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Zinc 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:

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 Antiviral Inhibitor Grl-06579A (pdb code 3ec0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-06579A, PDB code: 3ec0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3ec0

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Zinc binding site 1 out of 10 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 Zinc with other atoms in the Zn 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:Zn403

b:23.7
occ:0.50
 O A:HOH1007 1.4 19.5 0.5
N3 A:IMD304 2.0 20.2 0.5
CL A:CL508 2.2 17.6 0.5
OXT A:LEU99 2.3 32.7 1.0
O A:HOH1006 2.3 17.6 0.5
O A:LEU99 2.8 34.5 1.0
C A:LEU99 2.9 25.8 1.0
C4 A:IMD304 2.9 21.4 0.5
C2 A:IMD304 3.1 24.9 0.5
O A:HOH1178 3.6 19.6 0.5
C5 A:IMD304 4.1 25.4 0.5
N1 A:IMD304 4.2 28.3 0.5
CA A:LEU99 4.4 23.4 1.0
O A:HOH1097 4.4 23.2 1.0
N B:PRO101 4.9 28.8 1.0

Zinc binding site 2 out of 10 in 3ec0

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Zinc binding site 2 out of 10 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 Zinc with other atoms in the Zn 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:Zn405

b:19.3
occ:0.50
 O A:HOH1029 1.9 22.4 0.5
OD2 A:ASP79 2.0 24.1 1.0
O A:HOH1028 2.2 22.2 0.5
CG A:ASP79 2.8 20.2 1.0
OD1 A:ASP79 2.9 24.7 1.0
O A:HOH1180 4.2 37.7 1.0
CB A:ASP79 4.2 16.6 1.0
O A:HOH1162 4.2 33.7 1.0
O A:HOH1086 4.9 36.3 1.0

Zinc binding site 3 out of 10 in 3ec0

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Zinc binding site 3 out of 10 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 Zinc with other atoms in the Zn 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
A:Zn406

b:23.3
occ:0.50
 OE1 A:GLU65 2.1 48.6 1.0
O A:HOH1004 2.1 31.4 0.5
N3 A:IMD306 2.4 23.9 0.5
CD A:GLU65 2.7 47.4 1.0
OE2 A:GLU65 2.9 53.9 1.0
C2 A:IMD306 3.2 27.1 0.5
C4 A:IMD306 3.6 22.4 0.5
O A:HOH1171 4.0 27.4 0.2
CG A:GLU65 4.1 39.2 1.0
N1 A:IMD306 4.4 25.6 0.5
O A:HOH1011 4.5 20.0 0.5
CB A:GLU65 4.6 24.7 1.0
C5 A:IMD306 4.6 23.1 0.5
CD1 A:TYR14 4.9 34.4 1.0
CG A:TYR14 5.0 33.5 1.0

Zinc binding site 4 out of 10 in 3ec0

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Zinc binding site 4 out of 10 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 Zinc with other atoms in the Zn 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
A:Zn410

b:27.0
occ:0.50
 OE2 A:GLU63 1.9 40.1 1.0
O A:HOH1010 2.2 19.1 0.5
CL A:CL507 2.3 27.4 0.5
CD A:GLU63 3.0 48.5 1.0
OE1 A:GLU63 3.6 59.6 1.0
NZ A:LYS70 4.0 53.5 1.0
CG A:GLU63 4.2 43.8 1.0
CD A:LYS70 4.4 41.4 1.0
OE2 A:GLU65 4.8 53.9 1.0
CE A:LYS70 4.9 45.4 1.0

Zinc binding site 5 out of 10 in 3ec0

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Zinc binding site 5 out of 10 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 Zinc with other atoms in the Zn 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:Zn401

b:11.3
occ:1.00
 OE2 B:GLU121 1.9 13.2 1.0
N3 B:IMD301 2.0 10.1 1.0
N3 B:IMD302 2.0 17.6 1.0
CD B:GLU121 2.8 10.4 1.0
OE1 B:GLU121 2.9 15.6 1.0
C2 B:IMD301 3.0 11.9 1.0
C2 B:IMD302 3.0 17.8 1.0
C4 B:IMD301 3.0 11.2 1.0
C4 B:IMD302 3.1 23.3 1.0
O B:HOH1136 4.0 34.5 1.0
N1 B:IMD301 4.1 11.7 1.0
CG B:GLU121 4.2 9.9 1.0
N1 B:IMD302 4.2 24.6 1.0
C5 B:IMD301 4.2 12.8 1.0
C5 B:IMD302 4.2 26.1 1.0
CG1 B:VAL110 4.7 14.9 1.0
O B:HOH1142 4.9 40.6 1.0

Zinc binding site 6 out of 10 in 3ec0

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Zinc binding site 6 out of 10 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 Zinc with other atoms in the Zn 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:Zn402

b:23.1
occ:0.60
 ZN B:ZN409 1.3 18.6 0.4
N3 B:IMD303 1.8 16.9 0.6
O B:HOH1001 1.9 27.4 1.0
OD2 B:ASP130 1.9 22.1 1.0
CL B:CL502 2.6 23.3 0.6
C4 B:IMD303 2.8 16.5 0.6
C2 B:IMD303 2.8 16.4 0.6
CG B:ASP130 3.0 17.6 1.0
OD1 B:ASP130 3.4 25.3 1.0
CL B:CL506 3.6 31.4 0.4
N1 B:IMD303 3.9 16.0 0.6
C5 B:IMD303 4.0 14.2 0.6
C1 A:GRL201 4.1 12.4 1.0
O B:HOH1008 4.1 11.2 0.4
CB B:ASP130 4.3 12.5 1.0
OD2 B:ASP129 4.4 23.1 1.0
CB B:ASP129 4.5 14.1 1.0
C15 A:GRL201 4.6 13.5 1.0
CG2 B:VAL147 4.7 17.8 1.0
O1 A:GRL201 4.8 12.8 1.0
CE B:MET176 4.9 35.3 0.6

Zinc binding site 7 out of 10 in 3ec0

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Zinc binding site 7 out of 10 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 Zinc with other atoms in the Zn 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:Zn404

b:23.1
occ:0.50
 CL B:CL505 2.2 24.9 0.5
N3 B:IMD305 2.2 18.5 0.5
O B:HOH1009 2.3 16.8 0.5
CL B:CL504 2.4 18.2 0.5
C4 B:IMD305 3.1 15.7 0.5
C2 B:IMD305 3.2 17.1 0.5
CB B:TRP106 3.8 20.2 1.0
CD B:LYS107 4.2 28.8 1.0
O B:HOH1103 4.2 49.6 1.0
CG B:LYS107 4.3 24.9 1.0
C5 B:IMD305 4.3 14.6 0.5
N1 B:IMD305 4.3 16.7 0.5
CE B:LYS107 4.6 39.0 1.0
N B:LYS107 4.6 14.8 1.0
O B:HOH1095 4.6 40.5 1.0
CD1 B:TRP106 4.7 23.0 1.0
CG B:TRP106 4.7 20.6 1.0
CA B:TRP106 4.8 15.3 1.0
CB B:LYS107 4.8 17.6 1.0
C B:TRP106 4.9 15.8 1.0
N B:TRP106 5.0 14.4 1.0

Zinc binding site 8 out of 10 in 3ec0

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Zinc binding site 8 out of 10 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 Zinc with other atoms in the Zn 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:Zn407

b:25.9
occ:0.50
 O B:HOH1003 1.7 21.5 0.5
O B:HOH1005 1.9 22.4 0.5
O B:HOH1002 1.9 15.3 0.5
CL B:CL503 2.1 21.5 0.5
OE1 B:GLU165 2.3 47.1 1.0
CD B:GLU165 2.8 28.1 1.0
OE2 B:GLU165 2.9 33.2 1.0
O B:HOH1027 3.8 12.3 1.0
CG B:GLU165 4.1 17.1 1.0
NZ B:LYS170 4.3 59.4 1.0
CE B:LYS170 4.7 46.0 1.0
CA B:GLY117 4.9 12.7 1.0

Zinc binding site 9 out of 10 in 3ec0

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Zinc binding site 9 out of 10 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 Zinc with other atoms in the Zn binding site number 9 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:Zn408

b:45.2
occ:0.50
 OE1 B:GLU158 2.1 38.3 1.0
O B:HOH1150 2.5 27.2 0.5
CD B:GLU158 3.0 21.5 1.0
OE2 B:GLU158 3.4 36.1 1.0
O B:HOH1113 3.5 30.9 0.5
NZ B:LYS145 4.3 31.1 1.0
CG B:GLU158 4.3 13.8 1.0
CE B:MET176 4.3 35.1 0.4
NZ B:LYS160 4.3 52.7 1.0
O B:HOH1120 4.5 27.6 0.5
CE B:LYS145 4.6 21.4 1.0
CE B:LYS160 4.7 37.7 1.0
CG2 B:THR174 4.7 13.9 1.0
C5 B:IMD303 4.7 14.2 0.6
CE B:MET176 5.0 35.3 0.6

Zinc binding site 10 out of 10 in 3ec0

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Zinc binding site 10 out of 10 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 Zinc with other atoms in the Zn binding site number 10 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:Zn409

b:18.6
occ:0.40
 ZN B:ZN402 1.3 23.1 0.6
O B:HOH1001 1.8 27.4 1.0
OD2 B:ASP130 1.9 22.1 1.0
CL B:CL506 2.3 31.4 0.4
N3 B:IMD303 2.3 16.9 0.6
CG B:ASP130 2.7 17.6 1.0
C4 B:IMD303 2.7 16.5 0.6
OD1 B:ASP130 2.7 25.3 1.0
C2 B:IMD303 3.6 16.4 0.6
CL B:CL502 3.8 23.3 0.6
CB B:ASP129 3.9 14.1 1.0
C5 B:IMD303 4.0 14.2 0.6
OD2 B:ASP129 4.1 23.1 1.0
CB B:ASP130 4.2 12.5 1.0
N1 B:IMD303 4.4 16.0 0.6
CG B:ASP129 4.5 18.9 1.0
C1 A:GRL201 4.7 12.4 1.0
N B:ASP130 4.7 10.9 1.0
C B:ASP129 4.8 12.5 1.0
CA B:ASP130 4.9 10.8 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: Thu Oct 24 12:43:28 2024

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