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Zinc in PDB 3ecg: High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065

Enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065

All present enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065:
3.4.23.47;

Protein crystallography data

The structure of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065, PDB code: 3ecg 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 (°) 105.396, 30.964, 55.625, 90.00, 91.39, 90.00
R / Rfree (%) 14.2 / 18.8

Other elements in 3ecg:

The structure of High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065 (pdb code 3ecg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065, PDB code: 3ecg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 3ecg

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Zinc binding site 1 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.3
occ:0.50
 OD2 A:ASP30 1.9 19.3 1.0
O A:HOH1027 1.9 17.2 0.5
O A:HOH1028 2.0 23.9 0.5
CL A:CL503 2.1 27.4 0.5
O A:HOH1026 2.5 12.1 0.5
CG A:ASP30 2.9 18.8 1.0
OD1 A:ASP30 3.1 31.4 1.0
C40 A:065201 3.8 16.9 1.0
CB A:ASP30 4.3 15.2 1.0
CB A:ASP29 4.3 12.0 1.0
OD2 A:ASP29 4.4 20.3 1.0
O39 A:065201 4.5 16.6 1.0
CE A:MET76 4.5 84.9 1.0
O A:HOH1069 4.8 16.7 1.0
O41 A:065201 4.9 19.5 1.0
CG A:ASP29 4.9 13.0 1.0

Zinc binding site 2 out of 11 in 3ecg

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Zinc binding site 2 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:14.1
occ:0.50
 O A:HOH1008 1.8 17.1 0.5
N3 A:IMD304 1.9 13.6 0.5
OXT A:LEU99 2.1 25.9 1.0
O A:HOH1007 2.2 18.1 1.0
CL A:CL509 2.4 21.6 0.5
O A:LEU99 2.7 27.6 1.0
C A:LEU99 2.7 21.1 1.0
C2 A:IMD304 2.8 17.1 0.5
C4 A:IMD304 3.0 14.6 0.5
N1 A:IMD304 4.0 21.8 0.5
C5 A:IMD304 4.1 19.4 0.5
CA A:LEU99 4.2 20.1 1.0
O A:HOH1101 4.6 28.0 1.0
N A:LEU99 5.0 18.4 1.0

Zinc binding site 3 out of 11 in 3ecg

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Zinc binding site 3 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:22.4
occ:0.50
 OD2 A:ASP79 2.0 31.1 1.0
O A:HOH1033 2.1 22.7 0.5
O A:HOH1032 2.3 23.4 0.5
CG A:ASP79 2.8 26.1 1.0
OD1 A:ASP79 2.9 30.0 1.0
CB A:ASP79 4.2 20.3 1.0
O A:HOH1180 4.2 40.3 1.0
O A:HOH1154 4.4 31.6 1.0

Zinc binding site 4 out of 11 in 3ecg

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Zinc binding site 4 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:19.0
occ:0.50
 OE1 A:GLU65 2.0 26.7 0.5
N3 A:IMD306 2.0 18.8 0.5
O A:HOH1005 2.1 23.5 0.5
OE1 A:GLU65 2.4 39.4 0.5
CD A:GLU65 2.7 26.3 0.5
OE2 A:GLU65 2.7 40.3 0.5
C2 A:IMD306 2.9 19.4 0.5
CD A:GLU65 3.0 33.3 0.5
C4 A:IMD306 3.1 19.1 0.5
OE2 A:GLU65 3.2 44.3 0.5
O A:HOH1159 3.2 25.2 0.2
N1 A:IMD306 4.1 19.7 0.5
CG A:GLU65 4.2 24.1 0.5
C5 A:IMD306 4.2 19.8 0.5
CG A:GLU65 4.4 28.5 0.5
O A:HOH1011 4.4 18.9 0.5
CB A:GLU65 4.6 22.3 0.5
CB A:GLU65 4.6 22.1 0.5

Zinc binding site 5 out of 11 in 3ecg

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Zinc binding site 5 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:22.0
occ:0.50
 OE2 A:GLU63 1.9 34.0 1.0
O A:HOH1009 2.0 20.6 0.5
CL A:CL507 2.3 21.5 0.5
CD A:GLU63 3.0 37.9 1.0
OE1 A:GLU63 3.4 48.1 1.0
CG A:GLU63 4.2 31.6 1.0
CD A:LYS70 4.4 35.7 1.0
OE2 A:GLU65 4.5 44.3 0.5
CD A:GLU65 4.8 33.3 0.5

Zinc binding site 6 out of 11 in 3ecg

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Zinc binding site 6 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:11.8
occ:1.00
 OE2 B:GLU121 1.9 13.0 1.0
N3 B:IMD302 2.0 19.3 1.0
N3 B:IMD301 2.0 10.6 1.0
CD B:GLU121 2.8 12.1 1.0
C2 B:IMD302 2.9 19.5 1.0
OE1 B:GLU121 3.0 17.0 1.0
C2 B:IMD301 3.0 13.2 1.0
C4 B:IMD302 3.0 24.7 1.0
C4 B:IMD301 3.0 11.6 1.0
O B:HOH1186 3.9 32.0 1.0
N1 B:IMD302 4.1 28.3 1.0
N1 B:IMD301 4.1 12.0 1.0
O B:HOH1025 4.1 29.5 1.0
C5 B:IMD302 4.2 27.0 1.0
CG B:GLU121 4.2 9.7 1.0
C5 B:IMD301 4.2 11.4 1.0
O B:HOH1176 4.5 34.1 1.0
CG1 B:VAL110 4.7 16.1 1.0

Zinc binding site 7 out of 11 in 3ecg

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Zinc binding site 7 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:17.5
occ:0.60
 ZN B:ZN410 1.8 29.5 0.4
N3 B:IMD303 1.9 13.7 0.6
O B:HOH1001 2.0 21.0 1.0
OD2 B:ASP130 2.0 29.3 1.0
CL B:CL502 2.5 13.0 0.6
C4 B:IMD303 2.9 16.7 0.6
C2 B:IMD303 2.9 10.9 0.6
CG B:ASP130 3.1 22.1 1.0
OD1 B:ASP130 3.6 31.4 1.0
O B:HOH1004 3.9 36.8 1.0
C27 A:065201 3.9 15.4 1.0
N1 B:IMD303 4.1 13.4 0.6
C5 B:IMD303 4.1 14.3 0.6
CB B:ASP130 4.3 13.4 1.0
OD2 B:ASP129 4.4 18.1 1.0
O28 A:065201 4.5 14.4 1.0
O26 A:065201 4.6 13.1 1.0
CB B:ASP129 4.6 12.0 1.0
CG2 B:VAL147 4.7 16.0 1.0
C31 A:065201 4.8 14.6 1.0
CE B:MET176 4.9 25.0 0.6

Zinc binding site 8 out of 11 in 3ecg

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Zinc binding site 8 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:11.7
occ:0.50
 N3 B:IMD305 2.1 10.8 0.5
CL B:CL506 2.2 14.6 0.5
CL B:CL508 2.2 24.5 0.5
CL B:CL505 2.3 10.8 0.5
C2 B:IMD305 3.1 11.0 0.5
C4 B:IMD305 3.1 10.0 0.5
CB B:TRP106 4.0 15.5 1.0
N1 B:IMD305 4.2 10.9 0.5
C5 B:IMD305 4.2 11.4 0.5
CG B:LYS107 4.2 16.7 1.0
CD B:LYS107 4.4 18.4 1.0
CE B:LYS107 4.4 20.9 1.0
CD1 B:TRP106 4.6 16.9 1.0
N B:LYS107 4.6 14.2 1.0
O B:HOH1099 4.6 32.1 1.0
CG B:TRP106 4.7 15.7 1.0
CA B:TRP106 4.9 12.8 1.0
N B:TRP106 4.9 12.7 1.0
CB B:LYS107 5.0 14.5 1.0
C B:TRP106 5.0 15.2 1.0

Zinc binding site 9 out of 11 in 3ecg

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Zinc binding site 9 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn408

b:24.0
occ:0.50
 O B:HOH1003 1.5 17.0 0.5
CL B:CL504 2.1 19.5 0.5
O B:HOH1002 2.1 12.0 0.5
OE1 B:GLU165 2.4 58.5 1.0
CD B:GLU165 2.9 29.5 1.0
OE2 B:GLU165 3.1 36.0 1.0
O B:HOH1006 3.2 41.7 0.5
O B:HOH1031 3.6 10.6 1.0
CG B:GLU165 4.0 16.3 1.0
CA B:GLY117 4.7 12.0 1.0
N B:GLY117 4.8 11.2 1.0
OE1 B:GLU163 4.9 62.6 1.0

Zinc binding site 10 out of 11 in 3ecg

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Zinc binding site 10 out of 11 in the High Resolution Hiv-2 Protease Structure in Complex with Antiviral Inhibitor Grl-98065


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-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn409

b:48.5
occ:0.50
 OE1 B:GLU158 2.1 33.2 1.0
O B:HOH1010 2.2 24.0 0.5
O B:HOH1144 2.2 26.4 0.5
CD B:GLU158 2.9 20.1 1.0
O B:HOH1113 3.0 27.3 0.5
O B:HOH1184 3.2 34.4 1.0
OE2 B:GLU158 3.2 35.1 1.0
NZ B:LYS145 4.3 26.3 1.0
CG B:GLU158 4.3 13.5 1.0
CE B:MET176 4.3 22.7 0.4
CE B:LYS145 4.6 23.3 1.0
O B:HOH1120 4.6 22.8 0.5
CG2 B:THR174 4.7 13.4 1.0
C5 B:IMD303 4.8 14.3 0.6
CD B:LYS145 4.9 18.1 1.0
CE B:MET176 5.0 25.0 0.6

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 04:15:35 2020

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