Sodium in PDB 7qz1: Formate Dehydrogenase From Starkeya Novella

All present enzymatic activity of Formate Dehydrogenase From Starkeya Novella:
1.17.1.9;

The structure of Formate Dehydrogenase From Starkeya Novella, PDB code: 7qz1 was solved by N.Pontillo, D.J.Slotboom, A.Guskov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.87 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.255, 59.481, 122.673, 79.89, 85.41, 63.15
R / Rfree (%)	17.6 / 22.4

The structure of Formate Dehydrogenase From Starkeya Novella also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Formate Dehydrogenase From Starkeya Novella (pdb code 7qz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Formate Dehydrogenase From Starkeya Novella, PDB code: 7qz1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Formate Dehydrogenase From Starkeya Novella


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Formate Dehydrogenase From Starkeya Novella within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:48.9 occ:1.00 O A:HOH728 2.4 46.8 1.0 OE1 A:GLU355 2.7 41.4 1.0 NH2 A:ARG361 2.9 43.9 1.0 CB A:GLU355 3.6 37.8 1.0 O A:GLU352 3.8 36.8 1.0 CD A:GLU355 3.9 44.0 1.0 CG A:LYS42 3.9 48.0 1.0 O A:THR40 3.9 41.0 1.0 CZ A:ARG361 4.0 50.3 1.0 CG A:GLU352 4.0 36.5 1.0 N A:LYS42 4.1 40.6 1.0 SG A:CYS356 4.2 44.0 1.0 CD A:LYS42 4.2 49.7 1.0 NH1 A:ARG361 4.2 52.0 1.0 CE A:LYS42 4.2 52.7 1.0 CA A:GLU352 4.3 35.2 1.0 NZ A:LYS42 4.3 59.0 1.0 CG A:GLU355 4.4 39.2 1.0 CA A:PRO41 4.4 39.5 1.0 N A:CYS356 4.5 38.9 1.0 C A:GLU352 4.5 35.3 1.0 CB A:GLU352 4.7 35.1 1.0 C A:PRO41 4.7 40.5 1.0 O A:HOH626 4.7 47.4 1.0 C A:GLU355 4.8 40.2 1.0 CA A:GLU355 4.8 38.7 1.0 C A:THR40 4.9 38.4 1.0 CB A:LYS42 4.9 43.8 1.0 OE2 A:GLU355 4.9 42.6 1.0

Sodium binding site 2 out of 4 in the Formate Dehydrogenase From Starkeya Novella


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Formate Dehydrogenase From Starkeya Novella within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:45.1 occ:1.00 OD1 A:ASP183 2.4 37.9 1.0 O C:HOH639 2.8 38.1 1.0 O C:ASP12 3.0 40.4 1.0 O C:HOH707 3.5 50.1 1.0 CG A:ASP183 3.5 40.9 1.0 ND2 A:ASN180 3.7 40.5 1.0 CA A:ASN180 3.8 42.4 1.0 CG1 C:VAL14 4.0 46.8 1.0 C C:ASP12 4.0 43.6 1.0 CA C:PRO13 4.0 43.4 1.0 N C:VAL14 4.1 47.1 1.0 OD2 A:ASP183 4.1 42.6 1.0 CB A:ASN180 4.1 37.9 1.0 C A:ASN180 4.2 40.3 1.0 O C:ASP11 4.2 37.0 1.0 C C:PRO13 4.2 45.4 1.0 N A:ASP183 4.2 38.1 1.0 CG A:ASN180 4.3 41.9 1.0 O A:HOH701 4.3 36.4 1.0 CB A:ALA182 4.3 36.0 1.0 N C:PRO13 4.4 45.6 1.0 N A:ALA182 4.4 35.6 1.0 O A:HOH713 4.6 43.2 1.0 N A:ILE181 4.6 37.1 1.0 C C:ASP11 4.6 41.8 1.0 CB C:ASP11 4.6 41.4 1.0 O A:ASN180 4.7 39.4 1.0 CB A:ASP183 4.7 39.1 1.0 CA A:ALA182 4.8 36.5 1.0 N A:ASN180 4.9 41.9 1.0 CA C:VAL14 4.9 48.0 1.0 C A:ALA182 5.0 39.4 1.0

Sodium binding site 3 out of 4 in the Formate Dehydrogenase From Starkeya Novella


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Formate Dehydrogenase From Starkeya Novella within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:49.1 occ:1.00 O C:HOH673 2.4 38.6 1.0 OD2 C:ASP251 3.0 34.6 1.0 NZ C:LYS276 3.2 49.6 1.0 O A:HOH709 3.3 45.4 1.0 OD1 C:ASP251 3.5 38.3 1.0 CG C:ASP251 3.7 37.2 1.0 OG1 C:THR195 4.4 38.1 1.0 O A:HOH731 4.5 43.8 1.0 CG A:PRO27 4.5 37.5 1.0 O C:GLY193 4.6 36.9 1.0 CA A:PRO27 4.6 39.9 1.0 NH2 A:ARG23 4.6 37.9 1.0 CE C:LYS276 4.7 47.5 1.0 CB A:PRO27 4.7 38.5 1.0 N C:THR195 4.7 30.8 1.0 CA C:MET194 4.9 35.9 1.0 N A:PRO27 5.0 44.8 1.0

Sodium binding site 4 out of 4 in the Formate Dehydrogenase From Starkeya Novella


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Formate Dehydrogenase From Starkeya Novella within 5.0Å range: probe atom residue distance (Å) B Occ D:Na505 b:54.0 occ:1.00 O D:HOH645 2.4 40.1 1.0 OD2 D:ASP251 3.2 42.9 1.0 NZ D:LYS276 3.4 48.0 1.0 OD1 D:ASP251 3.7 39.7 1.0 CG D:ASP251 3.8 41.3 1.0 O D:GLY193 4.6 45.5 1.0 OG1 D:THR195 4.6 38.3 1.0 N D:THR195 4.6 40.8 1.0 CA D:MET194 4.8 40.2 1.0 CE D:LYS276 4.8 45.9 1.0

N.Pontillo, D.J.Slotboom, A.Guskov. Biochemical and Structural Insight Into the Chemical Resistance of the Formate Dehydrogenase From Starkeya Novella To Be Published.