HEADER DNA/ANTIBIOTIC 11-MAY-16 5JVW TITLE CRYSTAL STRUCTURE OF MITHRAMYCIN ANALOGUE MTM SA-TRP IN COMPLEX WITH A TITLE 2 10-MER DNA AGAGGCCTCT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS ANTI-CANCER AGENT, EWING SARCOMA, TRANSCRIPTION FACTOR, MINOR GROOVE, KEYWDS 2 DNA BINDING, DNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.HOU,J.ROHR,O.V.TSODIKOV REVDAT 3 06-MAR-24 5JVW 1 JRNL REMARK LINK REVDAT 2 26-OCT-16 5JVW 1 JRNL REVDAT 1 14-SEP-16 5JVW 0 JRNL AUTH C.HOU,S.WEIDENBACH,K.E.CANO,Z.WANG,P.MITRA,D.N.IVANOV, JRNL AUTH 2 J.ROHR,O.V.TSODIKOV JRNL TITL STRUCTURES OF MITHRAMYCIN ANALOGUES BOUND TO DNA AND JRNL TITL 2 IMPLICATIONS FOR TARGETING TRANSCRIPTION FACTOR FLI1. JRNL REF NUCLEIC ACIDS RES. V. 44 8990 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27587584 JRNL DOI 10.1093/NAR/GKW761 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 10435 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 + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 574 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 752 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 807 REMARK 3 HETEROGEN ATOMS : 368 REMARK 3 SOLVENT ATOMS : 210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.03000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : -1.71000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.201 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.135 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1342 ; 0.009 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 810 ; 0.013 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1971 ; 3.180 ; 1.708 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1779 ; 1.782 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 216 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 632 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 228 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1 ; 0.022 ; 1.527 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1342 ; 1.803 ; 1.625 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1343 ; 1.802 ; 1.624 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1976 ; 0.968 ; 2.422 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2048 ; 3.358 ;17.151 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2013 ; 3.232 ;17.067 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5JVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 1.0 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 : 10439 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SAD 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 (%): 62.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INCUBATION AGAINST 35% V/V 2-METHYL REMARK 280 -2,4-PENTANEDIOL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 17.28350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.03200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.32900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.03200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.28350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.32900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: 1 COMPLEX OF MTM SA-TRP WITH DOUBLE-STRANDED DNA 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 DA C 1 O5' 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 O9 6O6 C 101 O HOH C 201 1.34 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 C 254 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH C 255 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH D 237 DISTANCE = 6.07 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 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 1 N7 REMARK 620 2 HOH A 221 O 90.1 REMARK 620 3 HOH A 226 O 96.6 173.1 REMARK 620 4 HOH A 233 O 97.2 87.5 93.1 REMARK 620 5 HOH A 242 O 177.0 92.0 81.3 85.0 REMARK 620 6 HOH C 224 O 100.3 93.0 84.4 162.6 77.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 N7 REMARK 620 2 HOH A 217 O 105.9 REMARK 620 3 HOH A 218 O 87.9 107.0 REMARK 620 4 HOH A 224 O 95.4 82.4 168.8 REMARK 620 5 HOH A 230 O 94.0 151.4 93.8 75.3 REMARK 620 6 HOH A 243 O 174.1 69.9 89.4 88.1 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 6O6 B 101 O14 168.5 REMARK 620 3 6O6 B 101 O15 81.7 90.8 REMARK 620 4 6O6 C 101 O14 94.6 77.3 95.4 REMARK 620 5 6O6 C 101 O15 105.3 80.9 169.3 76.3 REMARK 620 6 HOH C 208 O 105.2 85.0 103.2 154.5 82.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 1 N7 REMARK 620 2 HOH B 219 O 91.2 REMARK 620 3 HOH B 223 O 87.2 177.5 REMARK 620 4 HOH B 246 O 95.1 95.7 86.4 REMARK 620 5 HOH B 261 O 173.0 82.8 98.5 89.2 REMARK 620 6 HOH D 212 O 97.9 88.3 90.0 166.3 78.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 4 N7 REMARK 620 2 HOH B 232 O 105.6 REMARK 620 3 HOH B 243 O 94.0 79.1 REMARK 620 4 HOH B 248 O 111.0 141.5 109.2 REMARK 620 5 HOH B 252 O 116.2 83.9 148.5 69.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 5 N7 REMARK 620 2 HOH B 248 O 109.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 106 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 5 OP2 REMARK 620 2 HOH B 258 O 107.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 6O6 B 102 O14 REMARK 620 2 6O6 B 102 O15 82.2 REMARK 620 3 HOH B 201 O 159.9 77.9 REMARK 620 4 6O6 C 102 O14 85.6 92.5 92.2 REMARK 620 5 6O6 C 102 O15 91.9 173.9 107.9 85.8 REMARK 620 6 HOH C 215 O 90.2 93.7 94.0 172.0 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 215 O REMARK 620 2 DA D 1 N7 91.5 REMARK 620 3 HOH D 213 O 92.3 99.1 REMARK 620 4 HOH D 220 O 90.1 92.1 168.5 REMARK 620 5 HOH D 223 O 172.6 93.6 92.1 84.4 REMARK 620 6 HOH D 232 O 89.4 178.5 82.0 86.8 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 108 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 218 O REMARK 620 2 DC C 7 OP1 130.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA C 1 N7 REMARK 620 2 HOH C 219 O 91.6 REMARK 620 3 HOH C 230 O 91.9 89.0 REMARK 620 4 HOH C 232 O 93.4 88.7 174.3 REMARK 620 5 HOH C 237 O 96.2 172.0 92.6 88.9 REMARK 620 6 HOH C 243 O 177.6 90.7 88.0 86.8 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 109 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 8 OP1 REMARK 620 2 6O6 C 102 O2 127.4 REMARK 620 3 HOH C 218 O 98.3 98.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 213 O REMARK 620 2 DA D 3 OP1 115.3 REMARK 620 3 HOH D 231 O 135.0 91.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 2 OP2 REMARK 620 2 HOH D 226 O 96.9 REMARK 620 3 HOH D 236 O 153.4 103.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 4 N7 REMARK 620 2 HOH D 215 O 107.6 REMARK 620 3 HOH D 225 O 94.7 157.2 REMARK 620 4 HOH D 233 O 174.5 73.0 84.3 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 ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6O6 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6O6 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6O6 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6O6 C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JW2 RELATED DB: PDB REMARK 900 RELATED ID: 5JVT RELATED DB: PDB REMARK 900 RELATED ID: 5JW0 RELATED DB: PDB DBREF 5JVW A 1 10 PDB 5JVW 5JVW 1 10 DBREF 5JVW B 1 10 PDB 5JVW 5JVW 1 10 DBREF 5JVW C 1 10 PDB 5JVW 5JVW 1 10 DBREF 5JVW D 1 10 PDB 5JVW 5JVW 1 10 SEQRES 1 A 10 DA DG DA DG DG DC DC DT DC DT SEQRES 1 B 10 DA DG DA DG DG DC DC DT DC DT SEQRES 1 C 10 DA DG DA DG DG DC DC DT DC DT SEQRES 1 D 10 DA DG DA DG DG DC DC DT DC DT HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HET NA A 104 1 HET 6O6 B 101 87 HET 6O6 B 102 87 HET ZN B 103 1 HET ZN B 104 1 HET ZN B 105 1 HET NA B 106 1 HET 6O6 C 101 87 HET 6O6 C 102 87 HET ZN C 103 1 HET ZN C 104 1 HET ZN C 105 1 HET ZN C 106 1 HET ZN C 107 1 HET NA C 108 1 HET NA C 109 1 HET ZN D 101 1 HET ZN D 102 1 HET NA D 103 1 HET NA D 104 1 HET NA D 105 1 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM 6O6 PLICAMYCIN, MITHRAMYCIN ANALOGUE MTM SA-TRP HETSYN 6O6 METHYL (2S)-2-({(2S)-2-[(2R,3S)-3-{[(2S,4R,5R,6R)-4- HETSYN 2 6O6 {[(2S,4R,5S,6R)-4-{[(2S,4S,5R,6R)-4,5-DIHYDROXY-4,6- HETSYN 3 6O6 DIMETHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-5-HYDROXY-6- HETSYN 4 6O6 METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-5-HYDROXY-6- HETSYN 5 6O6 METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-7-{[(2S,4R,5R,6R)- HETSYN 6 6O6 4-{[(2S,4R,5S,6R)-4,5-DIHYDROXY-6-METHYLTETRAHYDRO-2H- HETSYN 7 6O6 PYRAN-2-YL]OXY}-5-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN- HETSYN 8 6O6 2-YL]OXY}-5,10-DIHYDROXY-6-METHYL-4-OXO-1,2,3,4- HETSYN 9 6O6 TETRAHYDROANTHRACEN-2-YL]-2-METHOXYACETYL}AMINO)-3- HETSYN 10 6O6 (1H-INDOL-3-YL)PROPANOATE (NON-PREFERRED NAME) FORMUL 5 ZN 13(ZN 2+) FORMUL 8 NA 7(NA 1+) FORMUL 9 6O6 4(C61 H82 N2 O24) FORMUL 29 HOH *210(H2 O) LINK N7 DA A 1 ZN ZN A 103 1555 1555 2.07 LINK OP2 DA A 3 NA NA A 104 1555 1555 2.41 LINK N7 DG A 4 ZN ZN A 101 1555 1555 2.10 LINK ZN ZN A 101 O HOH A 217 1555 1555 2.00 LINK ZN ZN A 101 O HOH A 218 1555 1555 2.00 LINK ZN ZN A 101 O HOH A 224 1555 1555 2.00 LINK ZN ZN A 101 O HOH A 230 1555 1555 1.99 LINK ZN ZN A 101 O HOH A 243 1555 1555 1.98 LINK ZN ZN A 102 O HOH A 201 1555 1555 1.98 LINK ZN ZN A 102 O14 6O6 B 101 1555 1555 1.95 LINK ZN ZN A 102 O15 6O6 B 101 1555 1555 1.97 LINK ZN ZN A 102 O14 6O6 C 101 1555 1555 2.01 LINK ZN ZN A 102 O15 6O6 C 101 1555 1555 1.99 LINK ZN ZN A 102 O HOH C 208 1555 1555 1.98 LINK ZN ZN A 103 O HOH A 221 1555 1555 2.00 LINK ZN ZN A 103 O HOH A 226 1555 1555 1.99 LINK ZN ZN A 103 O HOH A 233 1555 1555 1.97 LINK ZN ZN A 103 O HOH A 242 1555 1555 2.00 LINK ZN ZN A 103 O HOH C 224 1555 2594 1.97 LINK N7 DA B 1 ZN ZN B 104 1555 1555 2.11 LINK N7 DG B 4 ZN ZN B 103 1555 1555 2.11 LINK N7 DG B 5 ZN ZN B 105 1555 1555 2.07 LINK OP2 DG B 5 NA NA B 106 1555 1555 2.50 LINK O14 6O6 B 102 ZN ZN C 105 1555 1555 2.01 LINK O15 6O6 B 102 ZN ZN C 105 1555 1555 1.87 LINK ZN ZN B 103 O HOH B 232 1555 1555 1.99 LINK ZN ZN B 103 O HOH B 243 1555 1555 1.99 LINK ZN ZN B 103 O HOH B 248 1555 1555 2.00 LINK ZN ZN B 103 O HOH B 252 1555 1555 2.00 LINK ZN ZN B 104 O HOH B 219 1555 1555 1.98 LINK ZN ZN B 104 O HOH B 223 1555 1555 2.00 LINK ZN ZN B 104 O HOH B 246 1555 1555 1.99 LINK ZN ZN B 104 O HOH B 261 1555 1555 2.00 LINK ZN ZN B 104 O HOH D 212 1555 1555 1.98 LINK ZN ZN B 105 O HOH B 248 1555 1555 2.42 LINK NA NA B 106 O HOH B 258 1555 1555 2.46 LINK O HOH B 201 ZN ZN C 105 1555 1555 1.99 LINK O HOH B 215 ZN ZN D 102 2595 1555 2.00 LINK O HOH B 218 NA NA C 108 2595 1555 2.44 LINK N7 DA C 1 ZN ZN C 104 1555 1555 2.08 LINK N7 DG C 2 ZN ZN C 107 1555 1555 2.07 LINK N7 DA C 3 ZN ZN C 106 1555 1555 2.08 LINK N7 DG C 4 ZN ZN C 103 1555 1555 2.10 LINK OP1 DC C 7 NA NA C 108 1555 1555 2.59 LINK OP1 DT C 8 NA NA C 109 1555 1555 2.32 LINK O14 6O6 C 102 ZN ZN C 105 1555 1555 2.00 LINK O15 6O6 C 102 ZN ZN C 105 1555 1555 1.92 LINK O2 6O6 C 102 NA NA C 109 1555 1555 3.04 LINK ZN ZN C 104 O HOH C 219 1555 1555 1.99 LINK ZN ZN C 104 O HOH C 230 1555 1555 1.99 LINK ZN ZN C 104 O HOH C 232 1555 1555 1.99 LINK ZN ZN C 104 O HOH C 237 1555 1555 2.00 LINK ZN ZN C 104 O HOH C 243 1555 1555 1.99 LINK ZN ZN C 105 O HOH C 215 1555 1555 1.98 LINK NA NA C 109 O HOH C 218 1555 1555 2.65 LINK O HOH C 213 NA NA D 103 3657 1555 2.93 LINK N7 DA D 1 ZN ZN D 102 1555 1555 2.09 LINK OP2 DG D 2 NA NA D 105 1555 1555 2.37 LINK OP1 DA D 3 NA NA D 103 1555 1555 2.55 LINK N7 DG D 4 ZN ZN D 101 1555 1555 2.13 LINK OP2 DG D 5 NA NA D 104 1555 1555 2.76 LINK ZN ZN D 101 O HOH D 215 1555 1555 2.00 LINK ZN ZN D 101 O HOH D 225 1555 1555 2.00 LINK ZN ZN D 101 O HOH D 233 1555 1555 1.99 LINK ZN ZN D 102 O HOH D 213 1555 1555 1.99 LINK ZN ZN D 102 O HOH D 220 1555 1555 1.99 LINK ZN ZN D 102 O HOH D 223 1555 1555 2.00 LINK ZN ZN D 102 O HOH D 232 1555 1555 2.00 LINK NA NA D 103 O HOH D 231 1555 1555 2.77 LINK NA NA D 105 O HOH D 226 1555 1555 2.98 LINK NA NA D 105 O HOH D 236 1555 1555 2.68 SITE 1 AC1 6 DG A 4 HOH A 217 HOH A 218 HOH A 224 SITE 2 AC1 6 HOH A 230 HOH A 243 SITE 1 AC2 4 HOH A 201 6O6 B 101 6O6 C 101 HOH C 208 SITE 1 AC3 5 DA A 1 HOH A 221 HOH A 226 HOH A 233 SITE 2 AC3 5 HOH A 242 SITE 1 AC4 2 DG A 2 DA A 3 SITE 1 AC5 23 DG A 4 DG A 5 DC A 7 ZN A 102 SITE 2 AC5 23 HOH A 201 DG B 5 DC B 6 DC B 7 SITE 3 AC5 23 DT B 8 DC B 9 HOH B 202 HOH B 205 SITE 4 AC5 23 HOH B 206 HOH B 212 HOH B 216 HOH B 222 SITE 5 AC5 23 HOH B 227 HOH B 228 HOH B 230 HOH B 242 SITE 6 AC5 23 HOH B 254 6O6 C 101 HOH C 208 SITE 1 AC6 24 DT A 10 DA B 1 HOH B 201 HOH B 208 SITE 2 AC6 24 HOH B 211 HOH B 217 HOH B 221 HOH B 224 SITE 3 AC6 24 HOH B 235 HOH B 237 HOH B 238 HOH B 244 SITE 4 AC6 24 DG C 4 DG C 5 6O6 C 102 ZN C 105 SITE 5 AC6 24 HOH C 215 DA D 3 DG D 5 DC D 6 SITE 6 AC6 24 DC D 7 DT D 8 DC D 9 HOH D 201 SITE 1 AC7 6 DG B 4 ZN B 105 HOH B 232 HOH B 243 SITE 2 AC7 6 HOH B 248 HOH B 252 SITE 1 AC8 6 DA B 1 HOH B 219 HOH B 223 HOH B 246 SITE 2 AC8 6 HOH B 261 HOH D 212 SITE 1 AC9 3 DG B 5 ZN B 103 HOH B 248 SITE 1 AD1 2 DG B 5 HOH B 258 SITE 1 AD2 18 DG A 5 DC A 6 DC A 7 DT A 8 SITE 2 AD2 18 ZN A 102 HOH A 201 DG B 4 DG B 5 SITE 3 AD2 18 6O6 B 101 DA C 1 HOH C 201 HOH C 202 SITE 4 AD2 18 HOH C 208 HOH C 210 HOH C 214 HOH C 228 SITE 5 AD2 18 HOH C 235 DT D 10 SITE 1 AD3 20 6O6 B 102 HOH B 201 DG C 5 DC C 6 SITE 2 AD3 20 DC C 7 DT C 8 DC C 9 ZN C 105 SITE 3 AD3 20 NA C 109 HOH C 207 HOH C 213 HOH C 215 SITE 4 AD3 20 HOH C 217 HOH C 218 HOH C 229 HOH C 234 SITE 5 AD3 20 HOH C 236 DG D 4 DG D 5 NA D 103 SITE 1 AD4 2 DG C 4 ZN C 106 SITE 1 AD5 7 DA C 1 ZN C 107 HOH C 219 HOH C 230 SITE 2 AD5 7 HOH C 232 HOH C 237 HOH C 243 SITE 1 AD6 4 6O6 B 102 HOH B 201 6O6 C 102 HOH C 215 SITE 1 AD7 2 DA C 3 ZN C 103 SITE 1 AD8 5 DA C 1 DG C 2 ZN C 104 HOH C 230 SITE 2 AD8 5 HOH C 237 SITE 1 AD9 1 DC C 7 SITE 1 AE1 3 DT C 8 6O6 C 102 HOH C 218 SITE 1 AE2 4 DG D 4 HOH D 215 HOH D 225 HOH D 233 SITE 1 AE3 5 DA D 1 HOH D 213 HOH D 220 HOH D 223 SITE 2 AE3 5 HOH D 232 SITE 1 AE4 4 6O6 C 102 HOH C 213 DA D 3 HOH D 231 SITE 1 AE5 1 DG D 5 SITE 1 AE6 4 DA D 1 DG D 2 HOH D 226 HOH D 236 CRYST1 34.567 50.658 92.064 90.00 90.00 90.00 P 21 21 21 16 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 0.028929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010862 0.00000