Chlorine in PDB 3vf7: Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7 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 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.820, 86.242, 46.005, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.5

Other elements in 3vf7:

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 (pdb code 3vf7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3vf7

Go back to Chlorine Binding Sites List in 3vf7
Chlorine binding site 1 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:11.9
occ:0.75
C1 A:GOL206 2.6 23.4 0.2
NE1 A:TRP6 3.2 11.5 1.0
O B:HOH604 3.3 12.4 1.0
O1 A:GOL206 3.3 20.7 0.2
CZ2 A:TRP6 3.8 10.5 1.0
CE2 A:TRP6 3.9 9.7 1.0
C2 A:GOL206 3.9 25.8 0.2
CG2 A:THR4 4.2 16.7 1.0
CD1 A:TRP6 4.4 10.8 1.0
O A:HOH1042 4.6 28.6 1.0
O2 A:GOL206 4.8 28.4 0.2
CB A:THR4 4.8 12.2 1.0

Chlorine binding site 2 out of 3 in 3vf7

Go back to Chlorine Binding Sites List in 3vf7
Chlorine binding site 2 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:16.8
occ:1.00
O A:HOH1015 3.0 16.0 1.0
ND2 A:ASN88 3.2 10.8 1.0
N A:THR74 3.2 9.4 1.0
OG1 A:THR74 3.7 12.8 1.0
CA A:GLY73 3.8 10.0 1.0
CB A:THR74 3.8 10.7 1.0
C2 A:GOL205 3.8 29.3 0.5
CB A:ASN88 3.9 10.2 1.0
C1 A:GOL205 3.9 29.1 0.5
C A:GLY73 4.0 8.7 1.0
CG A:ASN88 4.0 9.1 1.0
CA A:THR74 4.1 9.6 1.0
O A:HOH1009 4.1 13.2 1.0
O2 A:GOL205 4.2 38.6 0.5
NE2 A:GLN92 4.4 12.2 1.0
O A:ASN88 4.6 12.4 1.0
CD2 A:LEU89 4.6 14.9 1.0
O A:THR74 4.7 9.9 1.0
C A:ASN88 4.8 10.1 1.0
CA A:ASN88 4.8 8.8 1.0
C A:THR74 4.9 9.6 1.0

Chlorine binding site 3 out of 3 in 3vf7

Go back to Chlorine Binding Sites List in 3vf7
Chlorine binding site 3 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:13.6
occ:1.00
N B:THR74 3.2 9.7 1.0
ND2 B:ASN88 3.3 12.0 1.0
CA B:GLY73 3.8 10.2 1.0
CB B:ASN88 3.8 8.9 1.0
OG1 B:THR74 3.9 14.6 1.0
CB B:THR74 3.9 12.3 1.0
C B:GLY73 4.0 10.2 1.0
CG B:ASN88 4.1 9.5 1.0
CA B:THR74 4.2 9.5 1.0
O B:HOH614 4.4 21.8 1.0
O B:THR74 4.7 10.8 1.0
O B:ASN88 4.7 10.4 1.0
CA B:ASN88 4.9 8.7 1.0
C B:THR74 5.0 9.4 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: Sat Dec 12 10:17:22 2020

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