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Sodium in PDB 3nte: Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein

Protein crystallography data

The structure of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein, PDB code: 3nte was solved by L.Betts, J.I.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.910, 86.532, 55.589, 90.00, 99.73, 90.00
R / Rfree (%) 20.4 / 25.3

Other elements in 3nte:

The structure of Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein also contains other interesting chemical elements:

Iodine (I) 23 atoms
Iron (Fe) 23 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein (pdb code 3nte). 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 Wild-Type Full-Length Hiv-1 Capsid Protein, PDB code: 3nte:

Sodium binding site 1 out of 1 in 3nte

Go back to Sodium Binding Sites List in 3nte
Sodium binding site 1 out of 1 in the Crystal Structure of the Wild-Type Full-Length Hiv-1 Capsid Protein


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 Wild-Type Full-Length Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na238

b:37.1
occ:1.00
ND2 B:ASN74 3.1 37.3 1.0
O B:HOH245 3.3 40.0 1.0
CA B:SER102 3.9 31.5 1.0
CB B:ALA77 4.0 26.7 1.0
CB B:SER102 4.0 30.5 1.0
CB B:ALA105 4.1 28.3 1.0
CG B:ASN74 4.4 35.9 1.0
N B:SER102 4.4 29.2 1.0
CA B:ASN74 4.5 30.3 1.0
CG2 B:ILE73 4.6 28.6 1.0
O B:HOH299 4.6 33.3 0.9
OG1 B:THR107 4.7 41.4 1.0
O B:GLY101 4.7 25.9 1.0
C B:GLY101 4.8 25.0 1.0
N B:ASN74 4.9 29.2 1.0
O B:ILE73 4.9 26.5 1.0

Reference:

S.Du, L.Betts, R.Yang, H.Shi, J.Concel, J.Ahn, C.Aiken, P.Zhang, J.I.Yeh. Structure of the Hiv-1 Full-Length Capsid Protein in A Conformationally Trapped Unassembled State Induced By Small-Molecule Binding. J.Mol.Biol. V. 406 371 2011.
ISSN: ISSN 0022-2836
PubMed: 21146540
DOI: 10.1016/J.JMB.2010.11.027
Page generated: Tue Dec 15 06:19:20 2020

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