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Platinum in PDB 1y73: Hiv-1 Dis(Mal) Duplex Pt-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Pt-Soaked, PDB code: 1y73 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) 7.99 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.915, 58.915, 65.194, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 19.4

Other elements in 1y73:

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

Magnesium (Mg) 8 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Hiv-1 Dis(Mal) Duplex Pt-Soaked (pdb code 1y73). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Hiv-1 Dis(Mal) Duplex Pt-Soaked, PDB code: 1y73:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 1y73

Go back to Platinum Binding Sites List in 1y73
Platinum binding site 1 out of 2 in the Hiv-1 Dis(Mal) Duplex Pt-Soaked


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Hiv-1 Dis(Mal) Duplex Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt217

b:73.0
occ:0.39
O A:HOH235 2.4 42.8 0.7
N7 A:A14 3.0 56.4 1.0
C8 A:A14 3.9 56.8 1.0
N6 A:A14 4.0 56.3 1.0
C5 A:A14 4.0 56.7 1.0
C5 A:C13 4.2 62.5 1.0
N4 A:C15 4.2 51.4 1.0
OP2 A:A14 4.3 64.6 1.0
C4 A:C13 4.3 62.7 1.0
N4 A:C13 4.4 62.7 1.0
C6 A:A14 4.5 56.9 1.0
C6 A:C13 4.7 61.9 1.0
C5 A:C15 4.8 50.6 1.0
C4 A:C15 4.9 50.1 1.0
N3 A:C13 5.0 62.8 1.0

Platinum binding site 2 out of 2 in 1y73

Go back to Platinum Binding Sites List in 1y73
Platinum binding site 2 out of 2 in the Hiv-1 Dis(Mal) Duplex Pt-Soaked


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Hiv-1 Dis(Mal) Duplex Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt121

b:78.7
occ:0.43
N7 B:A14 2.6 55.8 1.0
C8 B:A14 3.6 55.1 1.0
C5 B:A14 3.6 54.5 1.0
N4 B:C15 3.7 48.7 1.0
N6 B:A14 3.7 51.8 1.0
C5 B:C13 4.0 50.3 1.0
C6 B:A14 4.1 53.6 1.0
C4 B:C13 4.1 50.1 1.0
N4 B:C13 4.2 48.5 1.0
C4 B:C15 4.4 49.9 1.0
C5 B:C15 4.5 49.9 1.0
C6 B:C13 4.5 50.8 1.0
OP2 B:A14 4.6 56.3 1.0
N3 B:C13 4.6 51.2 1.0
N9 B:A14 4.7 55.7 1.0
C4 B:A14 4.8 54.8 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: Wed Dec 16 02:03:54 2020

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