Sodium in PDB 8a1u: Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2

All present enzymatic activity of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2:
7.2.1.1;

The structure of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 (pdb code 8a1u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2, PDB code: 8a1u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na509 b:28.5 occ:1.00 O B:VAL275 2.3 37.6 1.0 HD11 B:ILE268 2.5 34.4 1.0 O B:HOH623 2.5 34.8 1.0 O B:VAL332 2.5 34.2 1.0 O B:ALA263 2.8 36.6 1.0 O B:HOH632 3.1 30.2 1.0 HD13 B:ILE268 3.2 34.5 1.0 CD1 B:ILE268 3.3 32.9 1.0 HA B:VAL275 3.3 33.0 1.0 C B:VAL275 3.3 37.6 1.0 C B:VAL332 3.7 28.5 1.0 C B:ALA263 3.8 35.5 1.0 HA2 B:GLY266 3.8 33.8 1.0 CA B:VAL275 3.9 30.3 1.0 HB1 B:ALA263 3.9 33.3 1.0 HG12 B:ILE268 3.9 34.6 1.0 OG1 B:THR277 3.9 39.8 1.0 HD12 B:ILE268 3.9 34.9 1.0 O B:GLU274 4.0 42.5 1.0 HA B:ALA263 4.0 33.9 1.0 HA B:LEU333 4.0 30.2 1.0 HG1 B:THR277 4.0 34.0 1.0 H B:THR277 4.1 33.4 1.0 CG1 B:ILE268 4.1 30.1 1.0 HB B:VAL332 4.2 32.1 1.0 HA B:VAL332 4.3 31.6 1.0 HG13 B:ILE268 4.4 33.9 1.0 CA B:ALA263 4.4 29.6 1.0 N B:SER276 4.5 36.5 1.0 HA B:SER276 4.5 33.3 1.0 O B:GLY334 4.5 31.1 1.0 O B:HOH602 4.5 31.4 1.0 N B:THR277 4.5 32.2 1.0 CA B:VAL332 4.6 25.9 1.0 CB B:ALA263 4.6 30.2 1.0 HB B:VAL275 4.7 32.8 1.0 N B:LEU333 4.7 32.1 1.0 HA B:PHE264 4.7 34.2 1.0 CA B:LEU333 4.7 27.2 1.0 CA B:GLY266 4.8 30.7 1.0 C B:GLU274 4.8 33.6 1.0 O B:HOH617 4.8 38.5 1.0 H B:GLY334 4.8 30.8 1.0 H B:GLY266 4.9 35.0 1.0 N B:VAL275 4.9 31.9 1.0 HD23 B:LEU333 4.9 30.6 1.0 CA B:SER276 4.9 29.3 1.0 CB B:VAL332 4.9 27.3 1.0 CB B:VAL275 4.9 27.3 1.0 N B:PHE264 4.9 32.7 1.0 C B:SER276 5.0 29.1 1.0

Sodium binding site 2 out of 2 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na510 b:35.3 occ:1.00 O B:ASN375 2.2 40.9 1.0 O B:TYR378 2.2 39.0 1.0 O B:HOH660 2.2 34.6 1.0 O B:ARG372 2.9 37.5 1.0 HA B:PRO379 2.9 37.1 1.0 O B:ILE371 3.1 32.1 1.0 C B:TYR378 3.2 37.5 1.0 C B:ASN375 3.3 37.6 1.0 HA B:ARG372 3.4 30.5 1.0 O B:HOH659 3.5 29.8 1.0 C B:ARG372 3.6 31.5 1.0 HA B:PRO376 3.6 31.9 1.0 CA B:PRO379 3.6 39.4 1.0 HB3 B:ASN375 3.7 31.3 1.0 N B:PRO379 3.8 46.5 1.0 O B:HOH607 3.8 44.4 1.0 O B:PRO379 3.8 40.4 1.0 H B:ASN375 3.9 30.6 1.0 C B:PRO379 3.9 33.6 1.0 H B:TYR378 3.9 32.0 1.0 CA B:ARG372 3.9 27.9 1.0 CA B:PRO376 4.1 31.4 1.0 N B:PRO376 4.2 33.9 1.0 C B:ILE371 4.2 27.0 1.0 N B:TYR378 4.2 34.8 1.0 CA B:ASN375 4.3 30.4 1.0 CA B:TYR378 4.3 30.1 1.0 C B:PRO376 4.3 29.4 1.0 N B:ASN375 4.4 27.2 1.0 CB B:ASN375 4.4 28.7 1.0 O B:HOH605 4.4 40.1 1.0 O B:PRO376 4.4 38.2 1.0 HB2 B:TYR378 4.5 31.4 1.0 N B:VAL373 4.6 30.3 1.0 N B:ARG372 4.6 30.1 1.0 N B:GLU380 4.8 30.4 1.0 O B:VAL373 4.8 30.4 1.0 N B:ALA377 4.9 27.5 1.0 HG3 B:MET322 4.9 36.3 1.0 HG22 B:ILE371 4.9 28.1 1.0 C B:VAL373 4.9 28.5 1.0 CB B:PRO379 5.0 39.1 1.0 HA B:VAL373 5.0 31.7 1.0 CB B:TYR378 5.0 29.9 1.0

J.-L.Hau, S.Kaltwasser, V.Muras, G.V.Casutt, G.Vohl, B.Clauben, W.Steffen, L.Leitner, E.Bill, G.E.Cutsail, S.D.Debeer, J.Vonck, J.Steuber, G.Fritz. Conformational Coupling of Redox-Driven Na+-Translocation in Vibrio Cholerae Nadh:Quinone Oxidoreductase Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01099-0