Iron in PDB 7xk4: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2

All present enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2:
7.2.1.1;

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2 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 2 (pdb code 7xk4). 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 2, PDB code: 7xk4:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:50.2 occ:1.00 FE1 D:FES301 0.0 50.2 1.0 S2 D:FES301 2.2 50.2 1.0 S1 D:FES301 2.2 50.2 1.0 SG E:CYS26 2.9 30.1 1.0 SG D:CYS112 3.0 41.0 1.0 FE2 D:FES301 3.1 50.2 1.0 CB D:CYS112 3.1 41.0 1.0 N D:CYS112 3.4 41.0 1.0 N D:GLY27 3.6 34.3 1.0 CA D:CYS112 3.8 41.0 1.0 CB E:CYS26 4.1 30.1 1.0 CA D:GLY27 4.2 34.3 1.0 OD1 D:ASN111 4.4 39.3 1.0 O D:THR110 4.4 40.2 1.0 C D:ASN111 4.4 39.3 1.0 N D:VAL28 4.6 31.3 1.0 C D:LEU26 4.6 36.9 1.0 CA D:LEU26 4.6 36.9 1.0 CA D:ASN111 4.6 39.3 1.0 C D:GLY27 4.9 34.3 1.0 SG E:CYS120 4.9 37.7 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:50.2 occ:1.00 FE2 D:FES301 0.0 50.2 1.0 S1 D:FES301 2.2 50.2 1.0 S2 D:FES301 2.2 50.2 1.0 SG D:CYS29 2.9 31.7 1.0 SG E:CYS120 2.9 37.7 1.0 CB E:CYS120 3.1 37.7 1.0 FE1 D:FES301 3.1 50.2 1.0 CB D:CYS29 3.4 31.7 1.0 N E:GLY24 3.9 28.7 1.0 CA E:GLY24 4.1 28.7 1.0 N E:CYS120 4.2 37.7 1.0 CA E:CYS120 4.2 37.7 1.0 N E:MET25 4.3 29.3 1.0 C E:GLY24 4.6 28.7 1.0 CA D:CYS29 4.7 31.7 1.0 N D:CYS29 4.7 31.7 1.0 O D:THR110 4.7 40.2 1.0 SG E:CYS26 4.7 30.1 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:176.9 occ:1.00 FE1 F:FES501 0.0 176.9 1.0 S1 F:FES501 2.2 176.9 1.0 S2 F:FES501 2.2 176.9 1.0 N F:GLY74 3.0 99.4 1.0 FE2 F:FES501 3.1 176.9 1.0 CB F:CYS111 3.3 91.8 1.0 CA F:GLY74 3.4 99.4 1.0 SG F:CYS111 3.5 91.8 1.0 C F:GLY72 3.9 99.7 1.0 N F:GLY73 3.9 97.1 1.0 CA F:GLY72 4.1 99.7 1.0 SG F:CYS76 4.1 104.0 1.0 SG F:CYS79 4.1 94.4 1.0 C F:GLY73 4.2 97.1 1.0 N F:GLY72 4.3 99.7 1.0 O F:GLY72 4.3 99.7 1.0 C F:GLY74 4.6 99.4 1.0 CA F:GLY73 4.6 97.1 1.0 CA F:CYS111 4.7 91.8 1.0 N F:SER75 4.9 106.1 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:176.9 occ:1.00 FE2 F:FES501 0.0 176.9 1.0 S1 F:FES501 2.2 176.9 1.0 S2 F:FES501 2.2 176.9 1.0 FE1 F:FES501 3.1 176.9 1.0 CA F:GLY72 3.1 99.7 1.0 O F:GLY71 3.6 98.8 1.0 N F:GLY72 3.6 99.7 1.0 C F:GLY71 3.8 98.8 1.0 CD2 F:LEU56 3.8 88.0 1.0 C F:GLY72 4.0 99.7 1.0 N F:GLY73 4.0 97.1 1.0 CB F:CYS111 4.1 91.8 1.0 CA F:GLY71 4.9 98.8 1.0 O F:GLY72 5.0 99.7 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