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Sodium in PDB 3i6o: Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A

Enzymatic activity of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A

All present enzymatic activity of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A, PDB code: 3i6o was solved by A.A.Chumanevich, Y.-F.Wang, A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.764, 86.328, 45.976, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.6

Other elements in 3i6o:

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A also contains other interesting chemical elements:

Iodine (I) 19 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A (pdb code 3i6o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A, PDB code: 3i6o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3i6o

Go back to Sodium Binding Sites List in 3i6o
Sodium binding site 1 out of 2 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


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 Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:21.5
occ:1.00
O A:HOH1023 2.3 19.1 1.0
O A:HOH1107 2.3 18.6 1.0
O A:ASP60 2.4 14.9 1.0
O A:HOH1055 2.5 23.9 1.0
O A:HOH1076 2.5 29.2 1.0
O A:HOH1094 2.6 31.7 1.0
C A:ASP60 3.4 13.5 1.0
N A:ASP60 3.8 12.6 1.0
CA A:ASP60 4.0 14.4 1.0
O A:ARG41 4.1 19.2 1.0
N A:ARG41 4.4 22.1 1.0
CB A:ASP60 4.4 15.7 1.0
CB A:GLN61 4.4 17.6 1.0
N A:GLN61 4.5 14.1 1.0
O A:PRO39 4.6 21.9 1.0
O A:GLN61 4.7 17.1 1.0
O A:HOH1139 4.7 37.1 1.0
CD1 A:ILE62 4.7 16.2 1.0
C A:TYR59 4.7 11.0 1.0
CA A:GLY40 4.8 22.4 1.0
CA A:GLN61 4.8 14.3 1.0
C A:GLN61 4.8 14.7 1.0
OE1 A:GLN61 4.9 41.6 1.0
C A:GLY40 5.0 21.0 1.0

Sodium binding site 2 out of 2 in 3i6o

Go back to Sodium Binding Sites List in 3i6o
Sodium binding site 2 out of 2 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


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 Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:22.8
occ:1.00
O B:HOH1034 2.3 19.6 1.0
O B:HOH1069 2.3 29.1 1.0
O B:HOH1048 2.4 20.9 1.0
O B:ASP160 2.5 15.5 1.0
O B:HOH1098 2.6 37.3 1.0
O B:HOH1068 2.7 25.9 1.0
C B:ASP160 3.5 14.3 1.0
N B:ASP160 3.7 13.1 1.0
CA B:ASP160 4.0 13.2 1.0
O B:ARG141 4.1 14.1 1.0
CB B:GLN161 4.2 13.7 0.4
CB B:ASP160 4.4 14.4 1.0
O B:PRO139 4.4 16.8 1.0
N B:ARG141 4.5 12.0 1.0
N B:GLN161 4.6 13.0 1.0
C B:TYR159 4.6 11.7 1.0
CA B:GLY140 4.7 14.6 1.0
CD1 B:ILE162 4.7 15.8 1.0
CB B:GLN161 4.8 13.8 0.6
CA B:GLN161 4.8 13.9 0.4
O B:GLN161 4.8 19.3 1.0
C B:GLN161 4.9 13.9 1.0
CA B:TYR159 4.9 11.5 1.0
CA B:GLN161 5.0 14.2 0.6
C B:GLY140 5.0 12.2 1.0

Reference:

A.K.Ghosh, S.Kulkarni, D.D.Anderson, L.Hong, A.Baldridge, Y.F.Wang, A.A.Chumanevich, A.Y.Kovalevsky, Y.Tojo, M.Amano, Y.Koh, J.Tang, I.T.Weber, H.Mitsuya. Design, Synthesis, Protein-Ligand X-Ray Structure, and Biological Evaluation of A Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance. J.Med.Chem. V. 52 7689 2009.
ISSN: ISSN 0022-2623
PubMed: 19746963
DOI: 10.1021/JM900695W
Page generated: Tue Dec 15 06:14:17 2020

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