HEADER HYDROLASE/DNA 02-NOV-12 4HUF TITLE STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3'); COMPND 10 CHAIN: C, D, E, F; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DICKERSON DODECAMER DNA, CLU7 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: BH0863, RNHA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS 5-CHLORO-2'-DEOXYURIDINE, W-C BASE PAIR, WOBBLE BASE PAIR, DOUBLE KEYWDS 2 HELIX, WATSON-CRICK BASE PAIRING PATTERN, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATRA,M.EGLI REVDAT 5 20-SEP-23 4HUF 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 4HUF 1 AUTHOR REVDAT 3 27-MAR-13 4HUF 1 JRNL REVDAT 2 13-FEB-13 4HUF 1 JRNL REVDAT 1 19-DEC-12 4HUF 0 JRNL AUTH A.PATRA,J.HARP,P.S.PALLAN,L.ZHAO,M.ABRAMOV,P.HERDEWIJN, JRNL AUTH 2 M.EGLI JRNL TITL STRUCTURE, STABILITY AND FUNCTION OF 5-CHLOROURACIL MODIFIED JRNL TITL 2 A:U AND G:U BASE PAIRS. JRNL REF NUCLEIC ACIDS RES. V. 41 2689 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23275540 JRNL DOI 10.1093/NAR/GKS1316 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 5.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 54302 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2766 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 35.9042 - 4.5793 0.99 2803 143 0.2006 0.2114 REMARK 3 2 4.5793 - 3.6359 1.00 2698 141 0.1693 0.1925 REMARK 3 3 3.6359 - 3.1766 0.99 2651 147 0.1853 0.2095 REMARK 3 4 3.1766 - 2.8863 0.99 2646 117 0.2046 0.2843 REMARK 3 5 2.8863 - 2.6795 1.00 2615 133 0.1982 0.2398 REMARK 3 6 2.6795 - 2.5215 0.99 2586 163 0.1987 0.2382 REMARK 3 7 2.5215 - 2.3953 0.99 2611 128 0.1944 0.2388 REMARK 3 8 2.3953 - 2.2910 0.99 2576 134 0.1842 0.2318 REMARK 3 9 2.2910 - 2.2029 0.98 2601 122 0.1733 0.2274 REMARK 3 10 2.2029 - 2.1268 0.98 2543 154 0.1797 0.2113 REMARK 3 11 2.1268 - 2.0604 0.98 2571 136 0.1752 0.2187 REMARK 3 12 2.0604 - 2.0015 0.98 2553 125 0.1768 0.2043 REMARK 3 13 2.0015 - 1.9488 0.98 2530 140 0.1943 0.2673 REMARK 3 14 1.9488 - 1.9012 0.97 2513 142 0.1948 0.2114 REMARK 3 15 1.9012 - 1.8580 0.98 2546 142 0.2036 0.2358 REMARK 3 16 1.8580 - 1.8185 0.98 2542 121 0.2130 0.2548 REMARK 3 17 1.8185 - 1.7821 0.98 2510 141 0.2218 0.2833 REMARK 3 18 1.7821 - 1.7485 0.97 2497 145 0.2277 0.2555 REMARK 3 19 1.7485 - 1.7172 0.97 2484 168 0.2377 0.2802 REMARK 3 20 1.7172 - 1.6881 0.95 2460 124 0.2437 0.2993 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 : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.790 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 : 0.008 3208 REMARK 3 ANGLE : 1.329 4533 REMARK 3 CHIRALITY : 0.080 490 REMARK 3 PLANARITY : 0.005 429 REMARK 3 DIHEDRAL : 25.967 1261 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4HUF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-11 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 : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.67500 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: MOLREP REMARK 200 STARTING MODEL: 3D0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE (PH 6.5) AND 20% (W/V) PEG 8000 , VAPOR DIFFUSION, REMARK 280 HANGING 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 32.09650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.37400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.09650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.37400 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 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 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 ASP B 192 REMARK 465 TYR B 193 REMARK 465 GLY B 194 REMARK 465 DC E 9 REMARK 465 DG E 10 REMARK 465 DC E 11 REMARK 465 DG E 12 REMARK 465 DC F 13 REMARK 465 DG F 14 REMARK 465 DC F 15 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 GLU B 122 CD OE1 OE2 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 OE2 GLU A 175 O HOH A 343 2.01 REMARK 500 O HOH E 205 O HOH E 218 2.08 REMARK 500 OE1 GLU A 188 O HOH A 444 2.13 REMARK 500 O HOH A 402 O HOH A 440 2.14 REMARK 500 NH1 ARG A 118 O HOH A 430 2.14 REMARK 500 O HOH A 385 O HOH A 420 2.17 REMARK 500 O HOH B 301 O HOH B 312 2.17 REMARK 500 OE1 GLU B 92 O HOH B 319 2.17 REMARK 500 O HOH A 419 O HOH A 439 2.18 REMARK 500 O HOH B 283 O HOH B 302 2.18 REMARK 500 O HOH E 212 O HOH E 218 2.18 REMARK 500 O HOH E 218 O HOH F 204 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 386 O HOH A 408 4455 2.16 REMARK 500 O HOH A 447 O HOH B 275 4555 2.19 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 C 10 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC C 11 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 13 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 13 C2 - N1 - C1' ANGL. DEV. = 6.8 DEGREES REMARK 500 DG D 14 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC D 21 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC D 23 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DC D 23 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG E 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT E 8 C1' - O4' - C4' ANGL. DEV. = -9.8 DEGREES REMARK 500 DT E 8 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DA F 18 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT F 20 O4' - C1' - N1 ANGL. DEV. = 3.5 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE2 88.2 REMARK 620 3 HOH A 338 O 88.3 171.6 REMARK 620 4 HOH A 346 O 98.7 107.6 80.5 REMARK 620 5 HOH A 384 O 169.9 91.3 90.8 91.1 REMARK 620 6 HOH A 394 O 104.5 73.9 99.7 156.8 65.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 2 OP2 REMARK 620 2 HOH E 205 O 103.4 REMARK 620 3 HOH E 212 O 96.4 97.0 REMARK 620 4 HOH E 213 O 82.1 91.3 171.7 REMARK 620 5 HOH E 216 O 160.9 90.4 94.9 84.5 REMARK 620 6 HOH E 217 O 83.0 173.6 82.1 89.6 83.4 REMARK 620 7 HOH E 218 O 114.2 47.7 50.6 137.4 84.9 129.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO F 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO F 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HTU RELATED DB: PDB REMARK 900 STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR DBREF 4HUF A 61 194 UNP Q9KEI9 RNH1_BACHD 61 194 DBREF 4HUF B 61 194 UNP Q9KEI9 RNH1_BACHD 61 194 DBREF 4HUF C 1 12 PDB 4HUF 4HUF 1 12 DBREF 4HUF D 13 24 PDB 4HUF 4HUF 13 24 DBREF 4HUF E 1 12 PDB 4HUF 4HUF 1 12 DBREF 4HUF F 13 24 PDB 4HUF 4HUF 13 24 SEQADV 4HUF ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQADV 4HUF ASN B 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 134 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 A 134 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 A 134 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 A 134 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 A 134 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 A 134 ARG LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS SEQRES 7 A 134 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 A 134 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 A 134 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 A 134 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 A 134 ALA ASP TYR GLY SEQRES 1 B 134 GLU GLU ILE ILE TRP GLU SER LEU SER VAL ASP VAL GLY SEQRES 2 B 134 SER GLN GLY ASN PRO GLY ILE VAL GLU TYR LYS GLY VAL SEQRES 3 B 134 ASP THR LYS THR GLY GLU VAL LEU PHE GLU ARG GLU PRO SEQRES 4 B 134 ILE PRO ILE GLY THR ASN ASN MET GLY GLU PHE LEU ALA SEQRES 5 B 134 ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU ARG ASN SER SEQRES 6 B 134 ARG LYS PRO ILE TYR SER ASN SER GLN THR ALA ILE LYS SEQRES 7 B 134 TRP VAL LYS ASP LYS LYS ALA LYS SER THR LEU VAL ARG SEQRES 8 B 134 ASN GLU GLU THR ALA LEU ILE TRP LYS LEU VAL ASP GLU SEQRES 9 B 134 ALA GLU GLU TRP LEU ASN THR HIS THR TYR GLU THR PRO SEQRES 10 B 134 ILE LEU LYS TRP GLN THR ASP LYS TRP GLY GLU ILE LYS SEQRES 11 B 134 ALA ASP TYR GLY SEQRES 1 C 12 DC DG DC DG DA DA UCL DT DC DG DC DG SEQRES 1 D 12 DC DG DC DG DA DA UCL DT DC DG DC DG SEQRES 1 E 12 DC DG DC DG DA DA UCL DT DC DG DC DG SEQRES 1 F 12 DC DG DC DG DA DA UCL DT DC DG DC DG MODRES 4HUF UCL C 7 DU MODRES 4HUF UCL D 19 DU MODRES 4HUF UCL E 7 DU MODRES 4HUF UCL F 19 DU HET UCL C 7 20 HET UCL D 19 20 HET UCL E 7 20 HET UCL F 19 20 HET GOL A 201 6 HET MG A 202 1 HET GOL C 101 6 HET MG E 101 1 HET EDO F 101 4 HET EDO F 102 4 HETNAM UCL 5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 UCL 4(C9 H12 CL N2 O8 P) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 8 MG 2(MG 2+) FORMUL 11 EDO 2(C2 H6 O2) FORMUL 13 HOH *450(H2 O) HELIX 1 1 THR A 104 ARG A 123 1 20 HELIX 2 2 SER A 133 ASP A 142 1 10 HELIX 3 3 THR A 155 HIS A 172 1 18 HELIX 4 4 GLN A 182 GLY A 187 1 6 HELIX 5 5 THR B 104 ASN B 124 1 21 HELIX 6 6 SER B 133 LYS B 143 1 11 HELIX 7 7 THR B 155 HIS B 172 1 18 HELIX 8 8 GLN B 182 GLY B 187 1 6 SHEET 1 A 5 VAL A 93 GLY A 103 0 SHEET 2 A 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 A 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 A 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 A 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 SHEET 1 B 5 VAL B 93 GLY B 103 0 SHEET 2 B 5 GLY B 79 ASP B 87 -1 N GLY B 85 O LEU B 94 SHEET 3 B 5 LEU B 68 GLN B 75 -1 N SER B 69 O VAL B 86 SHEET 4 B 5 ILE B 129 SER B 131 1 O TYR B 130 N LEU B 68 SHEET 5 B 5 ILE B 178 LYS B 180 1 O LEU B 179 N ILE B 129 LINK O3' DA C 6 P UCL C 7 1555 1555 1.61 LINK O3' DA D 18 P UCL D 19 1555 1555 1.61 LINK O3' DA E 6 P UCL E 7 1555 1555 1.61 LINK O3' DA F 18 P UCL F 19 1555 1555 1.62 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.28 LINK OE2 GLU A 109 MG MG A 202 1555 1555 1.93 LINK MG MG A 202 O HOH A 338 1555 1555 2.05 LINK MG MG A 202 O HOH A 346 1555 1555 2.09 LINK MG MG A 202 O HOH A 384 1555 1555 2.05 LINK MG MG A 202 O HOH A 394 1555 1555 2.07 LINK OP2 DG E 2 MG MG E 101 1555 1555 2.08 LINK MG MG E 101 O HOH E 205 1555 1555 2.10 LINK MG MG E 101 O HOH E 212 1555 1555 2.06 LINK MG MG E 101 O HOH E 213 1555 1555 2.09 LINK MG MG E 101 O HOH E 216 1555 1555 2.07 LINK MG MG E 101 O HOH E 217 1555 1555 2.09 LINK MG MG E 101 O HOH E 218 1555 1555 2.80 CISPEP 1 ASN A 77 PRO A 78 0 -0.48 CISPEP 2 ASN B 77 PRO B 78 0 3.34 SITE 1 AC1 9 GLY A 76 ASN A 77 PRO A 78 HOH A 348 SITE 2 AC1 9 HOH A 356 HOH A 419 THR B 176 PRO B 177 SITE 3 AC1 9 ILE B 178 SITE 1 AC2 7 ASP A 71 GLU A 109 ASN A 132 HOH A 338 SITE 2 AC2 7 HOH A 346 HOH A 384 HOH A 394 SITE 1 AC3 11 THR A 135 DG C 2 HOH C 201 HOH C 204 SITE 2 AC3 11 HOH C 205 HOH C 206 HOH C 219 DG D 22 SITE 3 AC3 11 DC D 23 DG D 24 HOH D 107 SITE 1 AC4 7 DG E 2 HOH E 205 HOH E 212 HOH E 213 SITE 2 AC4 7 HOH E 216 HOH E 217 HOH E 218 SITE 1 AC5 5 LYS A 143 THR A 173 TYR A 174 DG F 24 SITE 2 AC5 5 HOH F 203 SITE 1 AC6 6 LYS A 141 DG E 2 DC E 3 HOH E 205 SITE 2 AC6 6 DG F 22 HOH F 204 CRYST1 64.193 64.748 116.470 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 0.015578 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008586 0.00000