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Sodium in PDB 3ebz: High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir

Enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir

All present enzymatic activity of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir:
3.4.23.47;

Protein crystallography data

The structure of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir, PDB code: 3ebz was solved by A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.408, 30.827, 55.768, 90.00, 91.41, 90.00
R / Rfree (%) 13.6 / 18.1

Other elements in 3ebz:

The structure of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Zinc (Zn) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir (pdb code 3ebz). 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 High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir, PDB code: 3ebz:

Sodium binding site 1 out of 1 in 3ebz

Go back to Sodium Binding Sites List in 3ebz
Sodium binding site 1 out of 1 in the High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Hiv-2 Protease Structure in Complex with Clinical Drug Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:27.0
occ:1.00
O A:HOH1109 2.2 26.0 1.0
OD1 A:ASN41 2.3 20.5 1.0
O A:HOH1090 2.3 27.0 1.0
O A:HOH1067 2.7 23.5 1.0
CG A:ASN41 3.4 20.1 1.0
O A:ASN40 3.5 25.7 1.0
CA A:ASN41 3.8 19.9 1.0
CB A:ASN41 4.1 21.6 1.0
C A:ASN40 4.2 22.3 1.0
N A:ASN41 4.3 20.6 1.0
ND2 A:ASN41 4.5 24.7 1.0
C A:ASN41 4.9 18.9 1.0

Reference:

A.Y.Kovalevsky, J.M.Louis, A.Aniana, A.K.Ghosh, I.T.Weber. Structural Evidence For Effectiveness of Darunavir and Two Related Antiviral Inhibitors Against Hiv-2 Protease J.Mol.Biol. V. 384 178 2008.
ISSN: ISSN 0022-2836
PubMed: 18834890
DOI: 10.1016/J.JMB.2008.09.031
Page generated: Tue Dec 15 06:09:39 2020

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