Iron in PDB 6f6h: R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6h 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)	43.53 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.395, 55.783, 69.607, 90.00, 114.06, 90.00
R / Rfree (%)	18.3 / 23.5

The structure of R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6h). 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 V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6h:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:32.6 occ:1.00 OE2 A:GLU102 2.1 34.3 1.0 OE2 A:GLU167 2.1 29.0 1.0 O A:HOH512 2.1 39.1 1.0 O2 A:PLM404 2.3 51.9 1.0 OE2 A:GLU202 2.3 33.5 1.0 ND1 A:HIS205 2.3 35.5 1.0 HG2 A:GLU167 2.9 30.2 1.0 CD A:GLU167 3.1 32.7 1.0 CD A:GLU102 3.1 30.8 1.0 CD A:GLU202 3.2 35.1 1.0 CE1 A:HIS205 3.2 25.9 1.0 CG A:HIS205 3.3 24.0 1.0 HE1 A:HIS205 3.3 31.1 1.0 C1 A:PLM404 3.3 48.1 1.0 OE1 A:GLU202 3.4 37.6 1.0 HD23 A:LEU72 3.4 52.6 1.0 OE1 A:GLU102 3.4 32.0 1.0 HB3 A:HIS205 3.4 32.7 1.0 MN A:MN3402 3.5 34.0 1.0 CG A:GLU167 3.5 25.2 1.0 HB2 A:HIS205 3.5 32.7 1.0 HE2 A:PHE98 3.6 35.4 1.0 CB A:HIS205 3.7 27.3 1.0 O1 A:PLM404 3.8 53.3 1.0 HA A:GLU202 3.9 36.7 1.0 HE1 A:HIS105 4.0 36.8 1.0 HG3 A:GLU167 4.0 30.2 1.0 OE1 A:GLU167 4.1 33.0 1.0 CE2 A:PHE98 4.2 29.5 1.0 CD2 A:LEU72 4.2 43.8 1.0 HE2 A:TYR162 4.3 40.8 1.0 HD22 A:LEU72 4.3 52.6 1.0 HZ A:PHE98 4.3 32.2 1.0 NE2 A:HIS205 4.3 26.3 1.0 CG A:GLU102 4.4 28.1 1.0 CD2 A:HIS205 4.4 29.2 1.0 HG2 A:GLU102 4.4 33.8 1.0 HD21 A:LEU72 4.5 52.6 1.0 HB3 A:GLU167 4.5 41.0 1.0 CG A:GLU202 4.6 34.7 1.0 CZ A:PHE98 4.6 26.8 1.0 HG3 A:GLU102 4.6 33.8 1.0 CE1 A:HIS105 4.6 30.6 1.0 C2 A:PLM404 4.6 46.0 1.0 CB A:GLU167 4.7 34.1 1.0 HG3 A:GLU202 4.7 41.6 1.0 ND1 A:HIS105 4.7 31.9 1.0 H22 A:PLM404 4.8 55.2 1.0 H21 A:PLM404 4.8 55.2 1.0 CA A:GLU202 4.8 30.6 1.0 O A:HOH501 4.9 39.8 1.0 HH A:TYR175 5.0 43.6 1.0 HB3 A:LEU72 5.0 39.8 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:34.5 occ:1.00 OE2 B:GLU167 2.0 29.3 1.0 O B:HOH501 2.0 39.3 1.0 OE2 B:GLU102 2.1 34.3 1.0 O1 B:PLM404 2.1 55.1 1.0 OE2 B:GLU202 2.1 30.4 1.0 ND1 B:HIS205 2.3 36.8 1.0 HG2 B:GLU167 2.8 38.6 1.0 CD B:GLU167 3.0 34.2 1.0 CD B:GLU202 3.1 38.6 1.0 CD B:GLU102 3.1 34.5 1.0 CE1 B:HIS205 3.1 30.2 1.0 HE1 B:HIS205 3.2 36.2 1.0 CG B:HIS205 3.3 30.7 1.0 OE1 B:GLU202 3.3 45.9 1.0 C1 B:PLM404 3.3 55.3 1.0 CG B:GLU167 3.4 32.2 1.0 HB3 B:HIS205 3.5 32.6 1.0 MN B:MN3401 3.5 35.3 1.0 OE1 B:GLU102 3.5 33.6 1.0 HE2 B:PHE98 3.6 42.8 1.0 HB2 B:HIS205 3.6 32.6 1.0 HD23 B:LEU72 3.6 51.5 1.0 CB B:HIS205 3.7 27.2 1.0 HA B:GLU202 3.9 37.8 1.0 HE1 B:HIS105 4.0 39.3 1.0 OE1 B:GLU167 4.0 35.4 1.0 HG3 B:GLU167 4.0 38.6 1.0 O2 B:PLM404 4.1 53.8 1.0 CE2 B:PHE98 4.1 35.7 1.0 HE2 B:TYR162 4.1 40.8 1.0 HZ B:PHE98 4.2 38.9 1.0 HB3 B:GLU167 4.3 34.2 1.0 NE2 B:HIS205 4.3 31.9 1.0 CG B:GLU202 4.4 36.6 1.0 CG B:GLU102 4.4 31.1 1.0 CD2 B:HIS205 4.4 34.6 1.0 CD2 B:LEU72 4.4 42.9 1.0 HG2 B:GLU102 4.5 37.4 1.0 CZ B:PHE98 4.5 32.4 1.0 CB B:GLU167 4.5 28.5 1.0 C2 B:PLM404 4.5 54.7 1.0 HD22 B:LEU72 4.5 51.5 1.0 HG3 B:GLU202 4.5 44.0 1.0 H21 B:PLM404 4.6 65.7 1.0 H22 B:PLM404 4.6 65.7 1.0 CE1 B:HIS105 4.6 32.7 1.0 HG3 B:GLU102 4.7 37.4 1.0 O B:HOH503 4.7 49.2 1.0 HD21 B:LEU72 4.7 51.5 1.0 ND1 B:HIS105 4.8 29.5 1.0 CA B:GLU202 4.8 31.5 1.0 HH B:TYR175 4.9 41.9 1.0 HB2 B:GLU202 5.0 45.3 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