Iron 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:

Sodium

(Na)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2, PDB code: 8a1u:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 E:Fe1001 b:98.1 occ:1.00 FE1 E:FES1001 0.0 98.1 1.0 S2 E:FES1001 2.2 88.8 1.0 S1 E:FES1001 2.2 91.8 1.0 SG E:CYS26 2.3 45.3 1.0 SG D:CYS112 2.3 62.3 1.0 HB2 E:CYS26 2.7 35.8 1.0 FE2 E:FES1001 2.7 91.8 1.0 CB E:CYS26 3.0 38.5 1.0 HB2 D:CYS112 3.2 52.1 1.0 H D:CYS112 3.2 51.7 1.0 H D:GLY27 3.3 47.3 1.0 CB D:CYS112 3.4 54.0 1.0 H E:CYS26 3.6 35.0 1.0 HB3 E:CYS26 3.6 35.8 1.0 HA D:LEU26 3.8 52.2 1.0 H D:VAL28 3.9 44.8 1.0 N D:CYS112 3.9 49.2 1.0 N D:GLY27 4.0 42.5 1.0 HB3 D:CYS112 4.1 52.9 1.0 N E:CYS26 4.2 29.0 1.0 CA E:CYS26 4.3 34.4 1.0 CA D:CYS112 4.3 50.9 1.0 SG D:CYS29 4.4 49.9 1.0 SG E:CYS120 4.4 50.0 1.0 HA2 D:GLY27 4.5 46.2 1.0 HA D:ASN111 4.5 47.1 1.0 HB2 E:CYS120 4.6 43.1 1.0 HA D:CYS112 4.7 52.1 1.0 H D:CYS29 4.7 44.2 1.0 CA D:LEU26 4.7 49.5 1.0 N D:VAL28 4.7 47.5 1.0 HA E:CYS26 4.8 35.2 1.0 O D:THR110 4.8 50.3 1.0 CA D:GLY27 4.8 41.6 1.0 H E:THR27 4.8 33.3 1.0 C D:LEU26 4.8 48.9 1.0 HD23 D:LEU26 4.9 52.0 1.0 HB D:VAL28 4.9 44.2 1.0 HA2 E:GLY24 4.9 38.6 1.0

Iron binding site 2 out of 4 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 E:Fe1001 b:91.8 occ:1.00 FE2 E:FES1001 0.0 91.8 1.0 S2 E:FES1001 2.2 88.8 1.0 S1 E:FES1001 2.2 91.8 1.0 SG E:CYS120 2.3 50.0 1.0 SG D:CYS29 2.3 49.9 1.0 HB2 E:CYS120 2.6 43.1 1.0 FE1 E:FES1001 2.7 98.1 1.0 CB E:CYS120 2.9 42.1 1.0 HB3 E:CYS120 3.3 42.3 1.0 H E:GLY24 3.6 39.4 1.0 H D:CYS29 3.7 44.2 1.0 HB2 D:CYS29 3.7 45.0 1.0 CB D:CYS29 3.8 45.1 1.0 H E:CYS120 4.0 43.9 1.0 HA2 E:GLY24 4.1 38.6 1.0 HA D:ASN111 4.1 47.1 1.0 H E:CYS26 4.3 35.0 1.0 CA E:CYS120 4.3 39.8 1.0 H D:CYS112 4.3 51.7 1.0 N E:GLY24 4.3 40.4 1.0 H E:MET25 4.3 36.3 1.0 HB3 D:CYS29 4.4 45.1 1.0 SG E:CYS26 4.4 45.3 1.0 H D:VAL28 4.4 44.8 1.0 N D:CYS29 4.5 41.8 1.0 O D:THR110 4.5 50.3 1.0 SG D:CYS112 4.5 62.3 1.0 N E:CYS120 4.6 43.4 1.0 CA E:GLY24 4.6 37.4 1.0 HB2 E:CYS26 4.7 35.8 1.0 HA E:CYS120 4.7 42.9 1.0 CA D:CYS29 4.8 41.4 1.0 HA2 D:GLY27 4.8 46.2 1.0 N E:MET25 4.8 39.1 1.0 H D:GLY27 4.8 47.3 1.0 HA E:LEU23 4.9 40.4 1.0 N D:CYS112 5.0 49.2 1.0

Iron binding site 3 out of 4 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1502 b:21.9 occ:1.00 FE1 F:FES1502 0.0 21.9 1.0 S2 F:FES1502 2.2 8.1 1.0 S1 F:FES1502 2.2 21.3 1.0 SG F:CYS70 2.3 25.6 1.0 SG F:CYS76 2.3 16.9 1.0 H F:GLY77 2.7 17.4 1.0 FE2 F:FES1502 2.7 10.0 1.0 H F:CYS76 2.7 17.4 1.0 CB F:CYS76 3.4 16.9 1.0 H F:CYS70 3.4 19.8 1.0 N F:CYS76 3.4 17.1 1.0 HB3 F:CYS76 3.4 16.9 1.0 N F:GLY77 3.4 19.8 1.0 H F:SER75 3.5 16.6 1.0 H F:GLY72 3.5 21.6 1.0 CB F:CYS70 3.7 20.6 1.0 CA F:CYS76 3.8 17.7 1.0 HB3 F:CYS70 3.8 20.6 1.0 H F:GLN78 4.0 17.4 1.0 C F:CYS76 4.1 16.6 1.0 N F:CYS70 4.1 17.0 1.0 HA F:SER68 4.1 21.2 1.0 N F:SER75 4.2 16.0 1.0 HB2 F:CYS76 4.2 17.1 1.0 H F:CYS79 4.2 16.6 1.0 N F:GLY72 4.3 18.4 1.0 H F:GLY74 4.3 18.1 1.0 HA2 F:GLY72 4.3 22.2 1.0 HA2 F:GLY77 4.4 17.7 1.0 CA F:CYS70 4.4 18.4 1.0 H F:GLY71 4.4 21.8 1.0 SG F:CYS79 4.4 17.2 1.0 CA F:GLY77 4.4 20.2 1.0 HB2 F:CYS70 4.4 20.4 1.0 C F:SER75 4.4 15.2 1.0 SG F:CYS111 4.5 19.4 1.0 HA2 F:GLY74 4.5 18.3 1.0 N F:GLN78 4.6 14.4 1.0 O F:GLY72 4.6 24.9 1.0 N F:GLY71 4.6 20.4 1.0 HB3 F:SER75 4.6 16.7 1.0 CA F:GLY72 4.7 22.4 1.0 C F:CYS70 4.7 20.9 1.0 H F:ALA69 4.7 20.2 1.0 HA F:CYS76 4.7 17.0 1.0 C F:GLY72 4.8 24.8 1.0 CA F:SER75 4.8 14.6 1.0 N F:GLY74 4.8 19.1 1.0 N F:ALA69 4.9 20.8 1.0 C F:GLY77 4.9 16.0 1.0 HB3 F:CYS79 4.9 18.0 1.0 CA F:GLY74 5.0 19.1 1.0 CA F:SER68 5.0 21.7 1.0 C F:GLY74 5.0 17.5 1.0

Iron binding site 4 out of 4 in the Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sodium Pumping Nadh-Quinone Oxidoreductase with Substrates Nadh and Q2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1502 b:10.0 occ:1.00 FE2 F:FES1502 0.0 10.0 1.0 S2 F:FES1502 2.2 8.1 1.0 S1 F:FES1502 2.2 21.3 1.0 SG F:CYS79 2.3 17.2 1.0 SG F:CYS111 2.3 19.4 1.0 FE1 F:FES1502 2.7 21.9 1.0 HB3 F:CYS111 2.9 19.5 1.0 CB F:CYS111 3.2 20.3 1.0 H F:CYS111 3.5 18.6 1.0 HB3 F:CYS79 3.6 18.0 1.0 CB F:CYS79 3.7 16.9 1.0 HA2 F:GLY72 3.7 22.2 1.0 HB2 F:CYS111 3.8 18.9 1.0 H F:GLY74 3.8 18.1 1.0 H F:CYS79 3.8 16.6 1.0 H F:GLY77 3.9 17.4 1.0 HA2 F:GLY74 4.0 18.3 1.0 HB3 F:LEU109 4.0 17.3 1.0 HD13 F:LEU109 4.0 17.8 1.0 H F:GLY72 4.1 21.6 1.0 HD12 F:LEU56 4.2 19.6 1.0 N F:CYS111 4.2 18.4 1.0 HB2 F:CYS79 4.2 17.0 1.0 HA2 F:GLY77 4.3 17.7 1.0 CA F:CYS111 4.3 19.6 1.0 HG2 F:GLN112 4.3 17.9 1.0 HD22 F:LEU109 4.3 16.7 1.0 SG F:CYS76 4.4 16.9 1.0 HD13 F:LEU56 4.4 19.0 1.0 SG F:CYS70 4.4 25.6 1.0 CA F:GLY72 4.5 22.4 1.0 N F:GLY74 4.6 19.1 1.0 N F:CYS79 4.6 13.0 1.0 N F:GLY77 4.6 19.8 1.0 H F:SER75 4.7 16.6 1.0 CD1 F:LEU56 4.7 21.9 1.0 CA F:GLY74 4.7 19.1 1.0 N F:GLY72 4.7 18.4 1.0 CA F:CYS79 4.7 11.6 1.0 HD11 F:LEU56 4.8 19.1 1.0 CA F:GLY77 4.8 20.2 1.0 H F:GLN112 4.9 17.1 1.0 HA F:SER68 4.9 21.2 1.0 C F:GLY72 4.9 24.8 1.0 CB F:LEU109 4.9 14.6 1.0 CD1 F:LEU109 5.0 20.6 1.0 C F:CYS111 5.0 18.9 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