Iron in PDB 6i92: R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6i92 was solved by J.J.Griese, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 1.85
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.236, 96.593, 127.638, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.9

The structure of R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6i92). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6i92:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:34.7 occ:1.00 OE2 A:GLU167 1.9 41.7 1.0 ND1 A:HIS205 2.0 32.6 1.0 OE2 A:GLU102 2.1 40.0 1.0 OE1 A:GLU167 2.1 36.0 1.0 OE1 A:GLU202 2.1 36.7 1.0 CD A:GLU167 2.3 38.9 1.0 OE2 A:GLU202 2.3 39.8 1.0 CD A:GLU202 2.5 40.4 1.0 CE1 A:HIS205 2.9 36.9 1.0 HE1 A:HIS205 3.0 44.3 1.0 CD A:GLU102 3.0 38.6 1.0 CG A:HIS205 3.1 33.1 1.0 OE1 A:GLU102 3.3 35.1 1.0 HB3 A:HIS205 3.4 42.4 1.0 HB2 A:HIS205 3.5 42.4 1.0 CB A:HIS205 3.6 35.3 1.0 MN A:MN401 3.6 37.5 1.0 HE2 A:PHE98 3.7 40.5 1.0 CG A:GLU167 3.8 37.8 1.0 CE2 A:PHE98 3.9 33.8 1.0 HA A:GLU202 4.0 42.0 1.0 CG A:GLU202 4.0 38.5 1.0 HZ A:PHE98 4.0 45.4 1.0 NE2 A:HIS205 4.0 32.9 1.0 HE2 A:TYR162 4.1 44.1 1.0 CZ A:PHE98 4.1 37.8 1.0 CD2 A:HIS205 4.1 37.0 1.0 HB3 A:GLU167 4.2 43.5 1.0 HG21 A:VAL72 4.2 50.5 1.0 HG2 A:GLU167 4.2 45.4 1.0 HG3 A:GLU167 4.3 45.4 1.0 O A:HOH504 4.3 49.0 1.0 CG A:GLU102 4.3 32.7 1.0 HE1 A:HIS105 4.3 44.4 1.0 HG3 A:GLU202 4.4 46.1 1.0 O A:HOH525 4.4 43.6 1.0 HG2 A:GLU102 4.4 39.2 1.0 HG2 A:GLU202 4.4 46.1 1.0 O A:HOH549 4.5 46.0 1.0 HG3 A:GLU102 4.6 39.2 1.0 CB A:GLU167 4.6 36.3 1.0 HB3 A:GLU202 4.6 44.8 1.0 CD2 A:PHE98 4.7 32.5 1.0 CB A:GLU202 4.7 37.3 1.0 HE2 A:HIS205 4.8 39.5 1.0 CA A:GLU202 4.8 35.0 1.0 HB A:VAL72 4.8 51.6 1.0 CE2 A:TYR162 4.9 36.8 1.0 HG23 A:VAL72 4.9 50.5 1.0 HD2 A:PHE98 4.9 39.0 1.0 CG2 A:VAL72 4.9 42.0 1.0 CE1 A:PHE98 5.0 41.4 1.0 CE1 A:HIS105 5.0 37.0 1.0 OH A:TYR162 5.0 39.6 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R2-Like Ligand-Binding Oxidase G68F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:0.8 occ:0.99 HE2 A:HIS130 1.6 90.4 1.0 NE2 A:HIS130 2.4 75.3 1.0 HD2 A:HIS130 3.2 87.2 1.0 CD2 A:HIS130 3.2 72.7 1.0 CE1 A:HIS130 3.6 73.8 1.0 OD2 A:ASP129 3.7 80.8 1.0 HE1 A:HIS130 3.8 88.6 1.0 OD1 A:ASP129 4.0 78.0 1.0 CG A:ASP129 4.3 78.1 1.0 CG A:HIS130 4.4 74.3 1.0 ND1 A:HIS130 4.6 74.0 1.0 HA3 A:GLY240 4.8 73.2 1.0

Y.Kutin, R.Kositzki, R.M.M.Branca, V.Srinivas, D.Lundin, M.Haumann, M.Hogbom, N.Cox, J.J.Griese. Chemical Flexibility of Heterobimetallic Mn/Fe Cofactors: R2LOX and R2C Proteins. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31591267
DOI: 10.1074/JBC.RA119.010570