Manganese in PDB 6f6e: R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

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

The structure of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6e 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 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.516, 55.654, 70.054, 90.00, 114.11, 90.00
R / Rfree (%)	17.5 / 20.1

The structure of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6e). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6e:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:21.4 occ:0.97 OE1 A:GLU102 2.1 23.2 1.0 OE1 A:GLU69 2.1 22.9 1.0 ND1 A:HIS105 2.2 19.5 1.0 O A:HOH508 2.2 26.8 1.0 OE2 A:GLU202 2.3 26.3 1.0 O1 A:PLM404 2.3 29.8 1.0 CE1 A:HIS105 3.0 23.5 1.0 HE1 A:HIS105 3.0 28.2 1.0 CD A:GLU69 3.1 23.8 1.0 CD A:GLU102 3.1 26.0 1.0 CD A:GLU202 3.2 27.7 1.0 H22 A:PLM404 3.2 36.2 1.0 CG A:HIS105 3.3 22.6 1.0 C1 A:PLM404 3.3 35.5 1.0 OE2 A:GLU69 3.4 26.2 1.0 FE A:FE2401 3.5 22.6 0.9 OE2 A:GLU102 3.5 23.9 1.0 HB2 A:HIS105 3.6 27.5 1.0 HB3 A:HIS105 3.7 27.5 1.0 HA A:GLU102 3.7 22.6 1.0 C2 A:PLM404 3.8 30.2 1.0 CB A:HIS105 3.8 22.9 1.0 H32 A:PLM404 3.8 36.0 1.0 HG A:LEU198 3.9 35.1 1.0 HG3 A:GLU202 3.9 33.4 1.0 OE1 A:GLU202 4.0 25.9 1.0 CG A:GLU202 4.0 27.9 1.0 HG2 A:GLU202 4.0 33.4 1.0 NE2 A:HIS105 4.2 25.3 1.0 HA A:GLU69 4.3 26.6 1.0 HE1 A:HIS205 4.3 26.7 1.0 CD2 A:HIS105 4.3 22.1 1.0 HD11 A:LEU198 4.4 33.2 1.0 C3 A:PLM404 4.4 30.0 1.0 HD21 A:LEU198 4.5 41.0 1.0 O2 A:PLM404 4.5 30.7 1.0 CG A:GLU69 4.5 25.9 1.0 HB3 A:GLU69 4.5 28.2 1.0 CG A:GLU102 4.5 20.9 1.0 HH A:TYR175 4.5 59.1 1.0 CA A:GLU102 4.6 18.8 1.0 HB3 A:ALA72 4.6 28.0 1.0 HB3 A:GLU102 4.7 24.9 1.0 CG A:LEU198 4.7 29.3 1.0 H21 A:PLM404 4.7 36.2 1.0 CB A:GLU102 4.8 20.7 1.0 CE1 A:HIS205 4.8 22.2 1.0 HB1 A:ALA72 4.8 28.0 1.0 HG3 A:GLU69 4.8 31.1 1.0 ND1 A:HIS205 4.9 22.7 1.0 CB A:GLU69 4.9 23.5 1.0 HE2 A:HIS105 4.9 30.3 1.0 CD1 A:LEU198 4.9 27.7 1.0 HG2 A:GLU102 5.0 25.1 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:18.5 occ:0.90 OE1 B:GLU102 2.1 21.2 1.0 OE1 B:GLU69 2.1 21.2 1.0 O B:HOH517 2.1 25.8 1.0 ND1 B:HIS105 2.2 21.4 1.0 O1 B:PLM404 2.2 30.6 1.0 OE2 B:GLU202 2.2 22.6 1.0 CE1 B:HIS105 3.0 20.4 1.0 HE1 B:HIS105 3.1 24.5 1.0 CD B:GLU69 3.1 24.2 1.0 CD B:GLU102 3.1 22.8 1.0 CD B:GLU202 3.2 23.9 1.0 CG B:HIS105 3.3 21.4 1.0 C1 B:PLM404 3.3 35.9 1.0 OE2 B:GLU69 3.4 25.5 1.0 FE B:FE2401 3.5 21.4 0.9 OE2 B:GLU102 3.5 23.6 1.0 HB2 B:HIS105 3.5 22.7 1.0 H21 B:PLM404 3.6 43.2 1.0 HA B:GLU102 3.6 22.7 1.0 HB3 B:HIS105 3.7 22.7 1.0 CB B:HIS105 3.7 18.9 1.0 HG3 B:GLU202 3.9 27.8 1.0 HG B:LEU198 3.9 35.0 1.0 HG2 B:GLU202 3.9 27.8 1.0 CG B:GLU202 3.9 23.2 1.0 C2 B:PLM404 4.0 36.0 1.0 OE1 B:GLU202 4.1 22.7 1.0 NE2 B:HIS105 4.2 22.7 1.0 HD11 B:LEU198 4.3 31.8 1.0 H31 B:PLM404 4.3 39.5 1.0 HD21 B:LEU198 4.3 41.7 1.0 HA B:GLU69 4.4 26.9 1.0 CD2 B:HIS105 4.4 22.6 1.0 O2 B:PLM404 4.4 29.9 1.0 HE1 B:HIS205 4.4 27.7 1.0 CG B:GLU69 4.5 25.2 1.0 HB3 B:GLU69 4.5 25.0 1.0 CG B:GLU102 4.5 21.6 1.0 CA B:GLU102 4.5 18.9 1.0 CG B:LEU198 4.7 29.2 1.0 C3 B:PLM404 4.7 32.9 1.0 HB3 B:GLU102 4.7 24.4 1.0 HB3 B:ALA72 4.7 27.1 1.0 HG3 B:GLU69 4.8 30.2 1.0 CB B:GLU102 4.8 20.3 1.0 ND1 B:HIS205 4.9 25.0 1.0 CD1 B:LEU198 4.9 26.5 1.0 CB B:GLU69 4.9 20.8 1.0 H32 B:PLM404 4.9 39.5 1.0 CE1 B:HIS205 4.9 23.1 1.0 HG2 B:GLU167 4.9 32.3 1.0 HB1 B:ALA72 4.9 27.1 1.0 CD2 B:LEU198 4.9 34.7 1.0 H22 B:PLM404 4.9 43.2 1.0 HE2 B:HIS105 5.0 27.2 1.0 HG2 B:GLU102 5.0 26.0 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