Iron in PDB 6f6c: R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6c 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)	43.57 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.462, 55.818, 69.741, 90.00, 114.09, 90.00
R / Rfree (%)	18 / 22.3

The structure of R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6c). 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6c:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:33.7 occ:1.00 OE2 A:GLU167 1.9 29.5 1.0 OE2 A:GLU102 2.0 30.9 1.0 O A:HOH502 2.0 37.8 1.0 OE2 A:GLU202 2.1 34.3 1.0 O2 A:PLM404 2.2 51.8 1.0 ND1 A:HIS205 2.4 37.9 1.0 C1 A:PLM404 2.8 42.6 1.0 O1 A:PLM404 2.9 41.6 1.0 CD A:GLU167 2.9 30.8 1.0 HG2 A:GLU167 3.0 34.5 1.0 CD A:GLU102 3.0 31.8 1.0 CE1 A:HIS205 3.2 29.4 1.0 CD A:GLU202 3.2 39.9 1.0 HE1 A:HIS205 3.3 35.2 1.0 OE1 A:GLU102 3.3 31.2 1.0 MN A:MN3402 3.4 29.4 1.0 CG A:HIS205 3.4 22.8 1.0 CG A:GLU167 3.5 28.8 1.0 HB3 A:HIS205 3.6 35.3 1.0 HB2 A:HIS205 3.6 35.3 1.0 OE1 A:GLU202 3.7 42.3 1.0 HE2 A:PHE98 3.7 41.6 1.0 CB A:HIS205 3.8 29.4 1.0 HE2 A:TYR162 3.9 34.3 1.0 OE1 A:GLU167 3.9 31.9 1.0 HA A:GLU202 4.0 33.0 1.0 HG3 A:GLU167 4.1 34.5 1.0 HE1 A:HIS105 4.1 35.1 1.0 CE2 A:PHE98 4.1 34.7 1.0 HZ A:PHE98 4.2 38.9 1.0 C2 A:PLM404 4.3 44.1 1.0 HB3 A:GLU167 4.4 34.7 1.0 CG A:GLU102 4.4 27.5 1.0 NE2 A:HIS205 4.4 30.0 1.0 CZ A:PHE98 4.4 32.4 1.0 CG A:GLU202 4.5 38.1 1.0 CD2 A:HIS205 4.5 29.4 1.0 HG2 A:GLU102 4.5 33.0 1.0 H22 A:PLM404 4.5 52.9 1.0 HG3 A:GLU202 4.5 45.8 1.0 HB1 A:ALA72 4.6 37.3 1.0 CB A:GLU167 4.6 28.9 1.0 HG3 A:GLU102 4.6 33.0 1.0 CE1 A:HIS105 4.7 29.3 1.0 O A:HOH501 4.8 40.3 1.0 CE2 A:TYR162 4.8 28.6 1.0 ND1 A:HIS105 4.8 21.6 1.0 H21 A:PLM404 4.9 52.9 1.0 H32 A:PLM404 4.9 44.6 1.0 CA A:GLU202 4.9 27.5 1.0 CD2 A:PHE98 5.0 30.2 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:35.2 occ:1.00 OE2 B:GLU167 2.0 32.3 1.0 OE2 B:GLU102 2.0 31.4 1.0 O B:HOH524 2.0 34.4 1.0 OE2 B:GLU202 2.1 33.3 1.0 ND1 B:HIS205 2.3 34.9 1.0 O2 B:PLM404 2.3 52.3 1.0 HG2 B:GLU167 2.9 35.6 1.0 CD B:GLU167 3.0 32.4 1.0 CD B:GLU102 3.0 28.9 1.0 CD B:GLU202 3.1 43.1 1.0 C1 B:PLM404 3.1 42.1 1.0 CE1 B:HIS205 3.2 32.3 1.0 HE1 B:HIS205 3.3 38.7 1.0 CG B:HIS205 3.3 26.7 1.0 O1 B:PLM404 3.4 56.1 1.0 OE1 B:GLU202 3.4 53.5 1.0 OE1 B:GLU102 3.4 34.2 1.0 MN B:MN3401 3.4 31.6 1.0 CG B:GLU167 3.4 29.7 1.0 HB3 B:HIS205 3.5 30.5 1.0 HB2 B:HIS205 3.5 30.5 1.0 HE2 B:PHE98 3.7 42.1 1.0 CB B:HIS205 3.7 25.4 1.0 HE2 B:TYR162 3.8 37.9 1.0 OE1 B:GLU167 4.0 32.2 1.0 HA B:GLU202 4.0 38.2 1.0 HE1 B:HIS105 4.1 35.1 1.0 HG3 B:GLU167 4.1 35.6 1.0 CE2 B:PHE98 4.1 35.1 1.0 HZ B:PHE98 4.2 39.4 1.0 HB3 B:GLU167 4.3 32.7 1.0 NE2 B:HIS205 4.3 29.4 1.0 CG B:GLU102 4.4 27.6 1.0 CZ B:PHE98 4.4 32.8 1.0 CD2 B:HIS205 4.4 31.2 1.0 CG B:GLU202 4.5 40.6 1.0 O B:HOH501 4.5 40.0 1.0 HG2 B:GLU102 4.5 33.2 1.0 CB B:GLU167 4.5 27.3 1.0 C2 B:PLM404 4.6 39.3 1.0 HG3 B:GLU202 4.6 48.7 1.0 HG3 B:GLU102 4.6 33.2 1.0 HB1 B:ALA72 4.7 36.6 1.0 CE1 B:HIS105 4.7 29.3 1.0 CE2 B:TYR162 4.7 31.6 1.0 H22 B:PLM404 4.7 47.2 1.0 ND1 B:HIS105 4.8 26.6 1.0 CA B:GLU202 4.9 31.9 1.0 CD2 B:PHE98 4.9 29.4 1.0 HB2 B:GLU202 5.0 42.2 1.0

J.J.Griese, R.M.M.Branca, V.Srinivas, M.Hogbom. Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 23 879 2018.
ISSN: ESSN 1432-1327
PubMed: 29946980
DOI: 10.1007/S00775-018-1583-3