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Chlorine in PDB 3nu5: Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5 was solved by Y.-F.Wang, C.H.Shen, 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 (°) 57.953, 86.011, 46.209, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19.3

Other elements in 3nu5:

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir (pdb code 3nu5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3nu5

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Chlorine binding site 1 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl511

b:14.8
occ:1.00
 O A:HOH1105 3.1 27.1 0.5
N A:THR74 3.2 10.4 1.0
ND2 A:ASN88 3.3 11.4 1.0
OG1 A:THR74 3.7 16.5 1.0
CA A:GLY73 3.8 10.9 1.0
CB A:ASN88 3.8 10.4 1.0
CB A:THR74 3.8 13.3 1.0
C A:GLY73 4.0 10.4 1.0
CG A:ASN88 4.1 11.3 1.0
CA A:THR74 4.2 11.0 1.0
O A:HOH1031 4.2 20.6 1.0
O A:ASN88 4.6 11.1 1.0
OD1 A:ASP30 4.8 21.9 0.6
O A:THR74 4.8 13.2 1.0
CA A:ASN88 4.8 10.8 1.0
C A:ASN88 5.0 10.4 1.0

Chlorine binding site 2 out of 7 in 3nu5

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Chlorine binding site 2 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl517

b:16.7
occ:0.50
 N A:LYS55 3.2 11.8 1.0
O A:HOH1068 3.2 36.7 1.0
CA A:ILE54 3.6 11.1 1.0
CB A:ILE54 3.9 12.4 1.0
C A:ILE54 3.9 11.2 1.0
CB A:LYS55 4.0 14.8 1.0
CA A:LYS55 4.2 11.0 1.0
CG A:PRO79 4.2 12.8 1.0
CG2 A:ILE54 4.3 17.3 1.0
O A:LYS55 4.3 12.3 1.0
O A:HOH1140 4.7 21.3 0.5
O A:PHE53 4.7 17.0 1.0
C A:LYS55 4.8 11.3 1.0
N A:ILE54 4.9 12.1 1.0
CD A:PRO79 4.9 11.7 1.0

Chlorine binding site 3 out of 7 in 3nu5

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Chlorine binding site 3 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl512

b:18.3
occ:1.00
 NE1 B:TRP106 3.2 12.9 1.0
O A:HOH1017 3.3 14.2 1.0
O B:HOH1106 3.3 24.0 0.5
CZ2 B:TRP106 3.8 13.4 1.0
CE2 B:TRP106 3.9 12.4 1.0
CG2 B:THR104 4.2 17.6 1.0
CD1 B:TRP106 4.4 12.1 1.0
O B:HOH1114 4.8 25.2 0.5
CB B:THR104 4.8 14.2 1.0

Chlorine binding site 4 out of 7 in 3nu5

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Chlorine binding site 4 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl513

b:19.8
occ:1.00
 O B:HOH1025 2.9 20.6 1.0
ND2 B:ASN188 3.1 13.9 1.0
N B:THR174 3.2 10.7 1.0
OG1 B:THR174 3.7 14.6 1.0
CA B:GLY173 3.8 10.4 1.0
CB B:THR174 3.8 12.8 1.0
CB B:ASN188 3.8 10.6 1.0
C B:GLY173 4.0 9.6 1.0
CG B:ASN188 4.0 11.0 1.0
CA B:THR174 4.1 11.0 1.0
O B:HOH1020 4.2 15.7 1.0
NE2 B:GLN192 4.3 14.9 1.0
O B:ASN188 4.5 14.9 1.0
CD2 B:LEU189 4.5 15.6 1.0
O B:THR174 4.6 12.3 1.0
C B:ASN188 4.8 10.9 1.0
CA B:ASN188 4.8 10.2 1.0
C B:THR174 4.9 10.3 1.0

Chlorine binding site 5 out of 7 in 3nu5

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Chlorine binding site 5 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl514

b:17.8
occ:0.50
 O B:HOH1174 3.1 24.7 0.5
O B:HOH1170 3.1 20.6 0.2
N B:THR112 3.3 10.8 1.0
CB B:VAL111 3.7 13.2 1.0
CA B:ALA167 3.8 13.0 1.0
CA B:VAL111 3.8 11.1 1.0
CB B:ALA167 3.9 16.0 1.0
CB B:THR112 4.0 14.2 1.0
C B:VAL111 4.0 10.5 1.0
O B:THR112 4.1 12.5 1.0
CA B:THR112 4.1 10.8 1.0
OG1 B:THR112 4.2 20.2 1.0
CG1 B:VAL111 4.3 16.8 1.0
C B:THR112 4.6 11.2 1.0
N B:ALA167 4.7 12.5 1.0
C B:ALA167 4.8 13.7 1.0
CG2 B:VAL111 5.0 14.9 1.0

Chlorine binding site 6 out of 7 in 3nu5

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Chlorine binding site 6 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl515

b:21.7
occ:0.50
 N B:GLU121 3.2 12.3 1.0
O B:HOH1059 3.5 29.7 1.0
CA B:LYS120 3.7 11.2 1.0
CB B:LYS120 3.7 12.7 1.0
C B:LYS120 3.9 10.9 1.0
O B:GLU121 4.1 12.5 1.0
CB B:GLU121 4.1 15.6 1.0
ND2 B:ASN183 4.1 14.3 1.0
CA B:GLU121 4.1 13.2 1.0
CG B:LYS120 4.3 17.8 1.0
C B:GLU121 4.6 11.7 1.0
O B:HOH1035 4.7 14.1 0.5
O B:HOH1171 4.8 18.8 0.2

Chlorine binding site 7 out of 7 in 3nu5

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Chlorine binding site 7 out of 7 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 I50V with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl516

b:25.4
occ:0.50
 N B:SER137 3.2 19.2 1.0
NE2 B:GLN118 3.5 57.1 1.0
CB B:MET136 3.7 20.7 1.0
CA B:MET136 3.8 17.7 1.0
CB B:SER137 3.9 23.8 0.7
CB B:SER137 4.0 22.7 0.3
C B:MET136 4.0 17.3 1.0
CA B:SER137 4.1 19.3 0.7
CA B:SER137 4.1 19.3 0.3
OE1 B:GLN118 4.2 42.8 1.0
OG B:SER137 4.2 21.8 0.3
CD B:GLN118 4.3 34.2 1.0
O B:HOH1149 4.3 28.9 0.5
CE B:MET136 4.4 28.6 1.0
O B:SER137 4.5 19.2 1.0
C B:SER137 4.8 16.4 1.0
CG B:MET136 4.8 25.0 1.0

Reference:

C.H.Shen, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Amprenavir Complexes with Hiv-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. Febs J. V. 277 3699 2010.
ISSN: ISSN 1742-464X
PubMed: 20695887
DOI: 10.1111/J.1742-4658.2010.07771.X
Page generated: Fri Jul 11 08:28:51 2025

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