Manganese in PDB 6f6k: R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

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

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k 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 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.612, 55.655, 70.075, 90.00, 114.16, 90.00
R / Rfree (%)	19.8 / 26.3

The structure of R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6k). 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:27.1 occ:1.00 O A:HOH549 2.1 36.5 1.0 OE1 A:GLU102 2.1 23.3 1.0 OE1 A:GLU69 2.2 20.9 1.0 ND1 A:HIS105 2.2 24.6 1.0 OE1 A:GLU202 2.3 36.2 1.0 CE1 A:HIS105 3.1 35.4 1.0 HE1 A:HIS105 3.1 42.5 1.0 CD A:GLU69 3.2 30.6 1.0 CD A:GLU102 3.2 29.8 1.0 HD23 A:LEU72 3.3 40.1 1.0 CG A:HIS105 3.3 27.9 1.0 CD A:GLU202 3.4 24.3 1.0 OE2 A:GLU69 3.4 32.5 1.0 HB2 A:HIS105 3.5 30.5 1.0 HA A:GLU102 3.5 29.0 1.0 OE2 A:GLU167 3.6 24.0 0.5 OE2 A:GLU102 3.6 29.0 1.0 HB3 A:HIS105 3.6 30.5 1.0 FE A:FE2402 3.7 25.7 1.0 CB A:HIS105 3.7 25.4 1.0 HG2 A:GLU202 3.9 27.1 1.0 HG3 A:GLU202 3.9 27.1 1.0 HG A:LEU198 4.0 30.5 1.0 HE1 A:HIS205 4.0 37.3 1.0 CG A:GLU202 4.0 22.6 1.0 CD2 A:LEU72 4.2 33.4 1.0 NE2 A:HIS105 4.2 29.5 1.0 HD11 A:LEU198 4.3 35.4 1.0 OE2 A:GLU202 4.3 25.6 1.0 HD21 A:LEU198 4.3 37.1 1.0 CD2 A:HIS105 4.4 23.5 1.0 HD21 A:LEU72 4.4 40.1 1.0 CA A:GLU102 4.5 24.1 1.0 HA A:GLU69 4.5 25.7 1.0 CG A:GLU102 4.5 30.3 1.0 CG A:GLU69 4.5 27.1 1.0 HB3 A:GLU69 4.6 25.4 1.0 HG A:LEU72 4.6 40.4 1.0 HB3 A:GLU102 4.6 38.9 1.0 CE1 A:HIS205 4.6 31.1 1.0 HB3 A:LEU72 4.6 24.7 1.0 CG A:LEU198 4.7 25.4 1.0 ND1 A:HIS205 4.7 27.4 1.0 CD A:GLU167 4.7 25.1 0.5 CB A:GLU102 4.8 32.4 1.0 HD22 A:LEU72 4.8 40.1 1.0 CD1 A:LEU198 4.9 29.5 1.0 HG3 A:GLU69 4.9 32.5 1.0 CG A:LEU72 4.9 33.7 1.0 HH A:TYR175 4.9 54.1 1.0 CD2 A:LEU198 5.0 30.9 1.0 HE2 A:HIS105 5.0 35.4 1.0 CB A:GLU69 5.0 21.2 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:28.6 occ:1.00 OE1 B:GLU69 2.1 29.0 1.0 OE1 B:GLU102 2.1 29.3 1.0 ND1 B:HIS105 2.1 24.8 1.0 O B:HOH521 2.2 36.6 1.0 OE2 B:GLU202 2.3 39.5 1.0 CD B:GLU69 3.0 34.5 1.0 CE1 B:HIS105 3.0 36.7 1.0 HE1 B:HIS105 3.2 44.0 1.0 CD B:GLU102 3.2 25.2 1.0 CG B:HIS105 3.2 27.5 1.0 CD B:GLU202 3.3 36.7 1.0 OE2 B:GLU69 3.3 43.7 1.0 HB2 B:HIS105 3.4 35.2 1.0 HD23 B:LEU72 3.4 51.5 1.0 HB3 B:HIS105 3.5 35.2 1.0 HA B:GLU102 3.6 32.1 1.0 CB B:HIS105 3.6 29.3 1.0 OE2 B:GLU102 3.6 27.8 1.0 OE2 B:GLU167 3.6 29.4 0.5 FE B:FE2402 3.7 30.6 1.0 HG B:LEU198 3.8 44.4 1.0 HD21 B:LEU198 3.9 55.0 1.0 OE1 B:GLU202 4.1 43.4 1.0 HG3 B:GLU202 4.1 47.5 1.0 CG B:GLU202 4.2 39.6 1.0 HG2 B:GLU202 4.2 47.5 1.0 HD11 B:LEU198 4.2 42.5 1.0 NE2 B:HIS105 4.2 25.6 1.0 HE1 B:HIS205 4.2 36.3 1.0 CD2 B:HIS105 4.3 34.9 1.0 CD2 B:LEU72 4.3 42.9 1.0 HA B:GLU69 4.4 35.2 1.0 CG B:GLU69 4.4 36.3 1.0 HG B:LEU72 4.4 45.5 1.0 HH B:TYR175 4.4 85.2 1.0 HB3 B:GLU102 4.4 33.1 1.0 CA B:GLU102 4.5 26.8 1.0 CG B:LEU198 4.5 37.0 1.0 CG B:GLU102 4.5 20.9 1.0 HB3 B:GLU69 4.5 33.9 1.0 CD2 B:LEU198 4.6 45.9 1.0 HD21 B:LEU72 4.6 51.5 1.0 HB3 B:LEU72 4.6 44.1 1.0 HG3 B:GLU69 4.6 43.5 1.0 CB B:GLU102 4.7 27.6 1.0 HB2 B:LEU72 4.7 44.1 1.0 HD23 B:LEU198 4.8 55.0 1.0 CD1 B:LEU198 4.8 35.4 1.0 CE1 B:HIS205 4.8 30.3 1.0 ND1 B:HIS205 4.8 29.6 1.0 CD B:GLU167 4.8 24.2 0.5 CG B:LEU72 4.8 37.9 1.0 CB B:GLU69 4.9 28.2 1.0 HE2 B:HIS105 5.0 30.7 1.0 HD22 B:LEU72 5.0 51.5 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