Iron in PDB 7xk5: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 3

All present enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 3:
7.2.1.1;

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 3 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 3 (pdb code 7xk5). 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 3, PDB code: 7xk5:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:64.6 occ:1.00 FE1 D:FES301 0.0 64.6 1.0 S2 D:FES301 2.2 64.6 1.0 S1 D:FES301 2.2 64.6 1.0 SG E:CYS26 3.0 32.4 1.0 SG D:CYS112 3.0 43.0 1.0 FE2 D:FES301 3.1 64.6 1.0 CB D:CYS112 3.1 43.0 1.0 N D:CYS112 3.4 43.0 1.0 N D:GLY27 3.7 42.5 1.0 CA D:CYS112 3.9 43.0 1.0 CB E:CYS26 4.0 32.4 1.0 CA D:GLY27 4.3 42.5 1.0 OD1 D:ASN111 4.3 38.0 1.0 O D:THR110 4.4 39.6 1.0 C D:ASN111 4.4 38.0 1.0 CA D:LEU26 4.6 44.3 1.0 CA D:ASN111 4.6 38.0 1.0 C D:LEU26 4.6 44.3 1.0 N D:VAL28 4.8 34.4 1.0 SG E:CYS120 4.9 38.3 1.0 C D:GLY27 5.0 42.5 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:64.6 occ:1.00 FE2 D:FES301 0.0 64.6 1.0 S1 D:FES301 2.2 64.6 1.0 S2 D:FES301 2.2 64.6 1.0 SG D:CYS29 2.9 37.2 1.0 SG E:CYS120 3.0 38.3 1.0 CB E:CYS120 3.0 38.3 1.0 FE1 D:FES301 3.1 64.6 1.0 CB D:CYS29 3.7 37.2 1.0 N E:GLY24 3.9 30.2 1.0 CA E:GLY24 4.1 30.2 1.0 N E:CYS120 4.2 38.3 1.0 CA E:CYS120 4.2 38.3 1.0 N E:MET25 4.4 31.4 1.0 C E:GLY24 4.6 30.2 1.0 SG E:CYS26 4.6 32.4 1.0 O D:THR110 4.7 39.6 1.0 N D:CYS29 4.9 37.2 1.0 CA D:CYS29 4.9 37.2 1.0 N E:CYS26 5.0 32.4 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:152.2 occ:1.00 FE1 F:FES501 0.0 152.2 1.0 S1 F:FES501 2.2 152.2 1.0 S2 F:FES501 2.2 152.2 1.0 N F:CYS76 2.7 118.7 1.0 N F:GLY77 2.8 113.7 1.0 N F:SER75 2.9 110.4 1.0 CB F:CYS70 3.0 109.5 1.0 FE2 F:FES501 3.1 152.2 1.0 C F:GLY74 3.2 101.3 1.0 CA F:GLY74 3.4 101.3 1.0 C F:SER75 3.5 110.4 1.0 OG F:SER75 3.5 110.4 1.0 CA F:CYS76 3.6 118.7 1.0 SG F:CYS70 3.6 109.5 1.0 C F:CYS76 3.6 118.7 1.0 CA F:SER75 3.6 110.4 1.0 CA F:GLY77 3.7 113.7 1.0 O F:GLY74 3.9 101.3 1.0 CA F:CYS70 3.9 109.5 1.0 N F:CYS70 4.1 109.5 1.0 CB F:CYS76 4.1 118.7 1.0 N F:GLY74 4.1 101.3 1.0 CB F:SER75 4.2 110.4 1.0 O F:SER75 4.5 110.4 1.0 N F:GLN78 4.6 114.9 1.0 C F:GLY77 4.7 113.7 1.0 O F:CYS76 4.7 118.7 1.0 C F:ALA69 4.9 111.0 1.0 OE1 F:GLN78 5.0 114.9 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:152.2 occ:1.00 FE2 F:FES501 0.0 152.2 1.0 S1 F:FES501 2.2 152.2 1.0 S2 F:FES501 2.2 152.2 1.0 FE1 F:FES501 3.1 152.2 1.0 SG F:CYS79 3.1 110.9 1.0 CB F:SER68 3.2 120.0 1.0 N F:GLN78 3.2 114.9 1.0 N F:CYS79 3.2 110.9 1.0 SG F:CYS70 3.5 109.5 1.0 CB F:CYS79 3.7 110.9 1.0 CA F:GLY77 3.8 113.7 1.0 N F:GLY77 3.8 113.7 1.0 CA F:SER68 3.8 120.0 1.0 C F:GLY77 3.9 113.7 1.0 CA F:GLN78 4.0 114.9 1.0 CA F:CYS79 4.1 110.9 1.0 C F:GLN78 4.1 114.9 1.0 OG F:SER68 4.2 120.0 1.0 CB F:CYS70 4.3 109.5 1.0 CB F:GLN78 4.4 114.9 1.0 OE1 F:GLN78 4.5 114.9 1.0 N F:ALA69 4.5 111.0 1.0 C F:SER68 4.7 120.0 1.0 N F:CYS70 4.7 109.5 1.0 O F:GLY77 5.0 113.7 1.0 N F:SER68 5.0 120.0 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