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Chlorine in PDB 3ec0: High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A

Enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A

All present enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A:
3.4.23.47;

Protein crystallography data

The structure of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A, PDB code: 3ec0 was solved by A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.360, 30.913, 55.954, 90.00, 91.79, 90.00
R / Rfree (%) 15.6 / 20.6

Other elements in 3ec0:

The structure of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A also contains other interesting chemical elements:

Zinc (Zn) 10 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A (pdb code 3ec0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A, PDB code: 3ec0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ec0

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Chlorine binding site 1 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:27.4
occ:0.50
 NZ A:LYS70 2.2 53.5 1.0
ZN A:ZN410 2.3 27.0 0.5
CE A:LYS70 3.5 45.4 1.0
OE2 A:GLU63 3.6 40.1 1.0
O A:HOH1010 3.8 19.1 0.5
CD A:LYS70 3.8 41.4 1.0
CD A:GLU63 4.7 48.5 1.0

Chlorine binding site 2 out of 8 in 3ec0

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Chlorine binding site 2 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:17.6
occ:0.50
 O A:HOH1007 1.9 19.5 0.5
ZN A:ZN403 2.2 23.7 0.5
O A:HOH1178 2.2 19.6 0.5
O A:HOH1097 2.5 23.2 1.0
OXT A:LEU99 2.6 32.7 1.0
O A:LEU99 2.8 34.5 1.0
C A:LEU99 2.9 25.8 1.0
O B:HOH1184 3.5 41.1 1.0
N3 A:IMD304 3.8 20.2 0.5
O A:HOH1006 4.0 17.6 0.5
C4 A:IMD304 4.0 21.4 0.5
CA A:LEU99 4.2 23.4 1.0
N A:LEU99 4.3 23.3 1.0
N B:PRO101 4.7 28.8 1.0
O B:PRO101 4.7 32.5 1.0
CB A:ASN98 4.7 18.6 1.0
C A:ASN98 4.9 20.8 1.0

Chlorine binding site 3 out of 8 in 3ec0

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Chlorine binding site 3 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:20.6
occ:1.00
 O B:HOH1049 2.6 25.8 1.0
N B:ILE146 3.3 8.9 1.0
N1 B:IMD303 3.4 16.0 0.6
CD B:LYS145 3.6 14.9 1.0
CA B:LYS145 3.8 9.5 1.0
O B:ILE146 4.0 13.1 1.0
CB B:LYS145 4.1 11.8 1.0
C B:LYS145 4.1 10.4 1.0
CA B:ILE146 4.2 9.4 1.0
CB B:ILE146 4.2 10.5 1.0
C5 B:IMD303 4.2 14.2 0.6
C2 B:IMD303 4.3 16.4 0.6
CG B:LYS145 4.4 11.7 1.0
C B:ILE146 4.6 10.0 1.0
CG1 B:ILE146 4.6 10.7 1.0
CE B:LYS145 4.8 21.4 1.0
O B:PRO144 4.9 10.9 1.0
CD1 B:ILE146 4.9 10.8 1.0

Chlorine binding site 4 out of 8 in 3ec0

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Chlorine binding site 4 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:23.3
occ:0.60
 O B:HOH1008 1.6 11.2 0.4
ZN B:ZN402 2.6 23.1 0.6
O B:HOH1001 3.1 27.4 1.0
N3 B:IMD303 3.3 16.9 0.6
C2 B:IMD303 3.3 16.4 0.6
C15 A:GRL201 3.5 13.5 1.0
O B:HOH1090 3.6 34.3 1.0
N B:GLY148 3.7 12.2 1.0
CA B:VAL147 3.7 12.3 1.0
ZN B:ZN409 3.8 18.6 0.4
C2 A:GRL201 4.0 13.1 1.0
OD2 B:ASP130 4.0 22.1 1.0
C1 A:GRL201 4.0 12.4 1.0
CG1 B:VAL147 4.1 16.2 1.0
O B:ILE146 4.1 13.1 1.0
O B:HOH1080 4.1 23.8 1.0
C B:VAL147 4.2 10.6 1.0
CB B:VAL147 4.2 13.9 1.0
CG2 B:VAL147 4.3 17.8 1.0
O B:GLY148 4.6 14.4 1.0
N1 B:IMD303 4.7 16.0 0.6
C4 B:IMD303 4.7 16.5 0.6
CA B:GLY148 4.7 14.0 1.0
N B:VAL147 4.7 9.8 1.0
C12 A:GRL201 4.7 13.1 1.0
C B:ILE146 4.8 10.0 1.0
O1 A:GRL201 4.9 12.8 1.0

Chlorine binding site 5 out of 8 in 3ec0

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Chlorine binding site 5 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:21.5
occ:0.50
 ZN B:ZN407 2.1 25.9 0.5
O B:HOH1005 2.5 22.4 0.5
O B:HOH1003 3.1 21.5 0.5
O B:HOH1002 3.6 15.3 0.5
OE2 B:GLU165 3.7 33.2 1.0
CA B:GLY117 3.8 12.7 1.0
OE1 B:GLU165 4.1 47.1 1.0
CD B:GLU165 4.1 28.1 1.0
CG B:TYR114 4.1 11.7 1.0
O B:HOH1027 4.3 12.3 1.0
CB B:TYR114 4.3 9.8 1.0
CD1 B:TYR114 4.3 12.4 1.0
N B:GLY117 4.4 11.4 1.0
CD2 B:TYR114 4.5 19.2 1.0
O B:GLY117 4.6 11.8 1.0
C B:GLY117 4.6 10.5 1.0
CE1 B:TYR114 4.9 15.7 1.0

Chlorine binding site 6 out of 8 in 3ec0

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Chlorine binding site 6 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:18.2
occ:0.50
 ZN B:ZN404 2.4 23.1 0.5
O B:HOH1095 3.1 40.5 1.0
N B:TRP106 3.4 14.4 1.0
N B:LYS107 3.5 14.8 1.0
CB B:TRP106 3.6 20.2 1.0
CG B:LYS107 3.6 24.9 1.0
CB B:SER104 3.7 25.1 1.0
N B:LEU105 3.7 13.8 1.0
N3 B:IMD305 3.8 18.5 0.5
CA B:TRP106 3.8 15.3 1.0
O B:HOH1009 3.8 16.8 0.5
C B:SER104 3.9 15.0 1.0
CL B:CL505 4.0 24.9 0.5
O B:HOH1070 4.0 15.5 1.0
N B:SER104 4.1 17.2 1.0
C B:TRP106 4.1 15.8 1.0
CA B:SER104 4.1 19.6 1.0
C4 B:IMD305 4.2 15.7 0.5
CD1 B:TRP106 4.2 23.0 1.0
CD B:LYS107 4.2 28.8 1.0
C B:LEU105 4.3 11.9 1.0
CG B:TRP106 4.4 20.6 1.0
CB B:LYS107 4.4 17.6 1.0
CA B:LEU105 4.5 12.9 1.0
CA B:LYS107 4.5 17.3 1.0
CE B:LYS107 4.5 39.0 1.0
NZ B:LYS107 4.5 63.7 1.0
O B:SER104 4.6 15.8 1.0
O B:LYS107 4.7 13.0 1.0
C2 B:IMD305 4.8 17.1 0.5
OG B:SER104 4.8 40.3 1.0

Chlorine binding site 7 out of 8 in 3ec0

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Chlorine binding site 7 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:24.9
occ:0.50
 ZN B:ZN404 2.2 23.1 0.5
O B:HOH1009 3.4 16.8 0.5
N3 B:IMD305 3.6 18.5 0.5
O B:HOH1103 3.8 49.6 1.0
CL B:CL504 4.0 18.2 0.5
CE B:LYS107 4.0 39.0 1.0
CD B:LYS107 4.1 28.8 1.0
C4 B:IMD305 4.3 15.7 0.5
C2 B:IMD305 4.6 17.1 0.5
CG B:LYS107 4.9 24.9 1.0
O B:HOH1095 4.9 40.5 1.0

Chlorine binding site 8 out of 8 in 3ec0

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Chlorine binding site 8 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:31.4
occ:0.40
 ZN B:ZN409 2.3 18.6 0.4
O B:HOH1001 3.0 27.4 1.0
OD1 B:ASP130 3.4 25.3 1.0
ZN B:ZN402 3.6 23.1 0.6
CB B:ASP129 3.7 14.1 1.0
OD2 B:ASP130 3.8 22.1 1.0
C4 B:IMD303 3.9 16.5 0.6
CG B:ASP130 4.0 17.6 1.0
OD2 B:ASP129 4.1 23.1 1.0
N3 B:IMD303 4.1 16.9 0.6
CG B:ASP129 4.3 18.9 1.0
O B:HOH1082 4.5 42.0 1.0
O B:ASP129 4.8 15.9 1.0
C B:ASP129 4.8 12.5 1.0
CA B:ASP129 4.9 11.9 1.0

Reference:

A.Y.Kovalevsky, J.M.Louis, A.Aniana, A.K.Ghosh, I.T.Weber. Structural Evidence For Effectiveness of Darunavir and Two Related Antiviral Inhibitors Against Hiv-2 Protease J.Mol.Biol. V. 384 178 2008.
ISSN: ISSN 0022-2836
PubMed: 18834890
DOI: 10.1016/J.JMB.2008.09.031
Page generated: Sat Dec 12 09:39:58 2020

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