Sodium in PDB 2vjm: Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate

All present enzymatic activity of Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate:
2.8.3.16;

The structure of Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate, PDB code: 2vjm was solved by C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.89
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	151.668, 151.668, 98.947, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.3

The binding sites of Sodium atom in the Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate (pdb code 2vjm). 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 Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate, PDB code: 2vjm:

Sodium binding site 1 out of 1 in the Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Formyl-Coa Transferase with Aspartyl-Formyl Anhydide Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1429 b:29.4 occ:1.00 O A:HOH2287 2.4 23.0 1.0 O A:ASP294 2.4 16.6 1.0 OD1 A:ASP297 2.5 19.5 0.5 C A:ASP294 3.4 16.9 1.0 CG A:ASP297 3.6 19.4 0.5 CA A:ASP294 4.1 17.2 1.0 OD2 A:ASP297 4.3 19.8 0.5 OH A:TYR343 4.4 19.9 1.0 CA A:ASP297 4.4 19.1 0.5 N A:ASP297 4.4 18.9 1.0 N A:MET295 4.4 16.7 1.0 CA A:ASP297 4.5 19.1 0.5 CB A:ASP294 4.6 17.2 1.0 O A:MET295 4.6 16.8 1.0 OD1 A:ASP297 4.6 19.5 0.5 CB A:ASP297 4.6 19.3 0.5 CB A:ASP297 4.6 19.2 0.5 C A:MET295 4.7 16.8 1.0 CA A:MET295 4.7 16.8 1.0 CG A:ASP297 4.8 19.5 0.5

C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist. Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, A Class III Coa-Transferase. J.Biol.Chem. V. 283 6519 2008.
ISSN: ISSN 0021-9258
PubMed: 18162462
DOI: 10.1074/JBC.M709353200