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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sat Dec 12 10:17:22 2020

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