Iron in PDB 7xk3: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1

All present enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1:
7.2.1.1;

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 (pdb code 7xk3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1, PDB code: 7xk3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:50.1 occ:1.00 FE1 D:FES301 0.0 50.1 1.0 S2 D:FES301 2.2 50.1 1.0 S1 D:FES301 2.2 50.1 1.0 SG E:CYS26 3.0 30.5 1.0 SG D:CYS112 3.0 35.6 1.0 FE2 D:FES301 3.1 50.1 1.0 CB D:CYS112 3.1 35.6 1.0 N D:CYS112 3.4 35.6 1.0 N D:GLY27 3.5 34.0 1.0 CA D:CYS112 3.9 35.6 1.0 CA D:GLY27 4.0 34.0 1.0 CB E:CYS26 4.0 30.5 1.0 OD1 D:ASN111 4.3 32.1 1.0 C D:ASN111 4.5 32.1 1.0 N D:VAL28 4.5 29.2 1.0 C D:LEU26 4.6 35.3 1.0 O D:THR110 4.6 33.4 1.0 CA D:ASN111 4.6 32.1 1.0 CA D:LEU26 4.7 35.3 1.0 C D:GLY27 4.8 34.0 1.0 SG D:CYS29 4.9 30.0 1.0 SG E:CYS120 5.0 34.9 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:50.1 occ:1.00 FE2 D:FES301 0.0 50.1 1.0 S1 D:FES301 2.2 50.1 1.0 S2 D:FES301 2.2 50.1 1.0 SG D:CYS29 2.9 30.0 1.0 CB E:CYS120 3.0 34.9 1.0 SG E:CYS120 3.0 34.9 1.0 FE1 D:FES301 3.1 50.1 1.0 N E:GLY24 3.8 29.8 1.0 CA E:GLY24 3.9 29.8 1.0 N E:CYS120 4.1 34.9 1.0 CB D:CYS29 4.1 30.0 1.0 CA E:CYS120 4.2 34.9 1.0 N E:MET25 4.2 30.2 1.0 C E:GLY24 4.5 29.8 1.0 O D:THR110 4.7 33.4 1.0 SG E:CYS26 4.7 30.5 1.0 ND2 E:ASN119 4.9 43.5 1.0 N E:CYS26 5.0 30.5 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:139.5 occ:1.00 FE1 F:FES501 0.0 139.5 1.0 S2 F:FES501 2.2 139.5 1.0 S1 F:FES501 2.2 139.5 1.0 CB F:CYS111 3.0 87.1 1.0 SG F:CYS111 3.0 87.1 1.0 FE2 F:FES501 3.1 139.5 1.0 N F:GLY74 3.3 79.2 1.0 SG F:CYS79 3.4 88.3 1.0 CA F:GLY74 3.6 79.2 1.0 SG F:CYS70 3.7 83.3 1.0 N F:GLY73 4.1 80.8 1.0 CA F:GLY72 4.3 79.0 1.0 CB F:CYS79 4.4 88.3 1.0 CA F:CYS111 4.4 87.1 1.0 N F:GLY72 4.4 79.0 1.0 C F:GLY73 4.5 80.8 1.0 C F:GLY72 4.5 79.0 1.0 N F:CYS111 4.7 87.1 1.0 OG F:SER68 4.8 84.8 1.0 C F:GLY74 4.8 79.2 1.0 CA F:GLY73 4.9 80.8 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:139.5 occ:1.00 FE2 F:FES501 0.0 139.5 1.0 S2 F:FES501 2.2 139.5 1.0 S1 F:FES501 2.2 139.5 1.0 FE1 F:FES501 3.1 139.5 1.0 SG F:CYS76 3.1 90.4 1.0 OG F:SER68 3.2 84.8 1.0 SG F:CYS70 3.2 83.3 1.0 N F:ALA69 3.5 80.3 1.0 N F:CYS70 3.5 83.3 1.0 CA F:SER68 3.7 84.8 1.0 C F:SER68 3.9 84.8 1.0 CB F:SER68 3.9 84.8 1.0 CB F:CYS70 4.0 83.3 1.0 CA F:CYS70 4.2 83.3 1.0 N F:GLY71 4.2 77.2 1.0 N F:GLN78 4.2 90.9 1.0 C F:ALA69 4.4 80.3 1.0 N F:CYS79 4.4 88.3 1.0 CA F:ALA69 4.4 80.3 1.0 N F:GLY72 4.5 79.0 1.0 C F:CYS70 4.5 83.3 1.0 N F:GLY77 4.6 90.9 1.0 CB F:CYS79 4.6 88.3 1.0 CB F:GLN78 4.7 90.9 1.0 SG F:CYS79 4.7 88.3 1.0 CB F:CYS76 4.7 90.4 1.0 CA F:GLN78 4.8 90.9 1.0 C F:GLN78 4.8 90.9 1.0 O F:SER68 4.9 84.8 1.0

J.I.Kishikawa, M.Ishikawa, T.Masuya, M.Murai, Y.Kitazumi, N.L.Butler, T.Kato, B.Barquera, H.Miyoshi. Cryo-Em Structures of Na + -Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae. Nat Commun V. 13 4082 2022.
ISSN: ESSN 2041-1723
PubMed: 35882843
DOI: 10.1038/S41467-022-31718-1