Cobalt in PDB 1y6t: Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked, PDB code: 1y6t 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)	7.97 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.797, 58.797, 65.097, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.5

The structure of Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Cobalt atom in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked (pdb code 1y6t). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Hiv-1 Dis(Mal) Duplex Co Hexamine-Soaked, PDB code: 1y6t:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-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 Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co902 b:59.2 occ:0.50 N7 A:G9 2.4 50.1 1.0 OP2 A:A8 2.6 49.8 1.0 O6 A:G9 3.2 50.3 1.0 C5 A:G9 3.3 50.1 1.0 O A:HOH132 3.4 56.1 1.0 C8 A:G9 3.5 50.4 1.0 C6 A:G9 3.6 50.0 1.0 P A:A8 3.9 50.0 1.0 O A:HOH133 4.0 46.1 1.0 O3' A:G7 4.5 48.9 1.0 C4 A:G9 4.5 50.2 1.0 C3' A:G7 4.6 47.0 1.0 C2' A:G7 4.6 46.4 1.0 N9 A:G9 4.6 50.5 1.0 OP1 A:A8 4.6 50.2 1.0 N7 A:G10 4.7 44.8 1.0 OP2 A:G9 4.9 56.6 1.0 N1 A:G9 5.0 49.9 1.0

Cobalt binding site 2 out of 5 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-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 Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Co901 b:26.4 occ:0.47 O4 A:U3 2.5 47.1 1.0 O6 A:G4 2.6 47.0 1.0 C4 A:U3 3.5 47.0 1.0 C6 A:G4 3.7 47.0 1.0 N7 A:G4 4.1 46.8 1.0 N6 B:A21 4.2 42.9 1.0 C5 A:U3 4.2 47.1 1.0 N4 B:C20 4.2 34.0 1.0 C5 A:G4 4.3 46.9 1.0 N3 A:U3 4.5 46.9 1.0 O6 B:G19 4.8 34.6 1.0 N1 A:G4 4.9 46.7 1.0 O4 A:U2 4.9 41.9 1.0 N4 A:C5 4.9 42.0 1.0

Cobalt binding site 3 out of 5 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-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 Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co906 b:54.2 occ:1.00 N7 B:G9 2.4 37.9 0.5 OP2 B:A8 2.6 38.1 0.5 N7 B:G9 2.7 35.7 0.5 OP2 B:A8 2.8 35.5 0.5 OP1 B:A8 2.8 38.1 0.5 O6 B:G9 2.9 37.6 0.5 O B:HOH100 3.0 43.0 1.0 P B:A8 3.1 38.1 0.5 C5 B:G9 3.1 37.8 0.5 O B:HOH124 3.2 38.2 1.0 C8 B:G9 3.3 35.7 0.5 C6 B:G9 3.3 37.6 0.5 C8 B:G9 3.5 38.0 0.5 P B:A8 3.9 35.4 0.5 C5 B:G9 3.9 35.5 0.5 OP1 B:A8 4.0 35.5 0.5 OP2 B:G9 4.3 37.5 0.5 O5' B:A8 4.3 38.1 0.5 O3' B:G7 4.3 38.2 0.5 C5' B:A8 4.4 38.1 0.5 C4 B:G9 4.4 37.8 0.5 O6 B:G9 4.4 35.4 0.5 C3' B:G7 4.5 38.3 0.5 C6 B:G9 4.6 35.4 0.5 N9 B:G9 4.6 38.1 0.5 N9 B:G9 4.6 36.0 0.5 C2' B:G7 4.7 38.2 0.5 N1 B:G9 4.7 37.5 0.5 O3' B:G7 4.8 35.0 0.5 C2' B:G7 4.9 34.0 0.5 N7 B:G10 4.9 33.7 1.0 C3' B:G7 4.9 34.3 0.5 C4 B:G9 4.9 35.6 0.5 O5' B:G9 5.0 37.1 0.5

Cobalt binding site 4 out of 5 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-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 Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co909 b:47.9 occ:1.00 O6 B:G23 4.5 50.1 1.0 N7 B:G23 4.6 50.3 1.0

Cobalt binding site 5 out of 5 in the Hiv-1 Dis(Mal) Duplex Co Hexamine-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 Co Hexamine-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Co900 b:49.8 occ:0.47 OP1 B:G9 4.2 37.4 0.5 O A:HOH132 4.3 56.1 1.0 OP2 A:G10 4.4 50.3 1.0 OP2 A:G9 4.4 56.6 1.0 OP2 B:G9 4.7 37.5 0.5 OP1 B:G10 4.7 37.2 1.0 P B:G9 5.0 37.4 0.5

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