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Sodium in PDB 3d20: Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia

Enzymatic activity of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia

All present enzymatic activity of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia, PDB code: 3d20 was solved by F.Liu, A.Y.Kovalesky, Y.Tie, A.K.Ghosh, 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 / 1.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.840, 86.110, 46.190, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18

Other elements in 3d20:

The structure of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia (pdb code 3d20). 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 of Hiv-1 Mutant I54V and Inhibitor Darunavia, PDB code: 3d20:

Sodium binding site 1 out of 1 in 3d20

Go back to Sodium Binding Sites List in 3d20
Sodium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Darunavia


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 Mutant I54V and Inhibitor Darunavia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:21.2
occ:1.00
O A:HOH1029 2.3 20.8 1.0
O A:ASP60 2.4 14.9 1.0
O A:HOH1023 2.4 20.5 1.0
O A:HOH1032 2.4 23.3 1.0
O A:HOH1104 2.5 29.6 1.0
O A:HOH1087 2.6 26.6 1.0
C A:ASP60 3.4 14.4 1.0
N A:ASP60 3.8 13.8 1.0
CA A:ASP60 4.0 14.4 1.0
O A:ARG41 4.1 17.9 1.0
CB A:GLN61 4.3 18.8 0.3
O A:HOH1149 4.3 30.3 1.0
CB A:ASP60 4.4 17.2 1.0
CB A:GLN61 4.4 18.6 0.7
NE2 A:GLN61 4.4 26.8 0.3
N A:ARG41 4.4 23.4 1.0
N A:GLN61 4.4 14.2 1.0
O A:HOH1193 4.6 43.4 1.0
O A:HOH1188 4.6 44.8 1.0
O A:PRO39 4.6 20.7 1.0
O A:GLN61 4.6 17.5 1.0
CD1 A:ILE62 4.6 15.7 1.0
CA A:GLN61 4.7 15.8 1.0
C A:TYR59 4.7 12.1 1.0
C A:GLN61 4.8 15.1 1.0
O A:HOH1201 4.8 46.9 1.0
CA A:GLY40 4.8 25.7 1.0
O A:HOH1166 5.0 55.4 1.0
C A:GLY40 5.0 21.5 1.0

Reference:

F.Liu, A.Y.Kovalevsky, Y.Tie, A.K.Ghosh, R.W.Harrison, I.T.Weber. Effect of Flap Mutations on Structure of Hiv-1 Protease and Inhibition By Saquinavir and Darunavir. J.Mol.Biol. V. 381 102 2008.
ISSN: ISSN 0022-2836
PubMed: 18597780
DOI: 10.1016/J.JMB.2008.05.062
Page generated: Tue Dec 15 06:08:18 2020

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