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Sodium in PDB 1zpk: Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2

Enzymatic activity of Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2

All present enzymatic activity of Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2, PDB code: 1zpk was solved by J.Duskova, T.Skalova, J.Dohnalek, H.Petrokova, J.Hasek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.65
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 62.483, 62.483, 82.412, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 25.3

Other elements in 1zpk:

The structure of Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2 (pdb code 1zpk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2, PDB code: 1zpk:

Sodium binding site 1 out of 1 in 1zpk

Go back to Sodium Binding Sites List in 1zpk
Sodium binding site 1 out of 1 in the Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Complex of Mutant Hiv-1 Protease (A71V, V82T, I84V) with A Hydroxyethylamine Peptidomimetic Inhibitor Boc-Phe- Psi[R-Ch(Oh)CH2NH]-Phe-Glu-Phe-NH2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:49.4
occ:1.00
 O B:HOH362 2.5 48.6 1.0
O B:HOH308 2.6 31.7 1.0
OD1 B:ASP130 2.7 40.7 1.0
CG B:ASP130 3.5 36.2 1.0
CB B:ASP130 3.8 32.4 1.0
CB B:THR174 3.8 38.2 1.0
CG2 B:THR174 3.9 39.6 1.0
ND2 B:ASN188 4.0 30.8 1.0
CG B:ASN188 4.1 22.3 1.0
CA B:ASP130 4.1 28.9 1.0
CB B:ASN188 4.2 26.5 1.0
O B:HOH404 4.3 37.6 0.5
OD2 B:ASP130 4.6 44.8 1.0
OD1 B:ASN188 4.6 26.9 1.0
OG1 B:THR174 4.6 47.1 1.0
O B:THR174 4.6 31.9 1.0
N B:THR131 4.8 25.6 1.0
O B:ASP129 4.9 27.0 1.0
C B:THR174 5.0 32.7 1.0
CA B:THR174 5.0 35.8 1.0
CL B:CL501 5.0 48.3 1.0

Reference:

J.Duskova, T.Skalova, J.Dohnalek, H.Petrokova, J.Hasek. Mutational Study of Pseudopeptide Inhibitor Binding to Hiv-1 Protease; Analysis of Four X-Ray Structures To Be Published.
Page generated: Sun Aug 17 10:00:15 2025

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