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Chlorine in PDB 3ndu: Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure

Enzymatic activity of Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure

All present enzymatic activity of Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure, PDB code: 3ndu 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) 10.00 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.190, 62.705, 59.296, 90.00, 98.32, 90.00
R / Rfree (%) 13.6 / 19.4

Other elements in 3ndu:

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 Complex Structure (pdb code 3ndu). 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 1:5 Complex Structure, PDB code: 3ndu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3ndu

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Chlorine binding site 1 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1010

b:72.1
occ:1.00
 NZ A:LYS15 4.1 28.8 0.5
O A:HOH569 4.8 29.1 0.5

Chlorine binding site 2 out of 7 in 3ndu

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Chlorine binding site 2 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1021

b:61.5
occ:0.50
 CL A:CL1021 0.0 61.5 0.5
CL A:CL1021 2.2 70.5 0.5
OE1 A:GLN59 2.7 29.4 1.0
NZ A:LYS46 3.4 41.1 1.0
CD A:GLN59 3.5 18.6 1.0
NE2 A:GLN59 3.5 24.6 1.0
NZ A:LYS44 3.8 46.2 1.0
CD A:LYS46 3.9 29.5 1.0
CE A:LYS44 4.0 36.8 1.0
CE A:LYS46 4.1 33.7 1.0
CG A:LYS46 4.5 26.2 1.0
CG A:GLN59 4.9 16.5 1.0

Chlorine binding site 3 out of 7 in 3ndu

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Chlorine binding site 3 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1021

b:70.5
occ:0.50
 CL A:CL1021 0.0 70.5 0.5
CL A:CL1021 2.2 61.5 0.5
NZ A:LYS44 3.2 46.2 1.0
NE2 A:GLN59 3.7 24.6 1.0
CE A:LYS44 4.0 36.8 1.0
OE1 A:GLN59 4.2 29.4 1.0
CD A:GLN59 4.4 18.6 1.0

Chlorine binding site 4 out of 7 in 3ndu

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Chlorine binding site 4 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:51.4
occ:1.00
 N B:SER38 3.2 23.3 1.0
OG B:SER38 3.6 37.8 1.0
CA B:MET37 3.8 21.6 1.0
C B:MET37 4.0 23.2 1.0
CB B:SER38 4.0 29.7 1.0
CB B:MET37 4.1 19.5 1.0
CA B:SER38 4.2 26.3 1.0
O B:SER38 4.8 30.5 1.0

Chlorine binding site 5 out of 7 in 3ndu

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Chlorine binding site 5 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1005

b:64.9
occ:1.00
 N B:GLY41 3.9 38.7 1.0
CA B:PRO40 4.0 28.3 1.0
CB B:PRO40 4.0 32.2 1.0
C B:PRO40 4.5 34.5 1.0
CA B:GLY41 4.9 42.8 1.0

Chlorine binding site 6 out of 7 in 3ndu

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Chlorine binding site 6 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1004

b:69.6
occ:1.00
 O A:HOH162 3.4 31.6 1.0
OE1 C:GLN2 4.2 54.2 1.0
O C:HOH304 4.4 31.4 1.0
CG2 D:THR96 4.6 31.7 1.0
O D:HOH130 4.9 38.0 1.0
O C:ACT1008 4.9 56.6 1.0
CD C:GLN2 4.9 51.0 1.0
NE2 C:GLN2 4.9 40.3 1.0

Chlorine binding site 7 out of 7 in 3ndu

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Chlorine binding site 7 out of 7 in the Hiv-1 Protease Saquinavir:Ritonavir 1:5 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 1:5 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1006

b:77.1
occ:1.00
 NZ C:LYS55 3.2 59.9 1.0
CE C:LYS55 3.5 45.5 1.0
CE C:MET46 4.3 50.1 0.5
CE C:MET46 4.8 50.3 0.5
SD C:MET46 4.9 47.6 0.5
CD C:LYS55 4.9 42.4 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 00:59:19 2024

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