A 7 DA DC DG DG DC DG DT SEQRES 1 B 7 DA DC DG 5CM DC DG DT SEQRES 1 D 8 DSN ALA N2C MVA DSN ALA NCY MVA SEQRES 1 E 8 DSN ALA N2C MVA DSN ALA NCY MVA HET 5CM B 4 40 HET DSN D 1 6 HET N2C D 3 8 HET MVA D 4 8 HET DSN D 5 6 HET NCY D 7 7 HET MVA D 8 8 HET DSN E 1 6 HET N2C E 3 8 HET MVA E 4 8 HET DSN E 5 6 HET NCY E 7 7 HET MVA E 8 8 HET MN A 101 1 HET MN A 102 1 HET MN B 101 1 HET QUI D 101 12 HET QUI D 102 12 HET QUI E 101 12 HET QUI E 102 12 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM DSN D-SERINE HETNAM N2C N,S-DIMETHYLCYSTEINE HETNAM MVA N-METHYLVALINE HETNAM NCY N-METHYLCYSTEINE HETNAM MN MANGANESE (II) ION HETNAM QUI 2-CARBOXYQUINOXALINE FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 3 DSN 4(C3 H7 N O3) FORMUL 3 N2C 2(C5 H11 N O2 S) FORMUL 3 MVA 4(C6 H13 N O2) FORMUL 3 NCY 2(C4 H9 N O2 S) FORMUL 5 MN 3(MN 2+) FORMUL 8 QUI 4(C9 H6 N2 O2) FORMUL 12 HOH *47(H2 O) SSBOND 1 N2C D 3 NCY D 7 1555 1555 2.91 SSBOND 2 N2C E 3 NCY E 7 1555 1555 2.83 LINK O3' DG B 3 P A5CM B 4 1555 1555 1.61 LINK O3' DG B 3 P B5CM B 4 1555 1555 1.61 LINK O3'A5CM B 4 P DC B 5 1555 1555 1.61 LINK O3'B5CM B 4 P DC B 5 1555 1555 1.61 LINK C DSN D 1 N ALA D 2 1555 1555 1.46 LINK OG DSN D 1 C MVA D 8 1555 1555 1.43 LINK N DSN D 1 C QUI D 101 1555 1555 1.48 LINK C ALA D 2 N N2C D 3 1555 1555 1.49 LINK C N2C D 3 N MVA D 4 1555 1555 1.51 LINK CB N2C D 3 SG NCY D 7 1555 1555 1.83 LINK C MVA D 4 OG DSN D 5 1555 1555 1.39 LINK C DSN D 5 N ALA D 6 1555 1555 1.45 LINK N DSN D 5 C QUI D 102 1555 1555 1.48 LINK C ALA D 6 N NCY D 7 1555 1555 1.48 LINK C NCY D 7 N MVA D 8 1555 1555 1.50 LINK C DSN E 1 N ALA E 2 1555 1555 1.47 LINK OG DSN E 1 C MVA E 8 1555 1555 1.41 LINK N DSN E 1 C QUI E 101 1555 1555 1.46 LINK C ALA E 2 N N2C E 3 1555 1555 1.48 LINK C N2C E 3 N MVA E 4 1555 1555 1.50 LINK CB N2C E 3 SG NCY E 7 1555 1555 1.83 LINK C MVA E 4 OG DSN E 5 1555 1555 1.38 LINK C DSN E 5 N ALA E 6 1555 1555 1.45 LINK N DSN E 5 C QUI E 102 1555 1555 1.47 LINK C ALA E 6 N NCY E 7 1555 1555 1.47 LINK C NCY E 7 N MVA E 8 1555 1555 1.49 LINK N7 DG A 3 MN MN A 102 1555 1555 2.22 LINK N7 DG A 6 MN MN A 101 1555 1555 2.30 LINK MN MN A 101 O HOH A 208 1555 1555 2.53 LINK MN MN A 101 O HOH A 212 1555 1555 2.25 LINK MN MN A 101 O HOH A 215 1555 1555 2.37 LINK MN MN A 101 O HOH A 217 1555 1555 2.21 LINK MN MN A 101 O HOH A 224 1555 1555 2.46 LINK MN MN A 102 O HOH A 207 1555 1555 2.28 LINK MN MN A 102 O HOH A 216 1555 1555 2.28 LINK MN MN A 102 N7 DG B 3 6557 1555 2.25 LINK MN MN A 102 O HOH B 205 1555 6557 2.24 LINK MN MN A 102 O HOH B 213 1555 6557 2.30 LINK N7 DG B 6 MN MN B 101 1555 1555 2.21 LINK MN MN B 101 O HOH B 212 1555 1555 2.26 LINK MN MN B 101 O HOH B 215 1555 1555 2.22 LINK MN MN B 101 O HOH B 218 1555 1555 2.23 CRYST1 46.329 46.329 47.954 90.00 90.00 120.00 P 31 1 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 0.021585 0.012462 0.000000 0.00000 SCALE2 0.000000 0.024924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020853 0.00000