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Sodium in PDB 4kb9: Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A

Enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A

All present enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A, PDB code: 4kb9 was solved by Y.-F.Wang, J.Agniswamy, 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 (°) 58.477, 86.300, 46.045, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 18

Other elements in 4kb9:

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A (pdb code 4kb9). 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 Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A, PDB code: 4kb9:

Sodium binding site 1 out of 1 in 4kb9

Go back to Sodium Binding Sites List in 4kb9
Sodium binding site 1 out of 1 in the Crystal Structure of Wild-Type Hiv-1 Protease with Novel Tricyclic P2- Ligands Grl-0739A


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 Novel Tricyclic P2- Ligands Grl-0739A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:22.0
occ:1.00
 O B:HOH602 2.3 19.9 1.0
O B:ASP60 2.3 14.2 1.0
O B:HOH603 2.4 24.4 1.0
O B:HOH601 2.4 18.6 1.0
O B:HOH607 2.4 35.0 1.0
O B:HOH606 2.9 29.4 1.0
C B:ASP60 3.4 13.0 1.0
N B:ASP60 3.7 12.6 1.0
CA B:ASP60 4.0 13.3 1.0
O B:ARG41 4.2 16.9 1.0
O B:HOH605 4.2 28.8 0.5
O B:HOH604 4.3 31.8 0.5
CB B:ASP60 4.4 15.2 1.0
CB B:GLN61 4.4 16.9 1.0
N B:GLN61 4.4 13.2 1.0
N B:ARG41 4.6 20.6 1.0
CD1 B:ILE62 4.6 14.6 1.0
O B:GLN61 4.6 17.3 1.0
C B:TYR59 4.7 11.5 1.0
O B:PRO39 4.7 19.6 1.0
CA B:GLY40 4.7 21.6 1.0
CA B:GLN61 4.8 14.2 1.0
C B:GLN61 4.8 13.9 1.0
OE1 B:GLN61 5.0 51.0 1.0

Reference:

A.K.Ghosh, G.L.Parham, C.D.Martyr, P.R.Nyalapatla, H.L.Osswald, J.Agniswamy, Y.F.Wang, M.Amano, I.T.Weber, H.Mitsuya. Highly Potent Hiv-1 Protease Inhibitors with Novel Tricyclic P2 Ligands: Design, Synthesis, and Protein-Ligand X-Ray Studies. J.Med.Chem. V. 56 6792 2013.
ISSN: ISSN 0022-2623
PubMed: 23947685
DOI: 10.1021/JM400768F
Page generated: Mon Oct 7 16:28:17 2024

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