Atomistry » Zinc » PDB 3e7l-3eg9 » 3ecg
Atomistry »
  Zinc »
    PDB 3e7l-3eg9 »
      3ecg »

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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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

Go back to Zinc Binding Sites List in 3ecg
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 Aug 20 08:51:31 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy