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Sodium in PDB 2nmy: Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir

Enzymatic activity of Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir

All present enzymatic activity of Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir, PDB code: 2nmy was solved by Y.Tie, A.Y.Kovalevsky, P.Boross, Y.F.Wang, A.K.Ghosh, J.Tozser, R.W.Harrison, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.988, 87.464, 47.190, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.1

Other elements in 2nmy:

The structure of Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir (pdb code 2nmy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir, PDB code: 2nmy:

Sodium binding site 1 out of 1 in 2nmy

Go back to Sodium Binding Sites List in 2nmy
Sodium binding site 1 out of 1 in the Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Hiv-1 Protease Mutant V82A with A Inhibitor Saquinavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:25.7
occ:1.00
 O A:HOH1157 2.1 46.6 1.0
O A:HOH1120 2.2 25.8 1.0
O A:HOH1057 2.4 24.6 1.0
O A:ASP60 2.5 15.1 1.0
O A:HOH1080 2.5 29.0 1.0
O A:HOH1112 3.1 43.7 1.0
C A:ASP60 3.4 14.5 1.0
N A:ASP60 3.8 13.4 1.0
CA A:ASP60 4.1 13.7 1.0
O A:HOH1184 4.1 37.7 1.0
O A:ARG41 4.3 20.1 1.0
CB A:ASP60 4.4 17.1 1.0
N A:GLN61 4.5 14.3 1.0
CB A:GLN61 4.5 18.3 1.0
N A:ARG41 4.6 24.7 1.0
O A:PRO39 4.7 23.5 1.0
O A:GLN61 4.7 19.0 1.0
C A:TYR59 4.8 10.5 1.0
CA A:GLN61 4.8 15.8 1.0
CA A:GLY40 4.8 25.3 1.0
C A:GLN61 4.9 14.8 1.0
CD1 A:ILE62 4.9 15.4 1.0

Reference:

Y.Tie, A.Y.Kovalevsky, P.Boross, Y.F.Wang, A.K.Ghosh, J.Tozser, R.W.Harrison, I.T.Weber. Atomic Resolution Crystal Structures of Hiv-1 Protease and Mutants V82A and I84V with Saquinavir. Proteins V. 67 232 2007.
ISSN: ISSN 0887-3585
PubMed: 17243183
DOI: 10.1002/PROT.21304
Page generated: Mon Oct 7 03:07:08 2024

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