Iron in PDB 5y6q: Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400

The structure of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400, PDB code: 5y6q was solved by B.Mikami, H.Uchida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.12 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.972, 77.972, 400.340, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.3

The structure of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

The binding sites of Iron atom in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 (pdb code 5y6q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400, PDB code: 5y6q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


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 An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:18.0 occ:1.00 FE1 A:FES201 0.0 18.0 1.0 S2 A:FES201 2.2 22.4 1.0 S1 A:FES201 2.2 18.2 1.0 SG A:CYS51 2.2 20.5 1.0 SG A:CYS63 2.3 20.0 1.0 FE2 A:FES201 2.9 20.0 1.0 CB A:CYS63 3.1 17.0 1.0 CB A:CYS51 3.3 17.0 1.0 SG A:CYS43 4.1 19.7 1.0 N A:GLY46 4.2 15.8 1.0 N A:CYS63 4.2 19.2 1.0 CA A:CYS63 4.3 16.2 1.0 CA A:GLY46 4.3 15.2 1.0 N A:ASP44 4.4 16.6 1.0 N A:CYS51 4.4 17.6 1.0 CA A:ASP44 4.5 15.2 1.0 CA A:CYS51 4.5 17.6 1.0 CB A:LEU61 4.5 17.4 1.0 N A:GLY49 4.7 16.6 1.0 SG A:CYS48 4.7 18.1 1.0 C A:ASP44 4.7 18.9 1.0 CD2 A:LEU27 4.9 16.7 1.0 CA A:GLY49 4.9 16.0 1.0 CD1 A:LEU61 5.0 17.5 1.0 CD2 A:LEU61 5.0 15.1 1.0

Iron binding site 2 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


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 An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:20.0 occ:1.00 FE2 A:FES201 0.0 20.0 1.0 SG A:CYS43 2.2 19.7 1.0 S2 A:FES201 2.2 22.4 1.0 SG A:CYS48 2.2 18.1 1.0 S1 A:FES201 2.2 18.2 1.0 FE1 A:FES201 2.9 18.0 1.0 CB A:CYS43 3.1 14.4 1.0 N A:CYS43 3.2 16.9 1.0 CB A:CYS48 3.3 16.9 1.0 N A:GLY49 3.6 16.6 1.0 CA A:CYS43 3.6 16.1 1.0 N A:ASP44 3.6 16.6 1.0 N A:CYS48 3.6 17.8 1.0 CA A:CYS48 3.9 14.9 1.0 C A:CYS43 4.1 17.8 1.0 C A:GLY42 4.2 18.1 1.0 C A:CYS48 4.2 17.0 1.0 N A:GLN47 4.3 15.8 1.0 N A:GLY42 4.3 16.8 1.0 N A:GLY46 4.3 15.8 1.0 N A:ALA50 4.4 15.8 1.0 CA A:GLY42 4.5 17.1 1.0 SG A:CYS63 4.6 20.0 1.0 CA A:ASP44 4.6 15.2 1.0 CA A:GLY49 4.6 16.0 1.0 CA A:GLY46 4.6 15.2 1.0 SG A:CYS51 4.7 20.5 1.0 C A:GLN47 4.7 15.0 1.0 C A:GLY46 4.7 18.3 1.0 N A:GLN45 4.8 15.9 1.0 C A:GLY49 5.0 17.5 1.0

Iron binding site 3 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


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 An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:19.8 occ:1.00 FE1 A:FES202 0.0 19.8 1.0 S1 A:FES202 2.2 18.5 1.0 SG A:CYS103 2.2 19.9 1.0 S2 A:FES202 2.2 21.4 1.0 SG A:CYS140 2.2 16.9 1.0 FE2 A:FES202 2.9 19.2 1.0 CB A:CYS103 3.2 18.2 1.0 CB A:CYS140 3.3 14.3 1.0 N A:CYS103 3.5 19.3 1.0 CA A:CYS103 3.8 17.8 1.0 O C:HOH908 3.8 14.1 1.0 N A:GLY104 3.9 19.8 1.0 N A:CYS140 4.1 16.2 1.0 C A:CYS103 4.2 16.6 1.0 CA A:CYS140 4.3 13.1 1.0 N A:TYR105 4.3 18.3 1.0 SG A:CYS138 4.5 15.5 1.0 C A:GLN102 4.6 16.2 1.0 O C:GLY259 4.7 15.7 1.0 N A:GLN102 4.8 15.2 1.0 SG A:CYS106 4.8 18.6 1.0 N A:CYS106 4.8 16.4 1.0 CB A:GLN102 4.9 16.0 1.0 N2' C:MCN802 4.9 18.9 1.0

Iron binding site 4 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:19.2 occ:1.00 FE2 A:FES202 0.0 19.2 1.0 S2 A:FES202 2.2 21.4 1.0 S1 A:FES202 2.2 18.5 1.0 SG A:CYS106 2.2 18.6 1.0 SG A:CYS138 2.2 15.5 1.0 FE1 A:FES202 2.9 19.8 1.0 CB A:CYS138 3.2 15.2 1.0 CB A:CYS106 3.4 15.8 1.0 CA A:CYS138 3.6 13.8 1.0 O A:HOH319 4.1 18.4 1.0 CB A:CYS140 4.2 14.3 1.0 C A:CYS138 4.2 14.3 1.0 N A:ARG139 4.2 12.6 1.0 N A:CYS106 4.3 16.4 1.0 N A:CYS140 4.3 16.2 1.0 SG A:CYS140 4.4 16.9 1.0 CA A:CYS106 4.4 16.1 1.0 O A:LEU137 4.7 16.5 1.0 N A:CYS138 4.8 12.8 1.0 SG A:CYS103 4.8 19.9 1.0 CA A:CYS140 4.9 13.1 1.0 C A:CYS106 4.9 16.1 1.0

Iron binding site 5 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:21.9 occ:1.00 FE1 B:SF4402 0.0 21.9 1.0 S3 B:SF4402 2.1 19.5 1.0 S2 B:SF4402 2.1 18.9 1.0 S4 B:SF4402 2.1 17.0 1.0 SG B:CYS118 2.3 19.4 1.0 FE3 B:SF4402 2.9 21.5 1.0 FE4 B:SF4402 3.0 22.3 1.0 FE2 B:SF4402 3.0 22.4 1.0 CB B:CYS118 3.3 16.5 1.0 S1 B:SF4402 3.7 22.3 1.0 CB B:TYR121 4.1 15.9 1.0 NE2 B:HIS149 4.2 15.8 1.0 CB B:ALA141 4.2 17.7 1.0 N B:TYR121 4.2 16.6 1.0 CB B:ALA160 4.3 19.4 1.0 CD2 B:HIS149 4.5 16.3 1.0 CA B:TYR121 4.7 13.9 1.0 SG B:CYS130 4.7 21.4 1.0 CA B:CYS118 4.8 18.2 1.0 CB B:TYR120 4.8 12.7 1.0 CA B:ALA160 4.9 15.5 1.0 SG B:CYS139 4.9 21.4 1.0 N B:ALA160 5.0 17.6 1.0 SG B:CYS158 5.0 21.6 1.0

Iron binding site 6 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:22.4 occ:1.00 FE2 B:SF4402 0.0 22.4 1.0 S1 B:SF4402 2.1 22.3 1.0 S3 B:SF4402 2.1 19.5 1.0 S4 B:SF4402 2.1 17.0 1.0 SG B:CYS139 2.2 21.4 1.0 FE4 B:SF4402 2.9 22.3 1.0 FE3 B:SF4402 2.9 21.5 1.0 FE1 B:SF4402 3.0 21.9 1.0 CB B:CYS139 3.1 16.9 1.0 CA B:CYS139 3.5 15.8 1.0 S2 B:SF4402 3.7 18.9 1.0 C B:CYS139 4.0 17.3 1.0 N B:ALA140 4.0 18.2 1.0 CB B:ALA141 4.0 17.7 1.0 N B:ALA141 4.0 17.3 1.0 O B:SER157 4.2 20.9 1.0 CA B:CYS158 4.5 18.5 1.0 N B:ILE159 4.6 20.6 1.0 CA B:ALA141 4.7 16.2 1.0 SG B:CYS158 4.7 21.6 1.0 O B:CYS139 4.8 20.5 1.0 CG1 B:ILE159 4.9 18.1 1.0 N B:CYS139 4.9 14.0 1.0 SG B:CYS118 5.0 19.4 1.0

Iron binding site 7 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:21.5 occ:1.00 FE3 B:SF4402 0.0 21.5 1.0 S4 B:SF4402 2.1 17.0 1.0 S2 B:SF4402 2.1 18.9 1.0 S1 B:SF4402 2.1 22.3 1.0 SG B:CYS130 2.2 21.4 1.0 FE2 B:SF4402 2.9 22.4 1.0 FE1 B:SF4402 2.9 21.9 1.0 FE4 B:SF4402 2.9 22.3 1.0 CB B:CYS130 3.2 17.3 1.0 CA B:CYS130 3.4 18.4 1.0 S3 B:SF4402 3.7 19.5 1.0 N B:ASN131 3.9 20.7 1.0 C B:CYS130 4.0 21.3 1.0 N B:LYS132 4.2 20.6 1.0 CB B:LYS132 4.3 19.2 1.0 CB B:TYR121 4.3 15.9 1.0 CA B:TYR121 4.6 13.9 1.0 O B:ALA129 4.7 15.7 1.0 CD1 B:TYR121 4.7 17.9 1.0 N B:CYS130 4.8 17.9 1.0 N B:TYR121 4.8 16.6 1.0 SG B:CYS118 4.8 19.4 1.0 CA B:LYS132 4.9 18.9 1.0 O B:CYS130 4.9 23.7 1.0 SG B:CYS158 5.0 21.6 1.0 SG B:CYS139 5.0 21.4 1.0

Iron binding site 8 out of 8 in the Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:22.3 occ:1.00 FE4 B:SF4402 0.0 22.3 1.0 S1 B:SF4402 2.1 22.3 1.0 S2 B:SF4402 2.1 18.9 1.0 S3 B:SF4402 2.1 19.5 1.0 SG B:CYS158 2.2 21.6 1.0 FE2 B:SF4402 2.9 22.4 1.0 FE3 B:SF4402 2.9 21.5 1.0 FE1 B:SF4402 3.0 21.9 1.0 CB B:CYS158 3.3 20.7 1.0 CB B:ALA160 3.6 19.4 1.0 CA B:CYS158 3.7 18.5 1.0 S4 B:SF4402 3.7 17.0 1.0 N B:ALA160 3.9 17.6 1.0 N B:ILE159 4.1 20.6 1.0 C B:CYS158 4.3 17.9 1.0 CA B:ALA160 4.3 15.5 1.0 CB B:LYS132 4.4 19.2 1.0 CE B:LYS132 4.5 21.1 1.0 O B:SER157 4.6 20.9 1.0 SG B:CYS139 4.7 21.4 1.0 SG B:CYS130 4.8 21.4 1.0 CD B:LYS132 4.9 16.4 1.0 C B:ILE159 4.9 18.6 1.0 N B:CYS158 4.9 17.3 1.0 N B:LYS132 5.0 20.6 1.0

H.Uchida, B.Mikami, A.Yamane-Tanabe, A.Ito, K.Hirano, M.Oki. Crystal Structure of An Aldehyde Oxidase From Methylobacillus Sp. KY4400. J. Biochem. V. 163 321 2018.
ISSN: ISSN 1756-2651
PubMed: 29319807
DOI: 10.1093/JB/MVY004