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Chlorine in PDB 3ndt: Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure

Enzymatic activity of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure

All present enzymatic activity of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure, PDB code: 3ndt was solved by S.Geremia, F.M.Olajuyigbe, N.Demitri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.294, 62.785, 59.171, 90.00, 98.32, 90.00
R / Rfree (%) 14 / 22.9

Other elements in 3ndt:

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure (pdb code 3ndt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure, PDB code: 3ndt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3ndt

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Chlorine binding site 1 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:62.3
occ:1.00
 CA A:PRO40 4.0 34.8 1.0
CB A:PRO40 4.1 38.3 1.0
O A:HOH107 4.2 39.5 1.0
N A:GLY41 4.3 33.7 1.0
C A:PRO40 4.8 35.9 1.0

Chlorine binding site 2 out of 7 in 3ndt

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Chlorine binding site 2 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:88.4
occ:1.00
 NZ B:LYS8 2.8 74.6 1.0
CE B:LYS8 4.1 59.9 1.0
CD B:LYS8 4.7 54.9 1.0

Chlorine binding site 3 out of 7 in 3ndt

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Chlorine binding site 3 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:73.3
occ:1.00
 CD1 B:ILE64 3.4 43.5 1.0
CG1 B:ILE64 4.8 38.9 1.0

Chlorine binding site 4 out of 7 in 3ndt

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Chlorine binding site 4 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl104

b:85.1
occ:1.00
 O A:TRP7 3.8 34.6 1.0
O B:HOH297 3.9 46.1 1.0
NH1 B:ARG88 4.3 26.5 1.0
CE3 A:TRP7 4.3 40.2 1.0
CA A:TRP7 4.5 26.4 1.0
C A:TRP7 4.5 30.4 1.0
CA B:ASN89 4.6 23.6 1.0
O B:ARG88 4.6 25.3 1.0
O A:LEU6 4.6 20.2 1.0
CG2 B:THR92 4.7 27.6 1.0
CZ3 A:TRP7 4.7 44.6 1.0
OG1 B:THR92 4.8 27.4 1.0
N B:ASN89 4.9 20.8 1.0
C B:ARG88 4.9 20.1 1.0

Chlorine binding site 5 out of 7 in 3ndt

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Chlorine binding site 5 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl105

b:0.5
occ:1.00
 O B:ASP61 3.9 27.3 1.0
CB B:GLN62 4.0 29.7 1.0
CG B:GLN62 4.0 38.7 1.0
CB B:ASP61 4.3 28.7 1.0
C B:ASP61 4.3 23.8 1.0
O B:HOH117 4.5 39.9 1.0
O B:HOH268 4.5 48.3 1.0
N B:GLN62 4.8 24.3 1.0
CA B:ASP61 4.8 23.3 1.0

Chlorine binding site 6 out of 7 in 3ndt

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Chlorine binding site 6 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl106

b:0.3
occ:1.00
 CZ2 B:TRP43 3.9 30.1 1.0
CD B:ARG58 4.0 25.1 1.0
NE B:ARG58 4.3 33.6 1.0
NH1 B:ARG58 4.5 32.3 1.0
CE2 B:TRP43 4.5 29.6 1.0
CZ B:ARG58 4.5 27.6 1.0
CH2 B:TRP43 4.6 27.2 1.0
NE1 B:TRP43 4.7 30.3 1.0

Chlorine binding site 7 out of 7 in 3ndt

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Chlorine binding site 7 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl101

b:62.2
occ:1.00
 N C:SER37 3.9 32.3 1.0
CB C:SER37 4.4 37.1 1.0
CA C:MET36 4.4 29.7 1.0
OG C:SER37 4.5 46.1 1.0
NE2 C:GLN18 4.7 55.2 1.0
C C:MET36 4.7 31.4 1.0
CB C:MET36 4.8 28.8 1.0
CA C:SER37 4.8 31.4 1.0

Reference:

F.M.Olajuyigbe, N.Demitri, S.Geremia. Investigation of 2-Fold Disorder of Inhibitors and Relative Potency By Crystallizations of Hiv-1 Protease in Ritonavir and Saquinavir Mixtures Cryst.Growth Des. V. 11 4378 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG200514Z
Page generated: Sun Jul 21 00:59:14 2024

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