Sodium in PDB 1vel: Mycobacterium Smegmatis Dps Tetragonal Form

The structure of Mycobacterium Smegmatis Dps Tetragonal Form, PDB code: 1vel was solved by S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.21 / 2.99
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.643, 123.643, 262.328, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21

The structure of Mycobacterium Smegmatis Dps Tetragonal Form also contains other interesting chemical elements:

Cadmium

(Cd)

10 atoms

The binding sites of Sodium atom in the Mycobacterium Smegmatis Dps Tetragonal Form (pdb code 1vel). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mycobacterium Smegmatis Dps Tetragonal Form, PDB code: 1vel:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:44.7 occ:0.75 OE2 B:GLU128 2.5 72.2 1.0 OE2 A:GLU128 2.8 97.3 1.0 OE2 C:GLU128 2.8 93.6 1.0 O1 A:SO4601 3.0 97.1 1.0 CD B:GLU128 3.7 72.2 1.0 CD A:GLU128 3.8 97.3 1.0 CD C:GLU128 4.0 93.6 1.0 OE1 A:GLU128 4.1 97.3 1.0 OE1 B:GLU128 4.3 72.2 1.0 S A:SO4601 4.4 97.1 1.0 OE1 C:GLU128 4.5 93.6 1.0 CG B:GLU128 4.9 72.2 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na212 b:46.7 occ:0.75 O1 D:SO4602 2.9 88.4 1.0 OE2 E:GLU128 2.9 76.4 1.0 OE2 D:GLU128 3.0 90.6 1.0 CD E:GLU128 3.9 76.4 1.0 OE1 E:GLU128 4.1 76.4 1.0 OE1 F:GLU128 4.2 0.3 1.0 CD D:GLU128 4.2 90.6 1.0 S D:SO4602 4.4 88.4 1.0 OE1 D:GLU128 4.8 90.6 1.0 O4 D:SO4602 5.0 88.4 1.0 O2 D:SO4602 5.0 88.4 1.0

S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan. X-Ray Analysis of Mycobacterium Smegmatis Dps and A Comparative Study Involving Other Dps and Dps-Like Molecules J.Mol.Biol. V. 339 1103 2004.
ISSN: ISSN 0022-2836
PubMed: 15178251
DOI: 10.1016/J.JMB.2004.04.042