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Chlorine 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:

Zinc (Zn) 7 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir, PDB code: 3s45:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3s45

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Chlorine binding site 1 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl513

b:37.3
occ:0.50
 ZN A:ZN533 0.9 43.0 0.5
O A:LEU99 2.0 38.7 1.0
O A:HOH1080 2.4 25.5 1.0
C A:LEU99 3.0 34.1 1.0
N3 A:IMD524 3.0 30.1 0.5
C4 A:IMD524 3.3 30.2 0.5
OXT A:LEU99 3.5 41.5 1.0
CA A:LEU99 4.2 28.3 1.0
N A:LEU99 4.3 25.3 1.0
C2 A:IMD524 4.3 31.0 0.5
N B:PRO1 4.4 35.4 1.0
C5 A:IMD524 4.6 30.1 0.5
CB A:ASN98 4.9 24.1 1.0
CD B:PRO1 4.9 35.5 1.0
C A:ASN98 5.0 23.4 1.0

Chlorine binding site 2 out of 8 in 3s45

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Chlorine binding site 2 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl511

b:20.8
occ:1.00
 O B:HOH1043 2.9 21.5 1.0
O B:HOH1073 3.0 25.9 1.0
N B:ILE46 3.2 8.3 1.0
N1 B:IMD523 3.3 12.0 0.6
CD B:LYS45 3.7 16.0 1.0
C5 B:IMD523 3.7 11.6 0.6
CA B:LYS45 3.8 9.8 1.0
O B:ILE46 4.0 13.8 1.0
CB B:LYS45 4.0 10.6 1.0
C B:LYS45 4.0 8.8 1.0
CA B:ILE46 4.2 9.6 1.0
CB B:ILE46 4.2 10.2 1.0
CG B:LYS45 4.4 12.8 1.0
C2 B:IMD523 4.5 11.4 0.6
C B:ILE46 4.5 10.2 1.0
CG1 B:ILE46 4.6 10.4 1.0
O B:PRO44 4.9 11.1 1.0
CE B:LYS45 5.0 18.7 1.0
NZ B:LYS45 5.0 23.1 1.0

Chlorine binding site 3 out of 8 in 3s45

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Chlorine binding site 3 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl512

b:15.2
occ:0.60
 ZN B:ZN532 2.3 13.2 0.6
C2 B:IMD523 3.4 11.4 0.6
OD2 B:ASP30 3.5 21.5 1.0
CL B:CL517 3.5 39.2 0.5
N B:GLY48 3.6 13.2 1.0
CA B:VAL47 3.8 11.6 1.0
O B:HOH1068 3.8 30.6 1.0
N3 B:IMD523 3.9 12.5 0.6
C1 B:478201 4.0 24.3 1.0
CG1 B:VAL47 4.1 17.0 1.0
C B:VAL47 4.2 13.0 1.0
CB B:VAL47 4.3 11.9 1.0
CG2 B:VAL47 4.3 14.0 1.0
O B:ILE46 4.3 13.8 1.0
O B:GLY48 4.4 13.8 1.0
N1 B:IMD523 4.7 12.0 0.6
CA B:GLY48 4.7 13.1 1.0
CG B:ASP30 4.7 16.2 1.0
O6 B:478201 4.7 25.1 1.0
N B:VAL47 4.9 10.5 1.0

Chlorine binding site 4 out of 8 in 3s45

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Chlorine binding site 4 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl514

b:19.2
occ:0.50
 ZN B:ZN537 1.9 26.0 0.5
OE1 B:GLU65 3.0 25.4 1.0
O B:HOH1013 3.1 25.2 1.0
O B:HOH1007 3.6 26.8 0.5
OE2 B:GLU65 3.6 28.7 1.0
CD B:GLU65 3.7 20.5 1.0
CA B:GLY17 3.7 12.4 1.0
CG B:TYR14 4.1 13.4 1.0
CB B:TYR14 4.3 9.6 1.0
O B:HOH1024 4.3 15.0 1.0
CD2 B:TYR14 4.3 17.4 1.0
CD1 B:TYR14 4.4 16.0 1.0
N B:GLY17 4.4 11.9 1.0
C B:GLY17 4.6 12.2 1.0
O B:GLY17 4.6 11.4 1.0
CE2 B:TYR14 4.8 18.6 1.0
CE1 B:TYR14 4.9 16.9 1.0

Chlorine binding site 5 out of 8 in 3s45

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Chlorine binding site 5 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl515

b:24.0
occ:0.50
 ZN B:ZN534 2.4 21.9 0.5
N B:TRP6 3.1 15.5 1.0
CB B:SER4 3.4 22.6 1.0
N B:LYS7 3.4 17.1 1.0
CB B:TRP6 3.4 20.2 1.0
N B:LEU5 3.4 15.1 1.0
CA B:TRP6 3.6 18.3 1.0
C B:SER4 3.7 17.7 1.0
CL B:CL518 3.8 33.2 0.5
CL B:CL516 3.8 28.4 0.5
CG B:LYS7 3.8 19.0 1.0
CA B:SER4 3.8 20.3 1.0
N3 B:IMD525 3.9 14.1 0.5
N B:SER4 3.9 18.6 1.0
O B:HOH1059 3.9 14.8 1.0
C B:TRP6 4.0 18.1 1.0
CD1 B:TRP6 4.0 21.3 1.0
C B:LEU5 4.1 14.7 1.0
CG B:TRP6 4.1 21.4 1.0
C4 B:IMD525 4.2 13.5 0.5
CA B:LEU5 4.2 14.0 1.0
O B:SER4 4.4 16.8 1.0
CA B:LYS7 4.5 16.6 1.0
CB B:LYS7 4.5 18.0 1.0
O B:LYS7 4.5 14.1 1.0
OG B:SER4 4.6 28.1 1.0
CD B:LYS7 4.7 21.7 1.0
CE B:LYS7 4.7 22.9 1.0
C2 B:IMD525 4.8 13.4 0.5

Chlorine binding site 6 out of 8 in 3s45

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Chlorine binding site 6 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl516

b:28.4
occ:0.50
 ZN B:ZN534 2.0 21.9 0.5
CL B:CL518 3.1 33.2 0.5
N3 B:IMD525 3.3 14.1 0.5
CL B:CL515 3.8 24.0 0.5
C2 B:IMD525 3.8 13.4 0.5
CG B:LYS7 4.0 19.0 1.0
CB B:LYS7 4.0 18.0 1.0
CB B:TRP6 4.0 20.2 1.0
CD B:LYS7 4.1 21.7 1.0
N B:LYS7 4.3 17.1 1.0
C B:TRP6 4.5 18.1 1.0
C4 B:IMD525 4.5 13.5 0.5
CA B:LYS7 4.8 16.6 1.0
CE B:LYS7 4.8 22.9 1.0
CA B:TRP6 4.9 18.3 1.0
O B:TRP6 4.9 22.6 1.0

Chlorine binding site 7 out of 8 in 3s45

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Chlorine binding site 7 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl517

b:39.2
occ:0.50
 ZN B:ZN532 2.1 13.2 0.6
N3 B:IMD523 3.3 12.5 0.6
OD2 B:ASP30 3.4 21.5 1.0
CL B:CL512 3.5 15.2 0.6
CB B:ASP29 3.7 17.8 1.0
OD1 B:ASP30 3.7 21.2 1.0
C2 B:IMD523 3.9 11.4 0.6
CG B:ASP30 3.9 16.2 1.0
OD2 B:ASP29 4.2 34.2 1.0
CG B:ASP29 4.2 21.2 1.0
C4 B:IMD523 4.4 12.1 0.6

Chlorine binding site 8 out of 8 in 3s45

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Chlorine binding site 8 out of 8 in the Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Wild-Type Hiv-2 Protease with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl518

b:33.2
occ:0.50
 ZN B:ZN534 2.0 21.9 0.5
CL B:CL516 3.1 28.4 0.5
CL B:CL515 3.8 24.0 0.5
N3 B:IMD525 3.8 14.1 0.5
CE B:LYS7 3.8 22.9 1.0
NZ B:LYS7 4.1 25.0 1.0
C4 B:IMD525 4.2 13.5 0.5
CD B:LYS7 4.3 21.7 1.0
CG B:LYS7 4.6 19.0 1.0
C2 B:IMD525 5.0 13.4 0.5

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: Sun Jul 21 04:07:51 2024

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