Sodium in PDB 7ya4: Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide

All present enzymatic activity of Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide:
1.17.1.9;

The structure of Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide, PDB code: 7ya4 was solved by S.Kim, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.14 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.794, 95.789, 117.93, 90, 99.28, 90
R / Rfree (%)	15.5 / 19.1

The binding sites of Sodium atom in the Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide (pdb code 7ya4). 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 Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide, PDB code: 7ya4:

Sodium binding site 1 out of 1 in the Formate Dehydrogenase From Novosphingobium Sp. AP12 with Nad and Azide


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 Novosphingobium Sp. AP12 with Nad and Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:14.7 occ:1.00 HD1 B:HIS264 1.8 21.0 1.0 HD1 A:HIS264 1.8 29.4 0.0 ND1 A:HIS264 2.3 26.4 1.0 O B:HOH655 2.4 15.9 1.0 O A:HOH678 2.4 15.8 1.0 ND1 B:HIS264 2.4 21.8 1.0 CG A:HIS264 3.0 18.4 1.0 CG B:HIS264 3.1 18.8 1.0 HB3 A:HIS264 3.1 16.6 1.0 HB3 B:HIS264 3.1 17.0 1.0 HB2 A:HIS264 3.2 16.6 1.0 HB2 B:HIS264 3.2 17.0 1.0 CE1 B:HIS264 3.3 22.3 1.0 CE1 A:HIS264 3.3 25.9 1.0 CB A:HIS264 3.3 16.9 1.0 CB B:HIS264 3.4 16.4 1.0 HE1 B:HIS264 3.5 21.2 1.0 HE1 A:HIS264 3.6 24.4 1.0 HE2 A:HIS263 4.1 14.1 0.0 CD2 A:HIS264 4.1 18.8 1.0 HE2 B:HIS263 4.1 15.6 0.0 CD2 B:HIS264 4.2 19.3 1.0 NE2 A:HIS264 4.2 20.9 1.0 HD2 A:HIS263 4.2 13.6 1.0 NE2 B:HIS264 4.2 18.6 1.0 OD2 B:ASP290 4.3 17.8 1.0 OD2 A:ASP290 4.3 17.6 1.0 HD2 B:HIS263 4.4 15.5 1.0 HB2 B:ASP290 4.6 14.4 1.0 NE2 A:HIS263 4.6 14.1 1.0 NE2 B:HIS263 4.7 15.6 1.0 CD2 A:HIS263 4.7 13.6 1.0 HB2 A:ASP290 4.8 13.7 1.0 CD2 B:HIS263 4.8 15.9 1.0 CA A:HIS264 4.8 14.2 1.0 HD2 A:HIS264 4.9 19.3 1.0 CA B:HIS264 4.9 16.7 1.0 HD2 B:HIS264 5.0 19.0 1.0 HB3 B:ASP267 5.0 16.9 1.0 HE2 A:HIS264 5.0 20.8 0.0 HE2 B:HIS264 5.0 17.9 0.0

S.Kim, K.-J.Kim. Dual Cofactor Specific Formate Dehydrogenase From Novosphingobium Sp. AP12 with High Activity. To Be Published.