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Sodium in PDB 4inb: Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor, PDB code: 4inb was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.42 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.950, 89.210, 39.270, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4inb:

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor (pdb code 4inb). 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 N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor, PDB code: 4inb:

Sodium binding site 1 out of 1 in 4inb

Go back to Sodium Binding Sites List in 4inb
Sodium binding site 1 out of 1 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor


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 N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:31.6
occ:1.00
O A:GLY106 2.6 16.6 1.0
O A:HOH1014 2.7 30.6 1.0
O A:HOH1012 2.7 21.3 1.0
O A:SER109 2.7 16.9 1.0
C A:GLY106 3.8 17.6 1.0
O A:HOH1081 3.9 37.6 1.0
C A:SER109 3.9 15.0 1.0
O A:HOH1004 4.1 22.6 1.0
O A:HOH1080 4.2 32.7 1.0
O A:THR107 4.4 16.8 1.0
NE2 A:GLN114 4.4 15.3 1.0
N A:SER109 4.5 15.6 1.0
O A:HOH1070 4.6 42.2 1.0
CA A:GLY106 4.6 13.8 1.0
CA A:THR110 4.6 14.8 1.0
C A:THR107 4.6 16.0 1.0
NE2 A:GLN50 4.6 29.1 1.0
N A:THR110 4.7 14.8 1.0
N A:THR107 4.8 15.2 1.0
CA A:SER109 4.8 14.6 1.0
CA A:THR107 4.9 17.0 1.0

Reference:

N.Goudreau, R.Coulombe, A.M.Faucher, C.Grand-Maitre, J.E.Lacoste, C.T.Lemke, E.Malenfant, Y.Bousquet, L.Fader, B.Simoneau, J.F.Mercier, S.Titolo, S.W.Mason. Monitoring Binding of Hiv-1 Capsid Assembly Inhibitors Using (19) F Ligand-and (15) N Protein-Based uc(Nmr) and X-Ray Crystallography: Early Hit Validation of A Benzodiazepine Series. Chemmedchem V. 8 405 2013.
ISSN: ISSN 1860-7179
PubMed: 23401268
DOI: 10.1002/CMDC.201200580
Page generated: Tue Dec 15 06:45:01 2020

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