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Sodium in PDB 3vfb: Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031, PDB code: 3vfb was solved by X.X.Yu, Y.F.Wang, Y.C.E.Chang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.255, 86.386, 46.068, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 21.6

Other elements in 3vfb:

The structure of Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031 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 Protease Mutant N88D with Novel P1'-Ligands Grl-02031 (pdb code 3vfb). 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 Protease Mutant N88D with Novel P1'-Ligands Grl-02031, PDB code: 3vfb:

Sodium binding site 1 out of 1 in 3vfb

Go back to Sodium Binding Sites List in 3vfb
Sodium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Protease Mutant N88D with Novel P1'-Ligands Grl-02031


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 N88D with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:24.6
occ:1.00
 O B:HOH641 2.3 20.7 1.0
O B:ASP60 2.3 18.1 1.0
O B:HOH634 2.4 28.4 1.0
O B:HOH640 2.5 26.2 1.0
O B:HOH618 2.8 32.2 1.0
C B:ASP60 3.4 18.8 1.0
N B:ASP60 3.7 17.0 1.0
CA B:ASP60 4.0 19.6 1.0
O B:ARG41 4.2 20.3 1.0
N B:GLN61 4.4 18.3 1.0
CB B:GLN61 4.4 22.0 1.0
CB B:ASP60 4.5 22.8 1.0
O B:GLN61 4.5 22.4 1.0
CD1 B:ILE62 4.6 16.2 1.0
N B:ARG41 4.6 21.8 1.0
C B:GLN61 4.6 18.3 1.0
C B:TYR59 4.7 14.7 1.0
O B:PRO39 4.7 21.8 1.0
CA B:GLN61 4.7 19.6 1.0
OE1 B:GLN61 4.7 58.9 1.0

Reference:

Y.C.Chang, X.Yu, Y.Zhang, Y.Tie, Y.F.Wang, S.Yashchuk, A.K.Ghosh, R.W.Harrison, I.T.Weber. Potent Antiviral Hiv-1 Protease Inhibitor Grl-02031 Adapts to the Structures of Drug Resistant Mutants with Its P1'-Pyrrolidinone Ring. J.Med.Chem. V. 55 3387 2012.
ISSN: ISSN 0022-2623
PubMed: 22401672
DOI: 10.1021/JM300072D
Page generated: Mon Oct 7 13:49:28 2024

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