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Chlorine in PDB 3ebz: High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir

Enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir

All present enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir:
3.4.23.47;

Protein crystallography data

The structure of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir, PDB code: 3ebz 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 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.408, 30.827, 55.768, 90.00, 91.41, 90.00
R / Rfree (%) 13.6 / 18.1

Other elements in 3ebz:

The structure of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir also contains other interesting chemical elements:

Zinc (Zn) 9 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 Clinical Drug Darunavir (pdb code 3ebz). 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 Clinical Drug Darunavir, PDB code: 3ebz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ebz

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Chlorine binding site 1 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:18.8
occ:0.50
 O A:HOH1010 1.0 17.3 0.5
O A:HOH1011 1.8 17.1 0.5
ZN A:ZN403 2.1 19.9 0.5
O A:LEU99 2.9 38.7 1.0
OXT A:LEU99 3.3 34.6 1.0
C A:LEU99 3.4 28.4 1.0
N3 A:IMD304 3.5 17.4 0.5
O A:HOH1009 3.7 15.5 0.5
C4 A:IMD304 4.1 19.4 0.5
C2 A:IMD304 4.6 21.2 0.5
CA A:LEU99 4.7 25.5 1.0
N A:LEU99 4.9 23.2 1.0
N B:PRO101 4.9 28.8 1.0

Chlorine binding site 2 out of 8 in 3ebz

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Chlorine binding site 2 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:15.0
occ:1.00
 O B:HOH1050 2.9 24.1 1.0
N B:ILE146 3.3 9.2 1.0
N1 B:IMD303 3.3 11.8 0.6
CD B:LYS145 3.7 13.6 1.0
CA B:LYS145 3.8 9.9 1.0
O B:ILE146 4.0 12.6 1.0
CB B:LYS145 4.0 11.0 1.0
C B:LYS145 4.0 10.2 1.0
C2 B:IMD303 4.1 10.3 0.6
CA B:ILE146 4.2 9.8 1.0
CB B:ILE146 4.3 11.0 1.0
C5 B:IMD303 4.3 12.9 0.6
CG B:LYS145 4.4 10.9 1.0
C B:ILE146 4.6 10.6 1.0
CG1 B:ILE146 4.7 10.0 1.0
CE B:LYS145 4.9 19.1 1.0
O B:PRO144 5.0 10.8 1.0

Chlorine binding site 3 out of 8 in 3ebz

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Chlorine binding site 3 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:12.1
occ:0.60
 ZN B:ZN402 2.4 13.9 0.6
O A:HOH1184 3.3 38.2 0.5
O B:HOH1002 3.4 13.6 0.6
N3 B:IMD303 3.5 11.0 0.6
N B:GLY148 3.5 13.7 1.0
OD2 B:ASP130 3.7 22.4 1.0
C2 B:IMD303 3.7 10.3 0.6
C27 B:017201 3.8 11.7 1.0
CA B:VAL147 3.8 11.8 1.0
C31 B:017201 3.8 11.9 1.0
CG1 B:VAL147 3.9 14.6 1.0
ZN B:ZN409 4.0 25.1 0.4
C B:VAL147 4.2 11.5 1.0
O B:GLY148 4.2 23.9 1.0
CB B:VAL147 4.3 10.9 1.0
O B:ILE146 4.3 12.6 1.0
C30 B:017201 4.3 14.3 1.0
O28 B:017201 4.4 13.1 1.0
CG2 B:VAL147 4.5 13.0 1.0
CA B:GLY148 4.6 15.9 1.0
C4 B:IMD303 4.8 13.1 0.6
O26 B:017201 4.9 10.7 1.0
N B:VAL147 4.9 10.5 1.0
C B:GLY148 4.9 14.4 1.0
C29 B:017201 4.9 14.2 1.0
CG B:ASP130 5.0 14.8 1.0

Chlorine binding site 4 out of 8 in 3ebz

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Chlorine binding site 4 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:23.5
occ:0.50
 ZN B:ZN407 2.2 28.7 0.5
O B:HOH1005 3.1 26.5 0.5
O B:HOH1008 3.5 43.2 0.5
O B:HOH1003 3.6 21.8 0.5
CA B:GLY117 3.7 12.9 1.0
OE1 B:GLU165 3.7 58.3 1.0
OE2 B:GLU165 4.0 45.3 1.0
CD B:GLU165 4.1 34.8 1.0
CG B:TYR114 4.1 12.2 1.0
O B:HOH1028 4.3 12.8 1.0
CD1 B:TYR114 4.3 15.4 1.0
CB B:TYR114 4.3 10.6 1.0
N B:GLY117 4.4 12.2 1.0
CD2 B:TYR114 4.4 22.3 1.0
C B:GLY117 4.6 11.3 1.0
O B:GLY117 4.6 13.9 1.0
CE1 B:TYR114 4.8 17.5 1.0
CE2 B:TYR114 4.9 24.8 1.0

Chlorine binding site 5 out of 8 in 3ebz

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Chlorine binding site 5 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:17.0
occ:0.50
 ZN B:ZN404 2.3 18.9 0.5
O B:HOH1103 3.2 39.1 1.0
N B:TRP106 3.3 16.2 1.0
CB B:SER104 3.5 26.1 1.0
N3 B:IMD305 3.5 15.3 0.5
N B:LEU105 3.6 14.0 1.0
N B:LYS107 3.6 14.9 1.0
CB B:TRP106 3.7 21.3 1.0
O B:HOH1006 3.7 14.8 0.5
CL B:CL506 3.7 27.4 0.5
O B:HOH1004 3.7 15.8 0.5
CG B:LYS107 3.8 21.7 1.0
C B:SER104 3.8 15.8 1.0
CA B:TRP106 3.9 16.1 1.0
CA B:SER104 3.9 17.8 1.0
N B:SER104 3.9 15.6 1.0
O B:HOH1075 3.9 16.7 1.0
CD1 B:TRP106 4.1 25.0 1.0
C4 B:IMD305 4.1 13.8 0.5
C B:TRP106 4.2 16.1 1.0
C B:LEU105 4.3 13.4 1.0
CG B:TRP106 4.3 21.1 1.0
CA B:LEU105 4.4 13.4 1.0
C2 B:IMD305 4.5 15.3 0.5
O B:SER104 4.5 18.1 1.0
CB B:LYS107 4.5 19.8 1.0
CE B:LYS107 4.5 29.7 1.0
CD B:LYS107 4.5 20.8 1.0
CA B:LYS107 4.6 15.6 1.0
OG B:SER104 4.7 34.2 1.0
O B:LYS107 4.7 13.9 1.0

Chlorine binding site 6 out of 8 in 3ebz

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Chlorine binding site 6 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:27.4
occ:0.50
 ZN B:ZN404 2.2 18.9 0.5
O B:HOH1006 2.3 14.8 0.5
O B:HOH1112 2.6 39.8 1.0
N3 B:IMD305 3.5 15.3 0.5
C2 B:IMD305 3.6 15.3 0.5
O B:HOH1004 3.6 15.8 0.5
CL B:CL505 3.7 17.0 0.5
CB B:TRP106 3.9 21.3 1.0
CB B:LYS107 3.9 19.8 1.0
N B:LYS107 4.0 14.9 1.0
CG B:LYS107 4.0 21.7 1.0
C B:TRP106 4.2 16.1 1.0
CD B:LYS107 4.3 20.8 1.0
O B:HOH1086 4.4 30.4 1.0
CA B:LYS107 4.5 15.6 1.0
O B:TRP106 4.6 20.0 1.0
CA B:TRP106 4.6 16.1 1.0
C4 B:IMD305 4.8 13.8 0.5
N1 B:IMD305 4.9 15.5 0.5

Chlorine binding site 7 out of 8 in 3ebz

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Chlorine binding site 7 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl507

b:25.4
occ:0.50
 ZN B:ZN408 2.2 25.0 0.5
O B:HOH1133 2.8 26.4 0.5
NZ B:LYS145 3.2 20.7 1.0
OE1 B:GLU158 3.5 29.6 1.0
O B:HOH1170 3.5 20.1 0.5
O B:HOH1001 3.6 21.0 0.5
C5 B:IMD303 3.6 12.9 0.6
CE B:LYS145 3.7 19.1 1.0
O B:HOH1123 3.8 22.3 0.5
O B:HOH1050 4.0 24.1 1.0
CD B:LYS145 4.1 13.6 1.0
CD B:GLU158 4.3 20.0 1.0
OE2 B:GLU158 4.4 26.6 1.0
C4 B:IMD303 4.4 13.1 0.6
N1 B:IMD303 4.6 11.8 0.6
CG B:LYS145 5.0 10.9 1.0

Chlorine binding site 8 out of 8 in 3ebz

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Chlorine binding site 8 out of 8 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


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 Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl508

b:26.7
occ:0.40
 ZN B:ZN409 2.3 25.1 0.4
O B:HOH1002 2.9 13.6 0.6
OD1 B:ASP130 3.2 22.5 1.0
CB B:ASP129 3.8 13.5 1.0
C4 B:IMD303 3.8 13.1 0.6
CG B:ASP130 4.0 14.8 1.0
ZN B:ZN402 4.0 13.9 0.6
OD2 B:ASP130 4.0 22.4 1.0
OD2 B:ASP129 4.2 20.4 1.0
N3 B:IMD303 4.3 11.0 0.6
CG B:ASP129 4.4 17.9 1.0
O B:HOH1088 4.4 41.8 1.0
O B:HOH1170 4.4 20.1 0.5
O B:HOH1098 4.8 27.9 1.0
C B:ASP129 4.8 10.5 1.0
O B:ASP129 4.8 13.5 1.0
C5 B:IMD303 4.9 12.9 0.6
CA B:ASP129 5.0 11.2 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: Fri Jul 11 04:45:59 2025

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