Sodium in PDB 8rtg: Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form

All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form:
1.12.7.2;

The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form, PDB code: 8rtg was solved by K.Bikbaev, I.Span, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.06 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.15, 84.786, 88.036, 90, 90, 90
R / Rfree (%)	16.5 / 18.9

The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form (pdb code 8rtg). 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 Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form, PDB code: 8rtg:

Sodium binding site 1 out of 1 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:14.3 occ:1.00 H A:ILE204 2.4 10.7 1.0 HZ2 A:LYS237 2.4 9.5 1.0 O A:HOH852 2.5 18.3 1.0 HB2 A:PRO203 2.8 11.7 1.0 O A:HOH806 2.9 24.8 1.0 HZ3 A:LYS237 3.0 9.5 1.0 HB A:ILE204 3.0 10.6 1.0 HG23 A:ILE204 3.0 10.7 1.0 NZ A:LYS237 3.0 9.5 1.0 HD2 A:PRO203 3.1 11.3 1.0 HE3 A:LYS237 3.1 9.6 1.0 N A:ILE204 3.1 10.7 1.0 HB2 A:SER202 3.2 11.4 1.0 HG21 A:THR145 3.3 9.3 1.0 CE A:LYS237 3.6 9.6 1.0 CB A:PRO203 3.6 11.7 1.0 CB A:ILE204 3.7 10.6 1.0 HE1 A:MET232 3.7 11.6 1.0 CG2 A:ILE204 3.7 10.7 1.0 CD A:PRO203 3.7 11.3 1.0 N A:PRO203 3.8 10.7 1.0 HZ1 A:LYS237 3.8 9.5 1.0 HD2 A:LYS237 3.8 10.2 1.0 HG A:SER202 3.8 10.8 0.0 HG2 A:PRO203 3.9 11.5 1.0 HG23 A:THR145 3.9 9.3 1.0 CG2 A:THR145 3.9 9.3 1.0 CA A:ILE204 4.0 10.1 1.0 HG21 A:ILE204 4.0 10.7 1.0 C A:PRO203 4.0 11.3 1.0 CA A:PRO203 4.0 11.3 1.0 OG A:SER202 4.0 10.8 1.0 CB A:SER202 4.0 11.4 1.0 CG A:PRO203 4.0 11.5 1.0 HG22 A:THR145 4.1 9.3 1.0 CD A:LYS237 4.3 10.2 1.0 SD A:MET232 4.3 11.0 1.0 CE A:MET232 4.3 11.6 1.0 HE2 A:LYS237 4.4 9.6 1.0 HA A:ILE204 4.4 10.1 1.0 HB3 A:PRO203 4.4 11.7 1.0 HE3 A:MET232 4.4 11.6 1.0 C A:SER202 4.4 10.7 1.0 HG22 A:ILE204 4.5 10.7 1.0 HD3 A:PRO203 4.6 11.3 1.0 HB2 A:CYS178 4.6 13.2 1.0 HB3 A:SER202 4.7 11.4 1.0 H A:GLY205 4.7 9.9 1.0 O A:HOH835 4.7 26.5 1.0 O A:HOH854 4.7 19.4 1.0 CA A:SER202 4.8 10.9 1.0 HD3 A:LYS237 4.8 10.2 1.0 O A:CYS178 4.8 12.5 1.0 HA A:PRO203 5.0 11.3 1.0 HG3 A:PRO203 5.0 11.5 1.0

K.Bikbaev, M.A.Martini, D.Oberthuer, J.A.Birrell, I.Span. Structure of [Fefe] Hydrogenase in the Holo and Apo Forms at Room Temperature To Be Published.