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Zinc 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:

Chlorine (Cl) 8 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 9 binding sites of Zinc where determined in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir, PDB code: 3ebz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3ebz

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Zinc binding site 1 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn403

b:19.9
occ:0.50
 O A:HOH1011 1.4 17.1 0.5
N3 A:IMD304 2.0 17.4 0.5
CL A:CL503 2.1 18.8 0.5
OXT A:LEU99 2.2 34.6 1.0
O A:HOH1009 2.2 15.5 0.5
O A:HOH1010 2.4 17.3 0.5
O A:LEU99 2.7 38.7 1.0
C2 A:IMD304 2.8 21.2 0.5
C A:LEU99 2.8 28.4 1.0
C4 A:IMD304 3.2 19.4 0.5
N1 A:IMD304 4.0 23.8 0.5
O A:HOH1148 4.0 37.9 0.5
C5 A:IMD304 4.2 21.1 0.5
CA A:LEU99 4.4 25.5 1.0

Zinc binding site 2 out of 9 in 3ebz

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Zinc binding site 2 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn405

b:21.8
occ:0.50
 O A:HOH1030 1.6 30.9 0.5
OD2 A:ASP79 2.0 26.4 1.0
O A:HOH1029 2.2 28.5 0.5
CG A:ASP79 2.8 22.9 1.0
OD1 A:ASP79 2.9 29.8 1.0
CB A:ASP79 4.2 19.5 1.0
O A:HOH1186 4.2 44.8 1.0

Zinc binding site 3 out of 9 in 3ebz

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Zinc binding site 3 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn406

b:26.8
occ:0.50
 N3 A:IMD306 2.1 24.2 0.5
O A:HOH1007 2.1 25.8 0.5
OE1 A:GLU65 2.2 45.0 1.0
CD A:GLU65 2.7 46.2 1.0
OE2 A:GLU65 2.7 51.4 1.0
C2 A:IMD306 2.7 25.6 0.5
C4 A:IMD306 3.3 22.7 0.5
O A:HOH1197 3.4 30.5 0.2
N1 A:IMD306 4.0 23.5 0.5
CG A:GLU65 4.1 37.6 1.0
C5 A:IMD306 4.3 23.1 0.5
CB A:GLU65 4.6 28.6 1.0
CD1 A:TYR14 5.0 37.0 1.0
CG A:TYR14 5.0 35.3 1.0

Zinc binding site 4 out of 9 in 3ebz

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Zinc binding site 4 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn401

b:12.6
occ:1.00
 OE2 B:GLU121 1.9 14.3 1.0
N3 B:IMD301 2.0 11.7 1.0
N3 B:IMD302 2.0 18.6 1.0
CD B:GLU121 2.7 11.2 1.0
C2 B:IMD302 2.9 23.1 1.0
OE1 B:GLU121 2.9 17.2 1.0
C2 B:IMD301 3.0 15.1 1.0
C4 B:IMD301 3.0 12.1 1.0
C4 B:IMD302 3.1 25.8 1.0
O B:HOH1152 3.9 34.3 1.0
N1 B:IMD302 4.1 31.6 1.0
CG B:GLU121 4.1 9.9 1.0
N1 B:IMD301 4.1 13.0 1.0
C5 B:IMD301 4.2 13.7 1.0
O B:HOH1146 4.2 38.1 1.0
C5 B:IMD302 4.2 29.6 1.0
CG1 B:VAL110 4.6 17.9 1.0
O B:HOH1159 4.6 46.1 1.0

Zinc binding site 5 out of 9 in 3ebz

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Zinc binding site 5 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn402

b:13.9
occ:0.60
 ZN B:ZN409 1.7 25.1 0.4
OD2 B:ASP130 1.9 22.4 1.0
N3 B:IMD303 1.9 11.0 0.6
O B:HOH1002 2.1 13.6 0.6
CL B:CL502 2.4 12.1 0.6
C4 B:IMD303 2.9 13.1 0.6
CG B:ASP130 3.0 14.8 1.0
C2 B:IMD303 3.0 10.3 0.6
OD1 B:ASP130 3.4 22.5 1.0
C27 B:017201 3.9 11.7 1.0
CL B:CL508 4.0 26.7 0.4
O A:HOH1184 4.0 38.2 0.5
C5 B:IMD303 4.1 12.9 0.6
N1 B:IMD303 4.1 11.8 0.6
CB B:ASP130 4.3 11.4 1.0
OD2 B:ASP129 4.5 20.4 1.0
O28 B:017201 4.5 13.1 1.0
O26 B:017201 4.6 10.7 1.0
CB B:ASP129 4.6 13.5 1.0
CG2 B:VAL147 4.6 13.0 1.0
C31 B:017201 4.8 11.9 1.0
CG1 B:VAL147 4.9 14.6 1.0
CE B:MET176 4.9 35.2 0.6

Zinc binding site 6 out of 9 in 3ebz

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Zinc binding site 6 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn404

b:18.9
occ:0.50
 O B:HOH1006 1.8 14.8 0.5
N3 B:IMD305 2.1 15.3 0.5
O B:HOH1004 2.2 15.8 0.5
CL B:CL506 2.2 27.4 0.5
CL B:CL505 2.3 17.0 0.5
C2 B:IMD305 3.0 15.3 0.5
C4 B:IMD305 3.2 13.8 0.5
CB B:TRP106 4.0 21.3 1.0
N1 B:IMD305 4.2 15.5 0.5
O B:HOH1112 4.2 39.8 1.0
C5 B:IMD305 4.3 14.6 0.5
CG B:LYS107 4.3 21.7 1.0
CD B:LYS107 4.5 20.8 1.0
CD1 B:TRP106 4.6 25.0 1.0
O B:HOH1103 4.6 39.1 1.0
N B:LYS107 4.6 14.9 1.0
O B:HOH1086 4.6 30.4 1.0
CE B:LYS107 4.6 29.7 1.0
CG B:TRP106 4.7 21.1 1.0
CA B:TRP106 4.9 16.1 1.0
CB B:LYS107 4.9 19.8 1.0
N B:TRP106 4.9 16.2 1.0
CB B:SER104 4.9 26.1 1.0
C B:TRP106 5.0 16.1 1.0

Zinc binding site 7 out of 9 in 3ebz

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Zinc binding site 7 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn407

b:28.7
occ:0.50
 O B:HOH1005 1.8 26.5 0.5
O B:HOH1003 1.8 21.8 0.5
OE1 B:GLU165 1.9 58.3 1.0
CL B:CL504 2.2 23.5 0.5
CD B:GLU165 2.8 34.8 1.0
O B:HOH1008 3.0 43.2 0.5
OE2 B:GLU165 3.1 45.3 1.0
O B:HOH1028 3.8 12.8 1.0
CG B:GLU165 4.1 19.7 1.0
CA B:GLY117 4.9 12.9 1.0

Zinc binding site 8 out of 9 in 3ebz

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Zinc binding site 8 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn408

b:25.0
occ:0.50
 OE1 B:GLU158 2.0 29.6 1.0
O B:HOH1001 2.0 21.0 0.5
CL B:CL507 2.2 25.4 0.5
O B:HOH1170 2.4 20.1 0.5
CD B:GLU158 2.9 20.0 1.0
OE2 B:GLU158 3.3 26.6 1.0
O B:HOH1123 3.8 22.3 0.5
CG B:GLU158 4.3 14.3 1.0
CE B:MET176 4.3 30.6 0.4
CE B:LYS145 4.5 19.1 1.0
NZ B:LYS145 4.5 20.7 1.0
O B:HOH1133 4.6 26.4 0.5
C5 B:IMD303 4.6 12.9 0.6
CG2 B:THR174 4.7 14.5 1.0
CE B:MET176 4.8 35.2 0.6
O B:HOH1098 5.0 27.9 1.0

Zinc binding site 9 out of 9 in 3ebz

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Zinc binding site 9 out of 9 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 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:Zn409

b:25.1
occ:0.40
 ZN B:ZN402 1.7 13.9 0.6
O B:HOH1002 1.8 13.6 0.6
OD2 B:ASP130 2.2 22.4 1.0
CL B:CL508 2.3 26.7 0.4
N3 B:IMD303 2.4 11.0 0.6
OD1 B:ASP130 2.5 22.5 1.0
C4 B:IMD303 2.5 13.1 0.6
CG B:ASP130 2.7 14.8 1.0
C2 B:IMD303 3.7 10.3 0.6
C5 B:IMD303 3.9 12.9 0.6
CB B:ASP129 3.9 13.5 1.0
CL B:CL502 4.0 12.1 0.6
OD2 B:ASP129 4.1 20.4 1.0
CB B:ASP130 4.2 11.4 1.0
N1 B:IMD303 4.4 11.8 0.6
CG B:ASP129 4.5 17.9 1.0
O A:HOH1184 4.7 38.2 0.5
N B:ASP130 4.7 9.5 1.0
C27 B:017201 4.8 11.7 1.0
O B:HOH1170 4.9 20.1 0.5
C B:ASP129 4.9 10.5 1.0
CE B:MET176 4.9 35.2 0.6
CA B:ASP130 4.9 10.1 1.0
O B:HOH1098 4.9 27.9 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: Wed Dec 16 04:15:34 2020

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