Atomistry » Chlorine » PDB 3v6e-3vfb » 3vfa
Atomistry »
  Chlorine »
    PDB 3v6e-3vfb »
      3vfa »

Chlorine in PDB 3vfa: Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031, PDB code: 3vfa 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 / 1.43
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.644, 86.459, 45.441, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.8

Other elements in 3vfa:

The structure of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 (pdb code 3vfa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031, PDB code: 3vfa:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 1 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:17.5
occ:1.00
 ND2 A:ASN88 3.2 14.6 1.0
N A:THR74 3.2 14.2 1.0
OG1 A:THR74 3.8 20.3 1.0
CB A:ASN88 3.8 11.9 1.0
CA A:GLY73 3.8 13.2 1.0
CB A:THR74 3.8 16.0 1.0
CG A:ASN88 4.0 13.3 1.0
C A:GLY73 4.0 12.1 1.0
CA A:THR74 4.2 13.6 1.0
O A:HOH1018 4.5 21.7 1.0
O A:ASN88 4.7 13.9 1.0
O A:THR74 4.7 13.7 1.0
CA A:ASN88 4.9 12.3 1.0
C A:THR74 5.0 13.2 1.0
C A:ASN88 5.0 11.7 1.0

Chlorine binding site 2 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 2 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:21.9
occ:0.50
 OG A:SER37 3.1 29.8 0.3
NE2 A:GLN18 3.2 41.5 1.0
N A:SER37 3.3 19.6 1.0
CB A:MET36 3.8 18.6 1.0
CA A:MET36 3.8 17.0 1.0
C A:MET36 4.0 19.6 1.0
CD A:GLN18 4.2 31.5 1.0
CB A:SER37 4.2 21.9 0.3
OE1 A:GLN18 4.2 34.2 1.0
CB A:SER37 4.3 21.7 0.3
CB A:SER37 4.3 21.9 0.3
CA A:SER37 4.3 19.8 0.3
CA A:SER37 4.3 19.9 0.3
CA A:SER37 4.3 19.9 0.3
O A:SER37 4.3 21.2 1.0
CE A:MET36 4.8 19.5 1.0
C A:SER37 4.8 19.2 1.0
OG A:SER37 4.9 26.8 0.3
CG A:MET36 5.0 20.5 1.0

Chlorine binding site 3 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 3 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:17.2
occ:0.50
 N A:GLY48 3.2 13.5 1.0
C40 A:031201 3.7 24.3 0.7
CA A:ILE47 3.7 11.5 1.0
C31 A:031201 3.7 16.2 0.3
C30 A:031201 3.7 17.1 0.3
O A:GLY48 3.9 16.3 1.0
CB A:ILE47 3.9 12.1 1.0
C A:ILE47 4.0 12.6 1.0
C3 A:031201 4.2 15.5 0.7
CA A:GLY48 4.2 14.2 1.0
CG2 A:ILE47 4.2 15.6 1.0
C A:GLY48 4.5 13.1 1.0
C27 A:031201 4.5 16.3 0.3
O A:MET46 4.6 15.6 1.0
CE2 A:PHE53 4.6 16.2 1.0
O A:HOH1054 4.8 21.6 0.3
C29 A:031201 4.9 18.7 0.3
C24 A:031201 4.9 14.5 0.3
O A:HOH1039 4.9 23.0 0.5
N A:ILE47 4.9 12.7 1.0
O39 A:031201 4.9 17.9 0.7
C4 A:031201 5.0 12.8 0.7

Chlorine binding site 4 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 4 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 4 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:19.1
occ:0.50
 N A:LYS55 3.2 15.5 1.0
CA A:ILE54 3.7 12.4 1.0
CB A:ILE54 3.9 13.9 1.0
C A:ILE54 3.9 13.5 1.0
CB A:LYS55 4.0 21.8 1.0
CG A:PRO79 4.1 19.8 1.0
CA A:LYS55 4.1 15.9 1.0
CG2 A:ILE54 4.3 16.0 1.0
O A:LYS55 4.3 18.1 1.0
C A:LYS55 4.7 15.7 1.0
O A:PHE53 4.8 19.3 1.0
CD A:PRO79 4.8 17.3 1.0
N A:ILE54 4.9 13.9 1.0

Chlorine binding site 5 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 5 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 5 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:18.8
occ:1.00
 O A:HOH1013 3.3 15.0 1.0
NE1 B:TRP6 3.3 14.5 1.0
O B:HOH223 3.3 35.2 1.0
CZ2 B:TRP6 3.9 14.3 1.0
CE2 B:TRP6 4.0 13.8 1.0
CG2 B:THR4 4.2 20.3 1.0
CD1 B:TRP6 4.5 13.5 1.0
CB B:THR4 4.9 15.4 1.0

Chlorine binding site 6 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 6 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 6 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:20.7
occ:0.50
 N B:THR12 3.2 13.9 1.0
CB B:VAL11 3.6 18.0 1.0
CA B:VAL11 3.7 15.5 1.0
CB B:ALA67 3.8 34.0 1.0
CA B:ALA67 3.9 25.5 1.0
C B:VAL11 3.9 14.2 1.0
CB B:THR12 4.0 15.4 1.0
CA B:THR12 4.1 15.0 1.0
CG1 B:VAL11 4.2 22.1 1.0
O B:THR12 4.3 16.1 1.0
OG1 B:THR12 4.3 19.8 1.0
C B:THR12 4.7 13.5 1.0
N B:ALA67 4.7 21.0 1.0
C B:ALA67 4.9 24.8 1.0
CG2 B:VAL11 4.9 20.2 1.0

Chlorine binding site 7 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 7 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 7 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:23.8
occ:0.50
 N B:GLU21 3.2 15.8 1.0
O B:HOH242 3.2 29.4 1.0
CA B:LYS20 3.8 16.4 1.0
CB B:LYS20 3.8 19.4 1.0
ND2 B:ASN83 3.8 16.2 1.0
O B:GLU21 3.9 15.3 1.0
C B:LYS20 4.0 14.3 1.0
CB B:GLU21 4.1 22.5 1.0
CA B:GLU21 4.1 15.5 1.0
CG B:LYS20 4.2 23.1 1.0
C B:GLU21 4.5 15.1 1.0
O B:HOH234 4.9 31.2 1.0

Chlorine binding site 8 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 8 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 8 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl104

b:21.9
occ:0.20
 CL B:CL104 0.0 21.9 0.2
CL B:CL104 1.4 21.1 0.2
N B:LYS55 3.4 19.3 1.0
CB B:ILE54 3.8 26.6 1.0
CA B:ILE54 3.9 22.7 1.0
O B:LYS55 4.1 19.5 1.0
C B:ILE54 4.2 18.6 1.0
CA B:LYS55 4.3 19.3 1.0
CG2 B:ILE54 4.3 30.3 1.0
CB B:LYS55 4.3 21.9 1.0
CG B:PRO79 4.5 23.5 1.0
C B:LYS55 4.7 17.2 1.0
CG B:LYS55 4.7 36.9 1.0
O B:PHE53 5.0 38.2 1.0

Chlorine binding site 9 out of 9 in 3vfa

Go back to Chlorine Binding Sites List in 3vfa
Chlorine binding site 9 out of 9 in the Crystal Structure of Hiv-1 Protease Mutant V82A 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 9 of Crystal Structure of Hiv-1 Protease Mutant V82A with Novel P1'-Ligands Grl-02031 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl104

b:21.1
occ:0.20
 CL B:CL104 0.0 21.1 0.2
CL B:CL104 1.4 21.9 0.2
N B:LYS55 3.1 19.3 1.0
CA B:ILE54 3.7 22.7 1.0
CG B:LYS55 3.9 36.9 1.0
C B:ILE54 3.9 18.6 1.0
CB B:LYS55 3.9 21.9 1.0
CA B:LYS55 4.1 19.3 1.0
CB B:ILE54 4.2 26.6 1.0
O B:PHE53 4.5 38.2 1.0
O B:LYS55 4.6 19.5 1.0
CD B:LYS55 4.7 47.4 1.0
CG2 B:ILE54 4.8 30.3 1.0
C B:LYS55 4.9 17.2 1.0
N B:ILE54 4.9 23.8 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: Fri Jul 11 11:40:44 2025

Last articles

Mg in 1S8F
Mg in 1S83
Mg in 1S77
Mg in 1S76
Mg in 1S4E
Mg in 1S6P
Mg in 1S6H
Mg in 1S5J
Mg in 1S5G
Mg in 1S2V
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy