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Sodium in PDB 3dk1: Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A

Enzymatic activity of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A

All present enzymatic activity of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A:
3.4.23.16;

Protein crystallography data

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A, PDB code: 3dk1 was solved by Y.F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.07
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.003, 86.338, 45.833, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.7

Other elements in 3dk1:

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A (pdb code 3dk1). 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 Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A, PDB code: 3dk1:

Sodium binding site 1 out of 1 in 3dk1

Go back to Sodium Binding Sites List in 3dk1
Sodium binding site 1 out of 1 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:17.2
occ:1.00
 O A:HOH1013 2.3 16.2 1.0
O A:HOH1032 2.4 17.6 1.0
O A:HOH1026 2.4 21.2 1.0
O A:ASP60 2.4 12.6 1.0
O A:HOH1062 2.4 27.4 1.0
O A:HOH1055 2.7 23.0 1.0
C A:ASP60 3.4 12.3 1.0
N A:ASP60 3.8 11.9 1.0
CA A:ASP60 4.0 12.1 1.0
O A:ARG41 4.1 14.8 1.0
O A:HOH1113 4.2 28.9 1.0
O A:HOH1108 4.3 28.4 0.5
CB A:ASP60 4.4 14.4 1.0
CB A:GLN61 4.4 15.7 0.4
CB A:GLN61 4.4 15.5 0.6
N A:GLN61 4.5 12.7 1.0
N A:ARG41 4.5 18.4 1.0
O A:GLN61 4.6 14.6 1.0
O A:PRO39 4.7 18.4 1.0
C A:TYR59 4.7 10.5 1.0
CD1 A:ILE62 4.7 13.7 1.0
CA A:GLY40 4.7 21.1 1.0
CA A:GLN61 4.8 13.1 1.0
C A:GLN61 4.8 12.4 1.0

Reference:

A.K.Ghosh, S.Gemma, J.Takayama, A.Baldridge, S.Leshchenko-Yashchuk, H.B.Miller, Y.F.Wang, A.Y.Kovalevsky, Y.Koh, I.T.Weber, H.Mitsuya. Potent Hiv-1 Protease Inhibitors Incorporating Meso-Bicyclic Urethanes As P2-Ligands: Structure-Based Design, Synthesis, Biological Evaluation and Protein-Ligand X-Ray Studies Org.Biomol.Chem. V. 6 3703 2008.
ISSN: ISSN 1477-0520
PubMed: 18843400
DOI: 10.1039/B809178A
Page generated: Sun Aug 17 14:32:25 2025

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