Manganese in PDB 6f6m: R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

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

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6m 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)	43.52 / 1.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.300, 55.599, 69.970, 90.00, 113.97, 90.00
R / Rfree (%)	14.9 / 18.7

The structure of R2-Like Ligand-Binding Oxidase Y162F 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6m). 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6m:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase Y162F 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:20.1 occ:1.00 O1 A:PLM404 2.0 39.5 1.0 OE1 A:GLU102 2.0 19.6 1.0 O A:HOH501 2.1 29.5 1.0 OE1 A:GLU69 2.1 21.4 1.0 OE2 A:GLU202 2.2 21.0 1.0 ND1 A:HIS105 2.2 20.3 1.0 C1 A:PLM404 2.8 39.0 1.0 CE1 A:HIS105 3.0 20.2 1.0 O2 A:PLM404 3.1 31.8 1.0 CD A:GLU69 3.1 21.4 1.0 HE1 A:HIS105 3.1 24.2 1.0 CD A:GLU102 3.1 18.5 1.0 CD A:GLU202 3.2 21.4 1.0 CG A:HIS105 3.3 21.1 1.0 OE2 A:GLU69 3.4 23.9 1.0 HB2 A:HIS105 3.5 23.9 1.0 OE2 A:GLU102 3.6 21.4 1.0 FE A:FE2401 3.6 21.8 1.0 HA A:GLU102 3.6 22.6 1.0 HG21 A:VAL72 3.6 27.6 1.0 HB3 A:HIS105 3.7 23.9 1.0 CB A:HIS105 3.7 19.9 1.0 HG A:LEU198 3.9 31.2 1.0 HG2 A:GLU202 3.9 26.6 1.0 HG3 A:GLU202 3.9 26.6 1.0 CG A:GLU202 4.0 22.2 1.0 H31 A:PLM404 4.0 47.6 1.0 OE1 A:GLU202 4.1 22.3 1.0 HD11 A:LEU198 4.2 28.0 1.0 C2 A:PLM404 4.2 42.7 1.0 HE1 A:HIS205 4.2 26.4 1.0 NE2 A:HIS105 4.2 19.7 1.0 HD21 A:LEU198 4.2 37.1 1.0 HG23 A:VAL72 4.4 27.6 1.0 CD2 A:HIS105 4.4 20.8 1.0 HA A:GLU69 4.4 24.4 1.0 CG2 A:VAL72 4.4 23.0 1.0 H32 A:PLM404 4.5 47.6 1.0 CG A:GLU102 4.5 18.5 1.0 CA A:GLU102 4.5 18.9 1.0 CG A:GLU69 4.5 20.7 1.0 C3 A:PLM404 4.5 39.7 1.0 HH A:TYR175 4.5 59.6 1.0 HB3 A:GLU102 4.6 22.3 1.0 CG A:LEU198 4.6 26.0 1.0 HB3 A:GLU69 4.6 24.1 1.0 HG22 A:VAL72 4.7 27.6 1.0 CB A:GLU102 4.8 18.6 1.0 CE1 A:HIS205 4.8 22.0 1.0 CD1 A:LEU198 4.8 23.3 1.0 H22 A:PLM404 4.8 51.3 1.0 H21 A:PLM404 4.8 51.3 1.0 ND1 A:HIS205 4.8 20.8 1.0 HG3 A:GLU69 4.9 24.9 1.0 CD2 A:LEU198 4.9 31.0 1.0 HG2 A:GLU102 5.0 22.1 1.0 HE2 A:HIS105 5.0 23.6 1.0 CB A:GLU69 5.0 20.1 1.0 HD12 A:LEU198 5.0 28.0 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase Y162F 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:21.9 occ:1.00 O1 B:PLM404 2.0 32.9 1.0 OE1 B:GLU102 2.1 21.2 1.0 ND1 B:HIS105 2.1 19.3 1.0 OE1 B:GLU69 2.1 21.1 1.0 OE2 B:GLU202 2.2 22.2 1.0 O B:HOH501 2.2 37.0 1.0 C1 B:PLM404 2.6 35.9 1.0 O2 B:PLM404 2.9 34.0 1.0 CE1 B:HIS105 3.0 18.8 1.0 CD B:GLU69 3.1 24.7 1.0 HE1 B:HIS105 3.1 22.6 1.0 CD B:GLU102 3.2 19.5 1.0 CD B:GLU202 3.2 21.1 1.0 CG B:HIS105 3.2 18.1 1.0 OE2 B:GLU69 3.3 27.8 1.0 HB2 B:HIS105 3.5 22.7 1.0 OE2 B:GLU102 3.5 20.7 1.0 FE B:FE2401 3.5 22.9 1.0 HB3 B:HIS105 3.6 22.7 1.0 HA B:GLU102 3.6 23.2 1.0 HG21 B:VAL72 3.7 26.7 1.0 CB B:HIS105 3.7 18.9 1.0 HG B:LEU198 3.9 33.0 1.0 HG3 B:GLU202 4.0 26.9 1.0 OE1 B:GLU202 4.0 24.9 1.0 CG B:GLU202 4.0 22.4 1.0 HG2 B:GLU202 4.0 26.9 1.0 C2 B:PLM404 4.0 43.2 1.0 H31 B:PLM404 4.1 48.5 1.0 NE2 B:HIS105 4.2 20.8 1.0 HE1 B:HIS205 4.2 25.9 1.0 HD11 B:LEU198 4.2 31.9 1.0 HD21 B:LEU198 4.2 34.5 1.0 H32 B:PLM404 4.2 48.5 1.0 CD2 B:HIS105 4.3 19.2 1.0 HG23 B:VAL72 4.3 26.7 1.0 HA B:GLU69 4.3 23.9 1.0 C3 B:PLM404 4.4 40.4 1.0 CG2 B:VAL72 4.4 22.2 1.0 CG B:GLU69 4.5 23.5 1.0 CG B:GLU102 4.5 19.8 1.0 HH B:TYR175 4.5 54.6 1.0 CA B:GLU102 4.5 19.3 1.0 H22 B:PLM404 4.6 51.8 1.0 CG B:LEU198 4.6 27.5 1.0 HB3 B:GLU69 4.7 25.6 1.0 HB3 B:GLU102 4.7 22.8 1.0 HG22 B:VAL72 4.7 26.7 1.0 CE1 B:HIS205 4.7 21.6 1.0 H21 B:PLM404 4.7 51.8 1.0 ND1 B:HIS205 4.7 20.6 1.0 CB B:GLU102 4.8 19.0 1.0 HG3 B:GLU69 4.8 28.2 1.0 CD1 B:LEU198 4.8 26.6 1.0 CD2 B:LEU198 4.8 28.7 1.0 HE2 B:HIS105 4.9 25.0 1.0 HG2 B:GLU102 5.0 23.8 1.0 CB B:GLU69 5.0 21.3 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