Iron in PDB 6f6l: R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6l 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)	43.46 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.748, 55.730, 69.456, 90.00, 113.92, 90.00
R / Rfree (%)	16.6 / 20.4

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6l). 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 Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6l:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically 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 Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:38.5 occ:1.00 OE2 A:GLU167 2.0 34.9 1.0 O A:HOH521 2.1 39.2 1.0 OE2 A:GLU102 2.1 37.0 1.0 O2 A:PLM404 2.2 53.2 1.0 OE2 A:GLU202 2.2 38.7 1.0 ND1 A:HIS205 2.3 37.6 1.0 HG2 A:GLU167 2.9 46.3 1.0 CD A:GLU167 3.0 36.1 1.0 C1 A:PLM404 3.0 45.1 1.0 CD A:GLU102 3.1 35.0 1.0 CE1 A:HIS205 3.2 31.5 1.0 CD A:GLU202 3.2 45.0 1.0 HE1 A:HIS205 3.3 37.8 1.0 O1 A:PLM404 3.3 45.8 1.0 CG A:HIS205 3.3 27.8 1.0 MN A:MN3401 3.4 32.4 1.0 HE2 A:PHE98 3.4 47.1 1.0 OE1 A:GLU102 3.4 32.6 1.0 CG A:GLU167 3.4 38.6 1.0 HB3 A:HIS205 3.5 37.5 1.0 OE1 A:GLU202 3.5 47.7 1.0 HB2 A:HIS205 3.5 37.5 1.0 CB A:HIS205 3.7 31.3 1.0 HA A:GLU202 3.9 37.2 1.0 HG3 A:GLU167 4.0 46.3 1.0 CE2 A:PHE98 4.0 39.2 1.0 OE1 A:GLU167 4.1 39.6 1.0 HE1 A:HIS105 4.1 38.9 1.0 HG21 A:VAL72 4.2 42.4 1.0 HZ A:PHE98 4.2 40.6 1.0 HE2 A:PHE162 4.3 44.1 1.0 NE2 A:HIS205 4.3 31.4 1.0 HB3 A:GLU167 4.4 48.4 1.0 CG A:GLU102 4.4 34.6 1.0 CD2 A:HIS205 4.4 32.8 1.0 C2 A:PLM404 4.5 42.2 1.0 CZ A:PHE98 4.5 33.8 1.0 HG2 A:GLU102 4.5 41.5 1.0 H22 A:PLM404 4.5 50.6 1.0 CG A:GLU202 4.5 44.2 1.0 CB A:GLU167 4.6 40.4 1.0 HG3 A:GLU102 4.6 41.5 1.0 HG3 A:GLU202 4.7 53.0 1.0 CE1 A:HIS105 4.7 32.4 1.0 O A:HOH501 4.7 43.0 1.0 ND1 A:HIS105 4.8 29.0 1.0 CA A:GLU202 4.8 31.0 1.0 H21 A:PLM404 4.8 50.6 1.0 CD2 A:PHE98 4.9 39.1 1.0 HD2 A:PHE98 5.0 46.9 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically 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 Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:40.8 occ:1.00 OE2 B:GLU167 2.0 38.2 1.0 OE2 B:GLU202 2.0 37.0 1.0 OE2 B:GLU102 2.1 38.6 1.0 O2 B:PLM404 2.2 50.4 1.0 ND1 B:HIS205 2.2 36.6 1.0 OE1 B:GLU202 2.2 47.1 1.0 CD B:GLU202 2.4 52.8 1.0 HG2 B:GLU167 2.9 49.1 1.0 CD B:GLU167 3.0 39.8 1.0 CD B:GLU102 3.0 37.0 1.0 CE1 B:HIS205 3.0 36.9 1.0 HE1 B:HIS205 3.1 44.3 1.0 C1 B:PLM404 3.2 47.1 1.0 CG B:HIS205 3.3 34.7 1.0 OE1 B:GLU102 3.3 34.4 1.0 MN B:MN3401 3.4 37.2 1.0 CG B:GLU167 3.5 40.9 1.0 HE2 B:PHE98 3.5 51.0 1.0 HB3 B:HIS205 3.5 42.5 1.0 O1 B:PLM404 3.6 58.0 1.0 HB2 B:HIS205 3.6 42.5 1.0 CB B:HIS205 3.7 35.4 1.0 CG B:GLU202 3.9 52.9 1.0 HA B:GLU202 4.0 44.2 1.0 OE1 B:GLU167 4.0 43.3 1.0 CE2 B:PHE98 4.0 42.5 1.0 HE2 B:PHE162 4.0 46.0 1.0 HG3 B:GLU167 4.1 49.1 1.0 HG3 B:GLU202 4.1 63.5 1.0 HG21 B:VAL72 4.1 46.8 1.0 HE1 B:HIS105 4.2 38.0 1.0 NE2 B:HIS205 4.2 36.0 1.0 HZ B:PHE98 4.2 42.6 1.0 HB3 B:GLU167 4.3 43.3 1.0 HG2 B:GLU202 4.3 63.5 1.0 CD2 B:HIS205 4.4 33.5 1.0 CG B:GLU102 4.4 39.5 1.0 CZ B:PHE98 4.4 35.5 1.0 HG2 B:GLU102 4.5 47.5 1.0 CB B:GLU167 4.5 36.1 1.0 C2 B:PLM404 4.5 43.1 1.0 HG3 B:GLU102 4.6 47.5 1.0 H22 B:PLM404 4.7 51.7 1.0 O B:HOH501 4.7 48.9 1.0 H21 B:PLM404 4.7 51.7 1.0 CE1 B:HIS105 4.8 31.6 1.0 ND1 B:HIS105 4.8 31.7 1.0 CA B:GLU202 4.8 36.8 1.0 CD2 B:PHE98 4.9 36.1 1.0 CB B:GLU202 4.9 40.2 1.0 CE2 B:PHE162 5.0 38.3 1.0 HE2 B:HIS205 5.0 43.2 1.0 CG2 B:VAL72 5.0 39.0 1.0

J.J.Griese, R.Kositzki, M.Haumann, M.Hogbom. Assembly of A Heterodinuclear Mn/Fe Cofactor Is Coupled to Tyrosine-Valine Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 24 211 2019.
ISSN: ESSN 1432-1327
PubMed: 30689052
DOI: 10.1007/S00775-019-01639-4