Sodium in PDB 5c4i: Structure of An Oxalate Oxidoreductase

All present enzymatic activity of Structure of An Oxalate Oxidoreductase:
1.2.7.10;

The structure of Structure of An Oxalate Oxidoreductase, PDB code: 5c4i was solved by M.I.Gibson, E.J.Brignole, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.66 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.351, 152.203, 171.824, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.6

The structure of Structure of An Oxalate Oxidoreductase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Sodium atom in the Structure of An Oxalate Oxidoreductase (pdb code 5c4i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of An Oxalate Oxidoreductase, PDB code: 5c4i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Oxalate Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:24.9 occ:0.80 O B:ARG258 2.4 29.4 1.0 O B:HOH637 2.4 30.4 1.0 O B:CYS261 2.4 22.2 1.0 O B:HOH627 2.5 26.1 1.0 C B:CYS261 3.5 19.8 1.0 C B:ARG258 3.5 25.6 1.0 O B:HOH586 3.8 24.4 1.0 N B:CYS261 4.0 19.2 1.0 CB B:CYS261 4.0 11.3 1.0 CA B:CYS261 4.0 20.5 1.0 O B:HOH592 4.0 42.0 1.0 CA B:ARG258 4.3 21.3 1.0 C B:GLU259 4.4 23.0 1.0 N B:GLU259 4.4 20.6 1.0 O B:GLU259 4.5 20.7 1.0 O B:HOH654 4.5 12.7 1.0 CA B:GLU259 4.5 24.0 1.0 N B:THR262 4.6 15.2 1.0 C B:ALA260 4.7 17.8 1.0 N B:ALA260 4.8 21.0 1.0 CB B:ARG258 4.9 22.6 1.0 CA B:THR262 5.0 22.1 1.0

Sodium binding site 2 out of 2 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Oxalate Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ F:Na404 b:22.4 occ:0.78 OD2 F:ASP130 2.4 31.6 1.0 O F:GLN213 2.4 30.5 1.0 O F:HOH597 2.5 22.0 1.0 O F:LEU211 2.5 26.3 1.0 O F:HOH632 2.7 24.6 1.0 C F:LEU211 3.3 20.5 1.0 CG F:ASP130 3.5 25.5 1.0 CA F:LEU211 3.6 15.2 1.0 C F:GLN213 3.6 24.5 1.0 O F:HOH623 3.7 53.5 1.0 O F:GLY210 3.8 21.1 1.0 OD1 F:ASP130 4.0 30.6 1.0 N F:GLN213 4.1 21.7 1.0 O F:GLY215 4.1 22.4 1.0 N F:ASN212 4.3 17.8 1.0 CA F:GLN213 4.4 22.3 1.0 O F:HOH546 4.4 19.6 1.0 C F:ASN212 4.5 21.4 1.0 C F:GLY210 4.6 22.0 1.0 N F:LEU211 4.6 17.1 1.0 CB F:LEU211 4.6 15.5 1.0 N F:GLY215 4.6 24.8 1.0 N F:GLU214 4.7 27.5 1.0 C F:ASP130 4.7 19.6 1.0 CB F:ASP130 4.8 23.7 1.0 O F:ASP130 4.8 17.6 1.0 CB F:GLN213 4.8 19.7 1.0 CA F:GLU214 4.8 27.2 1.0 CD2 F:LEU211 4.8 16.2 1.0 CA F:ASN212 4.9 20.3 1.0 CA F:ASP130 5.0 20.0 1.0

M.I.Gibson, E.J.Brignole, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan. The Structure of An Oxalate Oxidoreductase Provides Insight Into Microbial 2-Oxoacid Metabolism. Biochemistry V. 54 4112 2015.
ISSN: ISSN 0006-2960
PubMed: 26061898
DOI: 10.1021/ACS.BIOCHEM.5B00521