Iron in PDB 5oc0: Structure of E. Coli Superoxide Oxidase

The structure of Structure of E. Coli Superoxide Oxidase, PDB code: 5oc0 was solved by C.A.K.Lundgren, D.Sjostrand, O.Biner, M.Bennett, C.Von Ballmoos, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.046, 91.102, 97.923, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.4

The structure of Structure of E. Coli Superoxide Oxidase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Structure of E. Coli Superoxide Oxidase (pdb code 5oc0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of E. Coli Superoxide Oxidase, PDB code: 5oc0:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of E. Coli Superoxide Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of E. Coli Superoxide Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:32.1 occ:1.00 FE A:HEM201 0.0 32.1 1.0 NE2 A:HIS13 1.9 27.6 1.0 NE2 A:HIS151 1.9 31.2 1.0 ND A:HEM201 2.0 30.9 1.0 NA A:HEM201 2.0 30.4 1.0 NC A:HEM201 2.1 31.0 1.0 NB A:HEM201 2.1 30.6 1.0 CE1 A:HIS151 2.9 34.2 1.0 CE1 A:HIS13 3.0 31.1 1.0 CD2 A:HIS13 3.0 31.6 1.0 C1D A:HEM201 3.0 32.4 1.0 C4D A:HEM201 3.0 31.1 1.0 CD2 A:HIS151 3.0 33.0 1.0 C4B A:HEM201 3.0 31.9 1.0 C1A A:HEM201 3.0 33.1 1.0 C4A A:HEM201 3.0 34.5 1.0 C1B A:HEM201 3.0 34.7 1.0 C4C A:HEM201 3.1 33.5 1.0 C1C A:HEM201 3.1 33.5 1.0 CHB A:HEM201 3.4 32.6 1.0 CHD A:HEM201 3.4 32.7 1.0 CHC A:HEM201 3.4 29.9 1.0 CHA A:HEM201 3.4 29.9 1.0 ND1 A:HIS151 4.0 32.9 1.0 ND1 A:HIS13 4.1 30.8 1.0 CG A:HIS13 4.1 30.6 1.0 CG A:HIS151 4.1 32.3 1.0 C3A A:HEM201 4.2 33.9 1.0 C2A A:HEM201 4.2 33.7 1.0 C2D A:HEM201 4.3 32.0 1.0 C3D A:HEM201 4.3 31.9 1.0 C3C A:HEM201 4.3 31.0 1.0 C3B A:HEM201 4.3 33.7 1.0 C2B A:HEM201 4.3 32.1 1.0 C2C A:HEM201 4.3 31.9 1.0 O A:HOH305 4.8 28.8 1.0

Iron binding site 2 out of 2 in the Structure of E. Coli Superoxide Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of E. Coli Superoxide Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:37.3 occ:1.00 FE A:HEM202 0.0 37.3 1.0 ND A:HEM202 1.9 41.4 1.0 NA A:HEM202 2.0 36.8 1.0 NE2 A:HIS137 2.0 37.4 1.0 NC A:HEM202 2.1 36.1 1.0 NB A:HEM202 2.1 35.2 1.0 NE2 A:HIS45 2.1 40.9 1.0 CE1 A:HIS137 3.0 39.6 1.0 C1D A:HEM202 3.0 41.7 1.0 C4D A:HEM202 3.0 41.2 1.0 C1A A:HEM202 3.0 41.1 1.0 C4A A:HEM202 3.0 38.4 1.0 C4C A:HEM202 3.0 41.1 1.0 C1B A:HEM202 3.1 38.3 1.0 C4B A:HEM202 3.1 36.5 1.0 CE1 A:HIS45 3.1 39.2 1.0 CD2 A:HIS137 3.1 37.7 1.0 C1C A:HEM202 3.1 40.1 1.0 CD2 A:HIS45 3.2 40.0 1.0 CHD A:HEM202 3.4 38.0 1.0 CHB A:HEM202 3.4 31.9 1.0 CHA A:HEM202 3.4 40.7 1.0 CHC A:HEM202 3.4 34.6 1.0 ND1 A:HIS137 4.1 38.7 1.0 CG A:HIS137 4.2 37.8 1.0 ND1 A:HIS45 4.2 40.8 1.0 C2A A:HEM202 4.2 40.4 1.0 C3A A:HEM202 4.2 37.7 1.0 C3D A:HEM202 4.2 46.4 1.0 C2D A:HEM202 4.2 44.1 1.0 C3C A:HEM202 4.3 36.2 1.0 C2C A:HEM202 4.3 33.8 1.0 CG A:HIS45 4.3 38.6 1.0 C2B A:HEM202 4.3 36.8 1.0 C3B A:HEM202 4.3 35.0 1.0 CG A:MSE27 4.9 41.4 1.0

C.A.K.Lundgren, D.Sjostrand, O.Biner, M.Bennett, A.Rudling, A.L.Johansson, P.Brzezinski, J.Carlsson, C.Von Ballmoos, M.Hogbom. Scavenging of Superoxide By A Membrane-Bound Superoxide Oxidase. Nat. Chem. Biol. V. 14 788 2018.
ISSN: ESSN 1552-4469
PubMed: 29915379
DOI: 10.1038/S41589-018-0072-X