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Gold in PDB 2oij: Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked

Protein crystallography data

The structure of Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked, PDB code: 2oij 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 / 2.31
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.560, 47.460, 57.960, 90.00, 90.00, 90.00
R / Rfree (%) 27.2 / 27.2

Other elements in 2oij:

The structure of Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked also contains other interesting chemical elements:

Potassium (K) 2 atoms

Gold Binding Sites:

The binding sites of Gold atom in the Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked (pdb code 2oij). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 2 binding sites of Gold where determined in the Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked, PDB code: 2oij:
Jump to Gold binding site number: 1; 2;

Gold binding site 1 out of 2 in 2oij

Go back to Gold Binding Sites List in 2oij
Gold binding site 1 out of 2 in the Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au102

b:38.6
occ:0.35
N1 A:G7 1.6 37.9 1.0
N3 B:C17 2.3 37.1 1.0
C2 A:G7 2.3 38.2 1.0
N2 A:G7 2.4 37.7 1.0
C6 A:G7 2.6 37.4 1.0
O2 B:C17 2.7 35.0 1.0
O6 A:G7 2.8 37.9 1.0
C2 B:C17 2.8 36.7 1.0
C5 B:G18 3.3 38.0 1.0
N7 B:G18 3.4 39.2 1.0
C4 B:C17 3.4 38.9 1.0
N3 A:G7 3.5 37.5 1.0
C6 B:G18 3.5 37.6 1.0
N1 B:A16 3.6 32.2 1.0
N6 B:A16 3.6 34.8 1.0
C5 A:G7 3.7 38.3 1.0
C6 B:A16 3.7 33.0 1.0
N4 B:C17 3.8 37.1 1.0
O6 B:G18 3.8 35.1 1.0
C4 B:G18 3.9 38.8 1.0
C8 B:G18 3.9 40.7 1.0
C4 A:G7 4.0 38.8 1.0
N9 B:G18 4.2 38.8 1.0
N1 B:C17 4.2 37.7 1.0
N1 B:G18 4.2 34.2 1.0
C2 B:A16 4.4 35.2 1.0
N3 B:G18 4.6 37.0 1.0
C2 B:G18 4.7 38.4 1.0
C5 B:A16 4.7 34.2 1.0
C5 B:C17 4.7 36.5 1.0
C6 B:C17 5.0 35.8 1.0
N7 A:G7 5.0 38.1 1.0

Gold binding site 2 out of 2 in 2oij

Go back to Gold Binding Sites List in 2oij
Gold binding site 2 out of 2 in the Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Hiv-1 Subtype B Dis Rna Extended Duplex AUCL3 Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au101

b:38.6
occ:0.35
N1 B:G7 1.7 40.3 1.0
N2 B:G7 2.3 40.6 1.0
C2 B:G7 2.3 40.2 1.0
N3 A:C17 2.4 40.2 1.0
O2 A:C17 2.6 38.3 1.0
C6 B:G7 2.8 40.0 1.0
C2 A:C17 2.8 40.0 1.0
C5 A:G18 3.2 36.0 1.0
O6 B:G7 3.2 40.1 1.0
N7 A:G18 3.4 39.4 1.0
C6 A:G18 3.5 36.5 1.0
C4 A:G18 3.5 37.8 1.0
N3 B:G7 3.5 40.1 1.0
C4 A:C17 3.6 42.2 1.0
N6 A:A16 3.7 40.8 1.0
C8 A:G18 3.8 40.5 1.0
N1 A:A16 3.9 40.0 1.0
N9 A:G18 3.9 37.7 1.0
C5 B:G7 3.9 40.1 1.0
N1 A:G18 3.9 37.8 1.0
O6 A:G18 4.0 32.2 1.0
C6 A:A16 4.0 40.7 1.0
N4 A:C17 4.0 43.0 1.0
C4 B:G7 4.1 40.7 1.0
N3 A:G18 4.1 36.7 1.0
C2 A:G18 4.2 34.0 1.0
N1 A:C17 4.2 40.8 1.0
C2 A:A16 4.7 42.0 1.0
C1' A:G18 4.8 38.9 1.0
C5 A:C17 4.8 43.5 1.0

Reference:

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
Page generated: Sat Dec 12 01:53:13 2020

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