HEADER HYDROLASE/DNA/RNA 20-JUN-17 5W7N TITLE 2-SE-T2/4-DNA AND NATIVE RNA HYBRID IN COMPLEX WITH RNASE H CATALYTIC TITLE 2 DOMAIN D132N MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*(US3)P*GP*(US3)P*CP*G)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RIBONUCLEASE H; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: RESIDUES 62-193; COMPND 13 SYNONYM: RNASE H; COMPND 14 EC: 3.1.26.4; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES 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: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 11 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 12 ORGANISM_TAXID: 272558; SOURCE 13 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 14 GENE: RNHA, BH0863; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,F.YANG,Z.HUANG REVDAT 2 04-OCT-23 5W7N 1 REMARK LINK REVDAT 1 28-JUN-17 5W7N 0 JRNL AUTH Z.FANG,F.YANG,Z.HUANG JRNL TITL 2-SE-T2/4-MODIFIED-DNA AND NATIVE RNA HYBRID IN COMPLEX WITH JRNL TITL 2 RNASE H CATALYTIC DOMAIN D132N MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 14562 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 757 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 499 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1076 REMARK 3 NUCLEIC ACID ATOMS : 245 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.680 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1370 ; 0.020 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 1158 ; 0.034 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1896 ; 2.238 ; 1.844 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2705 ; 1.442 ; 3.011 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 131 ; 6.105 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;34.029 ;25.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 202 ;15.232 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;15.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 205 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1334 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 275 ; 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): 527 ; 2.099 ; 1.849 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 526 ; 2.075 ; 1.845 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 657 ; 2.934 ; 2.758 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 658 ; 2.935 ; 2.761 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 843 ; 3.309 ; 2.289 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 844 ; 3.308 ; 2.289 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1240 ; 4.813 ; 3.321 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1725 ; 6.141 ;22.452 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1720 ; 6.135 ;22.390 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 5W7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-17 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17561 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 61.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.7 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 : 5.300 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: 2G8U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.5, 12%(W/V) PEG 20000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.34300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.34300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.84500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 103 O HOH C 106 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 A B 6 P A B 6 O5' -0.069 REMARK 500 US3 C 2 O3' DG C 3 P 0.092 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 A B 6 OP1 - P - OP2 ANGL. DEV. = -9.8 DEGREES REMARK 500 A B 6 P - O5' - C5' ANGL. DEV. = 12.1 DEGREES REMARK 500 DA C 1 C2' - C3' - O3' ANGL. DEV. = -17.0 DEGREES REMARK 500 US3 C 4 C3' - O3' - P ANGL. DEV. = 8.6 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 104 O REMARK 620 2 ASP A 71 OD2 173.4 REMARK 620 3 ASP A 192 OD1 93.2 93.4 REMARK 620 4 HOH A 303 O 85.1 88.6 170.0 REMARK 620 5 HOH A 308 O 85.1 93.6 96.6 93.0 REMARK 620 6 HOH A 311 O 97.6 82.8 91.8 78.8 171.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 98.2 REMARK 620 3 GLU A 109 OE2 101.1 52.9 REMARK 620 4 ASN A 132 OD1 139.8 122.0 102.7 REMARK 620 5 HOH A 305 O 103.5 78.2 127.6 86.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 DBREF 5W7N B 1 6 PDB 5W7N 5W7N 1 6 DBREF 5W7N C 1 4 PDB 5W7N 5W7N 1 4 DBREF 5W7N A 62 193 UNP Q9KEI9 RNH1_BACHD 62 193 SEQADV 5W7N ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 B 6 U C G A C A SEQRES 1 C 6 DA US3 DG US3 DC DG SEQRES 1 A 132 GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SER SEQRES 2 A 132 GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL ASP SEQRES 3 A 132 THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO ILE SEQRES 4 A 132 PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA ILE SEQRES 5 A 132 VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER ARG SEQRES 6 A 132 LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS TRP SEQRES 7 A 132 VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG ASN SEQRES 8 A 132 GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU ALA SEQRES 9 A 132 GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO ILE SEQRES 10 A 132 LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS ALA SEQRES 11 A 132 ASP TYR HET US3 C 2 20 HET US3 C 4 20 HET MG A 201 1 HET MG A 202 1 HETNAM US3 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 US3 PENTOFURANOSYL)-5-METHYL-2-SELANYLPYRIMIDIN-4(1H)-ONE HETNAM MG MAGNESIUM ION HETSYN US3 2-SE-THYMIDINE-5'-PHOSPHATE FORMUL 2 US3 2(C10 H15 N2 O7 P SE) FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *48(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 THR A 155 ASN A 170 1 16 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' DA C 1 P US3 C 2 1555 1555 1.60 LINK O3' US3 C 2 P DG C 3 1555 1555 1.70 LINK O3' DG C 3 P US3 C 4 1555 1555 1.65 LINK O3' US3 C 4 P DC C 5 1555 1555 1.63 LINK O HOH B 104 MG MG A 201 4546 1555 2.08 LINK OD2 ASP A 71 MG MG A 201 1555 1555 2.06 LINK OD1 ASP A 71 MG MG A 202 1555 1555 1.98 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.72 LINK OE2 GLU A 109 MG MG A 202 1555 1555 2.35 LINK OD1 ASN A 132 MG MG A 202 1555 1555 2.23 LINK OD1 ASP A 192 MG MG A 201 1555 1555 1.99 LINK MG MG A 201 O HOH A 303 1555 1555 2.21 LINK MG MG A 201 O HOH A 308 1555 1555 1.87 LINK MG MG A 201 O HOH A 311 1555 1555 2.00 LINK MG MG A 202 O HOH A 305 1555 1555 2.27 CISPEP 1 ASN A 77 PRO A 78 0 2.35 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 303 HOH A 308 SITE 2 AC1 6 HOH A 311 HOH B 104 SITE 1 AC2 6 ASP A 71 GLU A 109 ASN A 132 HOH A 303 SITE 2 AC2 6 HOH A 305 A B 6 CRYST1 80.686 37.690 62.180 90.00 95.95 90.00 C 1 2 1 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 0.012394 0.000000 0.001291 0.00000 SCALE2 0.000000 0.026532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016169 0.00000