Atomistry » Sodium » PDB 3nte-3off » 3nu5
Atomistry »
  Sodium »
    PDB 3nte-3off »
      3nu5 »

Sodium in PDB 3nu5: Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5 was solved by Y.-F.Wang, C.H.Shen, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.953, 86.011, 46.209, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19.3

Other elements in 3nu5:

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir (pdb code 3nu5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3nu5

Go back to Sodium Binding Sites List in 3nu5
Sodium binding site 1 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:20.6
occ:1.00
O A:HOH1085 2.2 32.7 1.0
O A:HOH1013 2.4 17.7 1.0
O A:HOH1022 2.4 19.8 1.0
O A:ASP60 2.4 14.2 1.0
O A:HOH1073 2.4 26.2 1.0
O A:HOH1066 2.7 27.2 1.0
C A:ASP60 3.4 13.7 1.0
N A:ASP60 3.8 12.2 1.0
CA A:ASP60 4.0 13.6 1.0
O A:ARG41 4.2 16.2 1.0
CB A:ASP60 4.4 16.0 1.0
CB A:GLN61 4.4 17.4 1.0
N A:GLN61 4.5 13.8 1.0
N A:ARG41 4.5 18.5 1.0
O A:HOH1119 4.5 24.8 0.5
O A:GLN61 4.7 16.3 1.0
O A:PRO39 4.7 19.4 1.0
C A:TYR59 4.7 10.3 1.0
CD1 A:ILE62 4.7 14.5 1.0
CA A:GLN61 4.8 14.4 1.0
OE1 A:GLN61 4.8 40.3 1.0
C A:GLN61 4.8 14.2 1.0
CA A:GLY40 4.8 17.9 1.0

Sodium binding site 2 out of 3 in 3nu5

Go back to Sodium Binding Sites List in 3nu5
Sodium binding site 2 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:21.8
occ:0.50
O B:HOH1023 2.3 21.4 1.0
O B:ASP160 2.4 14.7 1.0
O B:HOH1113 2.4 22.9 0.5
O B:HOH1177 3.0 17.2 0.5
C B:ASP160 3.4 12.4 1.0
N B:ASP160 3.7 14.0 1.0
CA B:ASP160 4.0 13.7 1.0
O B:HOH1046 4.1 32.2 1.0
CB B:ASP160 4.3 15.8 1.0
O B:ARG141 4.4 14.9 1.0
O B:PRO139 4.5 16.3 1.0
CD1 B:ILE162 4.5 17.8 1.0
N B:GLN161 4.5 12.7 1.0
C B:TYR159 4.6 10.2 1.0
CB B:GLN161 4.6 17.0 1.0
C B:GLN161 4.8 12.8 1.0
O B:GLN161 4.8 16.1 1.0
CA B:GLN161 4.9 12.8 1.0
CA B:GLY140 4.9 14.4 1.0
O B:HOH1147 4.9 26.8 0.5
CA B:TYR159 4.9 10.3 1.0

Sodium binding site 3 out of 3 in 3nu5

Go back to Sodium Binding Sites List in 3nu5
Sodium binding site 3 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:26.0
occ:0.50
O B:HOH1158 2.0 24.3 0.5
O B:HOH1159 2.4 23.2 0.5
O B:HOH1162 2.4 22.7 0.5
O B:HOH1160 2.5 24.7 0.5
O B:HOH1161 2.5 19.3 0.2
O B:HOH1157 2.7 19.5 1.0
OH B:TYR159 3.8 16.0 1.0
CA B:SER137 4.1 19.3 0.3
CA B:SER137 4.1 19.3 0.7
OG B:SER137 4.1 30.9 0.7
OG B:SER137 4.1 21.8 0.3
O B:HOH1050 4.2 18.5 1.0
O B:LEU138 4.3 16.1 1.0
N B:LEU138 4.4 15.6 1.0
CB B:SER137 4.4 22.7 0.3
NH2 B:ARG157 4.4 25.1 1.0
CB B:SER137 4.5 23.8 0.7
O B:MET136 4.5 19.6 1.0
C B:SER137 4.8 16.4 1.0
O B:HOH1129 4.9 19.0 0.2
CZ B:TYR159 4.9 14.2 1.0

Reference:

C.H.Shen, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Amprenavir Complexes with Hiv-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. Febs J. V. 277 3699 2010.
ISSN: ISSN 1742-464X
PubMed: 20695887
DOI: 10.1111/J.1742-4658.2010.07771.X
Page generated: Tue Dec 15 06:19:22 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy