Iron in PDB 4p6v: Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae

The structure of Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae, PDB code: 4p6v was solved by J.Steuber, M.S.Casutt, G.Vohl, T.Vorburger, K.Diederichs, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 3.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.350, 143.380, 104.490, 90.00, 110.96, 90.00
R / Rfree (%)	24.6 / 27.6

The structure of Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae (pdb code 4p6v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae, PDB code: 4p6v:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.4 occ:1.00 SG E:CYS120 2.2 0.2 1.0 SG D:CYS29 2.3 0.7 1.0 SG D:CYS112 2.3 0.4 1.0 SG E:CYS26 2.4 0.3 1.0 CB E:CYS120 3.5 0.4 1.0 CB D:CYS29 3.6 0.9 1.0 CB D:CYS112 3.7 0.9 1.0 CB E:CYS26 3.9 0.2 1.0 N D:CYS112 3.9 0.5 1.0 O D:THR110 3.9 0.4 1.0 N E:CYS120 4.2 0.1 1.0 O E:VAL118 4.2 1.0 1.0 CA D:GLY27 4.2 0.7 1.0 CA E:CYS120 4.3 0.8 1.0 CA D:CYS112 4.5 0.4 1.0 N D:CYS29 4.5 0.9 1.0 C D:GLY27 4.6 0.1 1.0 CA D:CYS29 4.7 0.7 1.0 CA D:ASN111 4.8 0.3 1.0 C D:ASN111 4.8 0.7 1.0 N D:VAL28 4.8 0.5 1.0 C E:MET25 4.9 0.1 1.0 O E:MET25 5.0 0.4 1.0 C D:THR110 5.0 0.7 1.0 N E:CYS26 5.0 0.9 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:0.3 occ:1.00 FE1 F:FES501 0.0 0.3 1.0 S1 F:FES501 2.2 1.0 1.0 S2 F:FES501 2.2 0.7 1.0 SG F:CYS76 2.3 0.7 1.0 SG F:CYS70 2.3 0.3 1.0 N F:CYS76 3.1 0.3 1.0 FE2 F:FES501 3.1 0.9 1.0 CB F:CYS76 3.2 0.5 1.0 CB F:CYS70 3.5 0.5 1.0 N F:SER75 3.5 0.8 1.0 SG F:CYS111 3.6 0.2 1.0 CA F:CYS76 3.6 0.3 1.0 C F:SER75 4.1 0.2 1.0 CA F:GLY74 4.1 0.1 1.0 N F:GLY77 4.1 0.4 1.0 N F:GLY74 4.1 1.0 1.0 OG F:SER68 4.2 0.8 1.0 C F:GLY74 4.2 0.5 1.0 C F:CYS76 4.3 0.2 1.0 CA F:SER75 4.4 0.0 1.0 CA F:CYS70 4.6 0.5 1.0 N F:CYS70 4.6 0.9 1.0 CB F:CYS111 4.8 0.5 1.0 CB F:SER68 4.9 1.0 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Na+-Translocating Nadh: Ubiquinone Oxidoreductase From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:0.9 occ:1.00 FE2 F:FES501 0.0 0.9 1.0 S1 F:FES501 2.2 1.0 1.0 S2 F:FES501 2.2 0.7 1.0 SG F:CYS79 2.3 0.6 1.0 SG F:CYS111 2.3 0.2 1.0 CB F:CYS79 2.9 0.7 1.0 FE1 F:FES501 3.1 0.3 1.0 N F:CYS79 3.6 0.7 1.0 CB F:CYS111 3.8 0.5 1.0 CA F:CYS79 3.9 0.7 1.0 SG F:CYS76 3.9 0.7 1.0 OG F:SER68 4.3 0.8 1.0 CB F:SER68 4.3 1.0 1.0 N F:CYS111 4.3 0.4 1.0 N F:GLN78 4.5 0.3 1.0 CA F:GLY74 4.7 0.1 1.0 CA F:CYS111 4.7 0.3 1.0 CD2 F:LEU109 4.8 0.6 1.0 C F:GLN78 4.8 0.5 1.0 N F:GLY77 4.8 0.4 1.0 CA F:SER68 4.9 0.8 1.0 C F:CYS79 5.0 0.4 1.0

J.Steuber, G.Vohl, M.S.Casutt, T.Vorburger, K.Diederichs, G.Fritz. Structure of the V. Cholerae NA1-Pumping Nadh:Quinone Oxidoreductase Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14003