Sodium in PDB 2eix: The Structure of Physarum Polycephalum Cytochrome B5 Reductase

All present enzymatic activity of The Structure of Physarum Polycephalum Cytochrome B5 Reductase:
1.6.2.2;

The structure of The Structure of Physarum Polycephalum Cytochrome B5 Reductase, PDB code: 2eix was solved by S.W.Kim, M.Suga, K.Ogasahara, T.Ikegami, Y.Minami, T.Yubisui, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.35 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.084, 136.369, 45.718, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.6

The structure of The Structure of Physarum Polycephalum Cytochrome B5 Reductase also contains other interesting chemical elements:

Iodine

(I)

4 atoms

The binding sites of Sodium atom in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase (pdb code 2eix). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase, PDB code: 2eix:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1602 b:11.5 occ:1.00 NA B:NA1601 3.6 11.5 1.0 N A:MET259 3.6 10.6 1.0 CB A:MET259 3.7 8.6 1.0 CD A:PRO258 3.8 12.3 1.0 CG A:PRO258 3.9 12.7 1.0 CB A:PRO257 4.1 12.2 1.0 CB B:MET259 4.1 9.8 1.0 N A:PRO258 4.1 11.4 1.0 CA A:MET259 4.3 9.1 1.0 C A:PRO257 4.5 11.3 1.0 C A:PRO258 4.6 9.6 1.0 O B:HOH1789 4.6 36.4 1.0 CA A:PRO258 4.7 10.8 1.0 CA A:PRO257 4.7 11.1 1.0 CG B:MET259 4.7 10.9 1.0 CB A:PRO258 4.7 11.8 1.0 O B:HOH1669 4.7 10.9 1.0 O3 B:GOL1401 4.9 27.6 1.0 N B:MET259 5.0 8.2 1.0

Sodium binding site 2 out of 2 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1601 b:11.5 occ:1.00 N B:MET259 3.5 8.2 1.0 NA A:NA1602 3.6 11.5 1.0 CB B:MET259 3.7 9.8 1.0 CG B:PRO258 3.8 12.7 1.0 CD B:PRO258 3.9 10.2 1.0 N B:PRO258 4.0 10.5 1.0 CB B:PRO257 4.1 10.6 1.0 CB A:MET259 4.1 8.6 1.0 CA B:MET259 4.2 8.1 1.0 C B:PRO257 4.4 11.1 1.0 C B:PRO258 4.5 10.4 1.0 CA B:PRO258 4.6 10.6 1.0 CB B:PRO258 4.7 13.5 1.0 O A:HOH1801 4.7 15.5 1.0 CA B:PRO257 4.7 10.7 1.0 CG A:MET259 4.9 11.6 1.0 N A:MET259 4.9 10.6 1.0 CA A:MET259 5.0 9.1 1.0 O1 A:GOL1402 5.0 20.9 1.0

S.Kim, M.Suga, K.Ogasahara, T.Ikegami, Y.Minami, T.Yubisui, T.Tsukihara. Structure of Physarum Polycephalum Cytochrome B5 Reductase at 1.56 A Resolution. Acta Crystallogr.,Sect.F V. 63 274 2007.
ISSN: ESSN 1744-3091
PubMed: 17401193
DOI: 10.1107/S1744309107010731