Sodium in PDB 2x7r: Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41

The structure of Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41, PDB code: 2x7r was solved by G.Natrajan, V.Buzon, W.Weissenhorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.729 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	57.422, 57.422, 182.768, 90.00, 90.00, 120.00
R / Rfree (%)	17.69 / 21.38

The structure of Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41 (pdb code 2x7r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41, PDB code: 2x7r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41


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 A Late Fusion Intermediate of Hiv-1 GP41 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1666 b:58.5 occ:1.00 O D:HOH2008 3.4 45.1 1.0 OE2 D:GLU560 3.7 42.8 1.0 OE2 B:GLU647 3.8 48.0 1.0 CD B:GLU647 4.0 45.5 1.0 OE1 B:GLU647 4.1 40.8 1.0 O D:HOH2010 4.3 33.8 1.0 CB B:GLU647 4.7 26.9 1.0 CG B:GLU647 4.7 33.7 1.0 CD D:GLU560 4.9 41.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1678 b:40.5 occ:1.00 OE2 E:GLU657 3.2 38.8 1.0 CL E:CL1679 3.4 65.1 1.0 OE1 E:GLU657 3.5 39.4 1.0 CD E:GLU657 3.7 30.6 1.0 CG E:GLN653 4.2 23.7 1.0 CG E:GLU654 5.0 32.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Late Fusion Intermediate of Hiv-1 GP41 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1581 b:58.9 occ:1.00 O A:HOH2006 3.2 52.9 1.0 NH1 A:ARG579 4.7 43.6 1.0

V.Buzon, G.Natrajan, D.Schibli, F.Campelo, M.M.Kozlov, W.Weissenhorn. Crystal Structure of Hiv-1 GP41 Including Both Fusion Peptide and Membrane Proximal External Regions. Plos Pathog. V. 6 880 2010.
ISSN: ISSN 1553-7366
PubMed: 20463810
DOI: 10.1371/JOURNAL.PPAT.1000880