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Zinc in PDB 3s45: Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir

Enzymatic activity of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir

All present enzymatic activity of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir:
3.4.23.47;

Protein crystallography data

The structure of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir, PDB code: 3s45 was solved by Y.-F.Tie, Y.-F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.51
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.998, 30.986, 56.161, 90.00, 91.66, 90.00
R / Rfree (%) 18.3 / 24.6

Other elements in 3s45:

The structure of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir 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 Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir (pdb code 3s45). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir, PDB code: 3s45:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3s45

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Zinc binding site 1 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn533

b:43.0
occ:0.50
 CL A:CL513 0.9 37.3 0.5
O A:LEU99 2.6 38.7 1.0
N3 A:IMD524 2.6 30.1 0.5
O A:HOH1080 2.7 25.5 1.0
C4 A:IMD524 3.0 30.2 0.5
C A:LEU99 3.5 34.1 1.0
OXT A:LEU99 3.6 41.5 1.0
C2 A:IMD524 3.9 31.0 0.5
C5 A:IMD524 4.3 30.1 0.5
N1 A:IMD524 4.7 30.8 0.5
CA A:LEU99 4.8 28.3 1.0

Zinc binding site 2 out of 7 in 3s45

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Zinc binding site 2 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn535

b:27.7
occ:0.50
 OD2 A:ASP79 1.9 30.5 1.0
CG A:ASP79 2.7 24.3 1.0
OD1 A:ASP79 2.8 32.6 1.0
CB A:ASP79 4.2 21.5 1.0

Zinc binding site 3 out of 7 in 3s45

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Zinc binding site 3 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn536

b:26.0
occ:0.50
 O A:HOH1002 1.4 26.3 0.5
N3 A:IMD526 1.8 24.3 0.5
O A:HOH1001 2.2 28.7 0.5
OE1 A:GLU65 2.2 41.1 1.0
C2 A:IMD526 2.6 25.1 0.5
C4 A:IMD526 2.9 23.9 0.5
CD A:GLU65 3.2 37.4 1.0
OE2 A:GLU65 3.6 36.6 1.0
N1 A:IMD526 3.8 24.6 0.5
C5 A:IMD526 4.0 24.1 0.5
CG A:GLU65 4.5 34.2 1.0
CB A:GLU65 4.7 31.0 1.0
CD1 A:TYR14 4.8 31.8 1.0
CG A:TYR14 4.9 30.9 1.0

Zinc binding site 4 out of 7 in 3s45

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Zinc binding site 4 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn531

b:13.8
occ:1.00
 N3 B:IMD522 1.8 34.2 1.0
OE2 B:GLU21 1.9 15.3 1.0
N3 B:IMD521 2.1 15.7 1.0
C2 B:IMD522 2.2 36.1 1.0
CD B:GLU21 2.7 14.2 1.0
OE1 B:GLU21 2.9 21.8 1.0
C2 B:IMD521 3.0 15.2 1.0
C4 B:IMD522 3.0 34.0 1.0
C4 B:IMD521 3.1 14.3 1.0
N1 B:IMD522 3.4 36.5 1.0
C5 B:IMD522 3.8 36.0 1.0
N1 B:IMD521 4.2 14.3 1.0
CG B:GLU21 4.2 12.7 1.0
C5 B:IMD521 4.2 13.8 1.0
CG1 B:VAL10 4.8 21.2 1.0

Zinc binding site 5 out of 7 in 3s45

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Zinc binding site 5 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn532

b:13.2
occ:0.60
 OD2 B:ASP30 1.9 21.5 1.0
CL B:CL517 2.1 39.2 0.5
CL B:CL512 2.3 15.2 0.6
N3 B:IMD523 2.3 12.5 0.6
C2 B:IMD523 2.6 11.4 0.6
CG B:ASP30 2.9 16.2 1.0
OD1 B:ASP30 3.1 21.2 1.0
C4 B:IMD523 3.6 12.1 0.6
N1 B:IMD523 4.0 12.0 0.6
CB B:ASP30 4.2 14.2 1.0
C5 B:IMD523 4.4 11.6 0.6
C1 B:478201 4.6 24.3 1.0
CB B:ASP29 4.6 17.8 1.0
O6 B:478201 4.6 25.1 1.0
CG2 B:VAL47 4.6 14.0 1.0
CE B:MET76 4.6 27.9 0.6
N B:ASP30 5.0 12.9 1.0

Zinc binding site 6 out of 7 in 3s45

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Zinc binding site 6 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn534

b:21.9
occ:0.50
 CL B:CL518 2.0 33.2 0.5
CL B:CL516 2.0 28.4 0.5
N3 B:IMD525 2.3 14.1 0.5
CL B:CL515 2.4 24.0 0.5
C4 B:IMD525 3.1 13.5 0.5
C2 B:IMD525 3.4 13.4 0.5
CB B:TRP6 4.0 20.2 1.0
CG B:LYS7 4.3 19.0 1.0
C5 B:IMD525 4.3 13.3 0.5
N1 B:IMD525 4.5 13.2 0.5
CD B:LYS7 4.6 21.7 1.0
N B:LYS7 4.6 17.1 1.0
CE B:LYS7 4.6 22.9 1.0
CG B:TRP6 4.7 21.4 1.0
CD1 B:TRP6 4.7 21.3 1.0
CB B:SER4 4.8 22.6 1.0
CA B:TRP6 4.8 18.3 1.0
CB B:LYS7 4.9 18.0 1.0
N B:TRP6 4.9 15.5 1.0
C B:TRP6 4.9 18.1 1.0

Zinc binding site 7 out of 7 in 3s45

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Zinc binding site 7 out of 7 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn537

b:26.0
occ:0.50
 OE1 B:GLU65 1.7 25.4 1.0
O B:HOH1013 1.7 25.2 1.0
CL B:CL514 1.9 19.2 0.5
O B:HOH1007 2.2 26.8 0.5
CD B:GLU65 2.5 20.5 1.0
OE2 B:GLU65 2.7 28.7 1.0
O B:HOH1024 3.5 15.0 1.0
CG B:GLU65 4.0 17.0 1.0
NZ B:LYS70 4.2 28.5 0.4
CA B:GLY17 4.6 12.4 1.0
N B:GLY17 4.7 11.9 1.0
CE B:LYS70 4.8 26.1 0.4
CB B:TYR14 4.9 9.6 1.0

Reference:

Y.Tie, Y.F.Wang, P.I.Boross, T.Y.Chiu, A.K.Ghosh, J.Tozser, J.M.Louis, R.W.Harrison, I.T.Weber. Critical Differences in Hiv-1 and Hiv-2 Protease Specificity For Clinical Inhibitors. Protein Sci. V. 21 339 2012.
ISSN: ISSN 0961-8368
PubMed: 22238126
DOI: 10.1002/PRO.2019
Page generated: Sat Oct 26 15:33:01 2024

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