HEADER VIRAL PROTEIN/DNA 01-OCT-10 2L45 TITLE C-TERMINAL ZINC KNUCKLE OF THE HIVNCP7 WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TERMINAL ZINC KNUCLE OF THE HIV-NCP7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*TP*AP*CP*GP*CP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11676; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS NCP7, HIV, PLATINUM, VIRAL PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR S.QUINTAL,A.VIEGAS,E.CABRITA,N.FARRELL,S.ERHARDT REVDAT 3 05-FEB-20 2L45 1 REMARK REVDAT 2 20-JUN-12 2L45 1 JRNL REVDAT 1 14-DEC-11 2L45 0 JRNL AUTH S.QUINTAL,A.VIEGAS,S.ERHARDT,E.J.CABRITA,N.P.FARRELL JRNL TITL PLATINATED DNA AFFECTS ZINC FINGER CONFORMATION. INTERACTION JRNL TITL 2 OF A PLATINATED SINGLE-STRANDED OLIGONUCLEOTIDE AND THE JRNL TITL 3 C-TERMINAL ZINC FINGER OF NUCLEOCAPSID PROTEIN HIVNCP7. JRNL REF BIOCHEMISTRY V. 51 1752 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22303928 JRNL DOI 10.1021/BI201834G REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000101933. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : 6.0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM C-TERMINAL ZINC KNUCKLE OF REMARK 210 THE HIVNCP7, 1 MM DNA, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.114 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 9 DC B 24 C5' DC B 24 C4' 0.044 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 1 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 21 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 22 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DC B 22 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC B 22 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG B 23 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG B 23 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DC B 24 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DC B 24 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 24 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC B 24 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC B 25 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DT B 20 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA B 21 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA B 21 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC B 22 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DC B 22 N1 - C2 - O2 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DC B 22 N3 - C2 - O2 ANGL. DEV. = -8.2 DEGREES REMARK 500 2 DG B 23 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DG B 23 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DG B 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DC B 24 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DC B 24 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DC B 24 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC B 25 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DC B 25 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT B 20 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DT B 20 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DA B 21 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 DC B 22 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 DC B 22 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 3 DG B 23 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 DG B 23 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 DG B 23 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 3 DC B 24 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 3 DC B 24 N3 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 3 DC B 25 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 331 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 1 CYS A 3 179.75 -59.24 REMARK 500 1 GLU A 9 38.46 -72.05 REMARK 500 1 HIS A 11 -161.98 -168.70 REMARK 500 1 CYS A 16 -77.06 -86.51 REMARK 500 2 HIS A 11 -166.92 -165.70 REMARK 500 2 CYS A 16 -78.26 -79.16 REMARK 500 3 GLU A 9 49.89 -76.33 REMARK 500 3 HIS A 11 -172.59 -170.75 REMARK 500 3 CYS A 16 -72.83 -77.99 REMARK 500 4 HIS A 11 -160.18 -164.71 REMARK 500 4 CYS A 16 -72.95 -84.50 REMARK 500 4 THR A 17 19.60 56.46 REMARK 500 5 HIS A 11 -165.98 -169.17 REMARK 500 5 THR A 17 18.15 53.38 REMARK 500 6 HIS A 11 -165.48 -166.28 REMARK 500 6 THR A 17 42.29 39.94 REMARK 500 7 HIS A 11 -168.04 -165.26 REMARK 500 7 CYS A 16 -71.25 -85.73 REMARK 500 7 THR A 17 12.46 55.39 REMARK 500 8 CYS A 16 -75.22 -78.44 REMARK 500 8 THR A 17 17.65 54.38 REMARK 500 9 GLU A 9 49.64 -74.92 REMARK 500 9 CYS A 16 -78.22 -77.76 REMARK 500 9 THR A 17 16.28 58.64 REMARK 500 10 HIS A 11 -168.15 -169.82 REMARK 500 10 CYS A 16 -74.77 -73.64 REMARK 500 10 THR A 17 1.88 57.82 REMARK 500 11 CYS A 16 -74.11 -79.84 REMARK 500 12 GLU A 9 43.41 -78.59 REMARK 500 12 HIS A 11 -173.39 -170.09 REMARK 500 12 CYS A 16 -83.30 -77.97 REMARK 500 13 CYS A 16 -71.21 -88.42 REMARK 500 14 HIS A 11 -160.61 -161.89 REMARK 500 14 CYS A 16 -75.66 -76.34 REMARK 500 15 GLU A 9 47.25 -77.21 REMARK 500 15 HIS A 11 -167.92 -172.76 REMARK 500 15 CYS A 16 -83.47 -68.49 REMARK 500 15 THR A 17 -3.32 63.70 REMARK 500 16 HIS A 11 -167.37 -173.56 REMARK 500 16 CYS A 16 -72.30 -80.65 REMARK 500 17 CYS A 16 -75.04 -91.09 REMARK 500 17 THR A 17 18.85 51.22 REMARK 500 18 HIS A 11 -162.97 -169.25 REMARK 500 18 CYS A 16 -71.08 -74.46 REMARK 500 18 THR A 17 13.90 56.38 REMARK 500 19 CYS A 3 174.59 -59.71 REMARK 500 19 GLU A 9 40.90 -73.09 REMARK 500 19 CYS A 16 -73.57 -70.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DG B 23 0.10 SIDE CHAIN REMARK 500 1 DC B 24 0.07 SIDE CHAIN REMARK 500 2 DG B 23 0.09 SIDE CHAIN REMARK 500 2 DC B 24 0.08 SIDE CHAIN REMARK 500 3 DG B 23 0.07 SIDE CHAIN REMARK 500 4 DC B 22 0.11 SIDE CHAIN REMARK 500 7 DG B 23 0.11 SIDE CHAIN REMARK 500 8 DA B 21 0.06 SIDE CHAIN REMARK 500 8 DC B 22 0.10 SIDE CHAIN REMARK 500 8 DG B 23 0.06 SIDE CHAIN REMARK 500 9 DT B 20 0.09 SIDE CHAIN REMARK 500 10 DC B 25 0.14 SIDE CHAIN REMARK 500 13 DA B 21 0.06 SIDE CHAIN REMARK 500 13 DC B 22 0.07 SIDE CHAIN REMARK 500 13 DG B 23 0.12 SIDE CHAIN REMARK 500 13 DC B 24 0.07 SIDE CHAIN REMARK 500 14 DT B 20 0.06 SIDE CHAIN REMARK 500 14 DG B 23 0.06 SIDE CHAIN REMARK 500 14 DC B 24 0.07 SIDE CHAIN REMARK 500 15 DC B 22 0.07 SIDE CHAIN REMARK 500 17 DT B 20 0.08 SIDE CHAIN REMARK 500 17 DA B 21 0.07 SIDE CHAIN REMARK 500 18 ARG A 19 0.08 SIDE CHAIN REMARK 500 18 DG B 23 0.10 SIDE CHAIN REMARK 500 18 DC B 24 0.07 SIDE CHAIN REMARK 500 19 DG B 23 0.09 SIDE CHAIN 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 ZN A 26 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 CYS A 3 SG 111.5 REMARK 620 3 CYS A 6 SG 114.4 111.8 REMARK 620 N 1 2 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 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17229 RELATED DB: BMRB REMARK 900 RELATED ID: 2L44 RELATED DB: PDB REMARK 900 RELATED ID: 2L46 RELATED DB: PDB DBREF 2L45 A 1 19 UNP Q9YP46 Q9YP46_9HIV1 411 429 DBREF 2L45 B 20 25 PDB 2L45 2L45 20 25 SEQRES 1 A 19 LYS GLY CYS TRP LYS CYS GLY LYS GLU GLY HIS GLN MET SEQRES 2 A 19 LYS ASP CYS THR GLU ARG SEQRES 1 B 6 DT DA DC DG DC DC HET ZN A 26 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 1 GLN A 12 THR A 17 1 6 LINK SG CYS A 16 ZN ZN A 26 1555 1555 1.96 LINK SG CYS A 3 ZN ZN A 26 1555 1555 1.97 LINK SG CYS A 6 ZN ZN A 26 1555 1555 1.97 SITE 1 AC1 3 CYS A 3 CYS A 6 CYS A 16 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1