Cobalt in PDB 1wvd: Hiv-1 Dis(Mal) Duplex COCL2-Soaked

The structure of Hiv-1 Dis(Mal) Duplex COCL2-Soaked, PDB code: 1wvd was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.168, 59.168, 63.996, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 23.9

The binding sites of Cobalt atom in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked (pdb code 1wvd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked, PDB code: 1wvd:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:34.0 occ:0.37 O4 A:U6 3.9 45.8 1.0 O6 A:G7 4.1 41.8 1.0 N7 A:G7 4.4 44.6 1.0 C4 A:U6 4.6 47.2 1.0 C5 A:U6 4.7 47.9 1.0 C6 A:G7 4.9 44.1 1.0

Cobalt binding site 2 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co502 b:34.4 occ:0.16 OP1 B:G9 2.3 45.9 0.5 OP1 A:G9 2.4 50.8 1.0 OP1 B:G9 2.7 45.9 0.5 OP2 B:G9 2.9 45.5 0.5 P B:G9 3.1 45.6 0.5 P A:G9 3.7 52.2 1.0 P B:G9 3.8 45.5 0.5 O3' B:A8 3.8 47.4 0.5 O3' A:A8 3.9 50.1 1.0 OP1 B:G10 4.4 47.5 1.0 O3' B:A8 4.5 47.2 0.5 O5' B:G9 4.6 44.4 0.5 OP2 A:G9 4.6 52.1 1.0 O5' B:G9 4.6 44.5 0.5 C5' B:G9 4.6 41.9 0.5 OP2 B:G9 4.7 45.9 0.5 OP2 A:G10 4.7 53.8 1.0 O5' A:G9 4.8 51.5 1.0 O3' B:G9 5.0 44.1 0.5 C5' A:G9 5.0 50.4 1.0

Cobalt binding site 3 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:39.0 occ:0.39 O4 A:U3 2.6 59.1 1.0 O6 A:G4 2.7 56.4 1.0 C4 A:U3 3.6 58.0 1.0 C6 A:G4 3.7 56.2 1.0 N7 A:G4 3.9 54.6 1.0 C5 A:G4 4.1 55.7 1.0 C5 A:U3 4.3 57.9 1.0 N6 B:A21 4.3 55.6 1.0 N4 B:C20 4.3 50.0 1.0 O6 B:G19 4.6 44.5 1.0 N3 A:U3 4.7 58.1 1.0 N4 A:C5 4.7 49.5 1.0 N1 A:G4 4.9 56.1 1.0

Cobalt binding site 4 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co504 b:33.0 occ:0.61 O6 B:G4 4.1 45.5 1.0 O4 B:U3 4.3 48.0 1.0 N7 B:G4 4.5 40.3 1.0 C5 B:U3 4.7 44.6 1.0 C4 B:U3 4.8 46.5 1.0 C6 B:G4 5.0 41.8 1.0

Cobalt binding site 5 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co505 b:43.9 occ:0.49 O6 B:G7 3.6 39.2 0.5 O4 B:U6 4.1 37.1 1.0 O6 B:G7 4.4 42.4 0.5 N7 B:G7 4.4 39.7 0.5 C6 B:G7 4.6 39.4 0.5 C4 B:U6 4.6 37.2 1.0 C5 B:U6 4.7 36.3 1.0 C5 B:G7 4.9 39.8 0.5 N7 B:G7 5.0 39.7 0.5

Cobalt binding site 6 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co506 b:37.5 occ:0.82 N7 B:G9 2.1 38.9 0.5 OP2 B:A8 2.2 42.1 0.5 OP2 B:A8 2.3 42.7 0.5 N7 B:G9 2.5 42.0 0.5 C5 B:G9 3.0 40.2 0.5 C8 B:G9 3.1 40.2 0.5 O6 B:G9 3.2 40.2 0.5 C8 B:G9 3.3 42.7 0.5 C6 B:G9 3.4 40.4 0.5 P B:A8 3.4 43.7 0.5 P B:A8 3.5 44.0 0.5 C5 B:G9 3.7 43.2 0.5 OP1 B:A8 3.9 45.2 0.5 OP1 B:A8 3.9 44.9 0.5 O6 B:G9 4.0 45.6 0.5 OP2 B:G9 4.1 45.9 0.5 C4 B:G9 4.1 40.7 0.5 N9 B:G9 4.2 41.4 0.5 C6 B:G9 4.3 43.9 0.5 O3' B:G7 4.4 43.4 0.5 C3' B:G7 4.6 41.6 0.5 C2' B:G7 4.6 41.7 0.5 O5' B:A8 4.6 45.8 0.5 O3' B:G7 4.6 44.1 0.5 O5' B:A8 4.6 46.1 0.5 N9 B:G9 4.6 42.7 0.5 C3' B:G7 4.7 42.3 0.5 C2' B:G7 4.7 42.3 0.5 N1 B:G9 4.7 40.7 0.5 C5' B:A8 4.7 48.4 0.5 C4 B:G9 4.8 42.6 0.5 N7 B:G10 4.9 43.6 1.0 O5' B:G9 5.0 44.5 0.5

Cobalt binding site 7 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co507 b:37.1 occ:0.71 OP2 A:A8 2.3 45.2 1.0 N7 A:G9 2.4 49.6 1.0 C8 A:G9 3.3 49.5 1.0 C5 A:G9 3.5 50.2 1.0 O6 A:G9 3.8 49.0 1.0 P A:A8 3.8 48.9 1.0 C6 A:G9 4.0 50.0 1.0 OP2 A:G9 4.4 52.1 1.0 C2' A:G7 4.5 47.3 1.0 O3' A:G7 4.5 47.7 1.0 N9 A:G9 4.6 49.4 1.0 OP1 A:A8 4.6 48.0 1.0 N7 A:G10 4.6 57.5 1.0 C3' A:G7 4.6 47.8 1.0 C4 A:G9 4.7 50.2 1.0 O5' A:A8 4.9 47.9 1.0 O6 A:G10 4.9 55.7 1.0

Cobalt binding site 8 out of 8 in the Hiv-1 Dis(Mal) Duplex COCL2-Soaked


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Hiv-1 Dis(Mal) Duplex COCL2-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co508 b:34.0 occ:0.22 O6 B:G12 2.9 48.6 1.0 O6 A:G12 3.3 59.5 1.0 N4 B:C13 3.5 59.1 1.0 N4 A:C13 3.7 56.2 1.0 C6 B:G12 4.0 48.7 1.0 O4 B:U11 4.2 49.8 1.0 C6 A:G12 4.5 60.0 1.0 C4 B:C13 4.6 58.1 1.0 N7 B:G12 4.7 49.4 1.0 C5 B:G12 4.7 49.5 1.0 C4 A:C13 4.9 56.5 1.0

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350