Manganese in PDB 6f6g: R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6g 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)	48.59 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.988, 98.467, 55.862, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24

The structure of R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6g). 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6g:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:30.5 occ:1.00 OE2 A:GLU102 2.1 30.9 1.0 OE2 A:GLU69 2.1 36.5 1.0 ND1 A:HIS105 2.1 34.2 1.0 O1 A:PLM404 2.1 68.4 1.0 OE1 A:GLU202 2.2 47.7 1.0 O A:HOH513 2.3 43.3 1.0 C1 A:PLM404 2.7 49.6 1.0 CE1 A:HIS105 3.0 37.1 1.0 O2 A:PLM404 3.0 44.5 1.0 HE1 A:HIS105 3.1 44.5 1.0 CD A:GLU69 3.1 42.5 1.0 CD A:GLU102 3.2 27.9 1.0 CG A:HIS105 3.2 31.5 1.0 CD A:GLU202 3.2 34.7 1.0 OE1 A:GLU69 3.5 49.9 1.0 HB2 A:HIS105 3.5 39.4 1.0 FE A:FE2402 3.5 30.5 1.0 HB3 A:HIS105 3.6 39.4 1.0 OE1 A:GLU102 3.6 32.7 1.0 HA A:GLU102 3.6 29.6 1.0 CB A:HIS105 3.7 32.9 1.0 HG A:LEU198 3.9 51.0 1.0 C2 A:PLM404 4.0 54.4 1.0 OE2 A:GLU202 4.0 34.0 1.0 HG3 A:GLU202 4.1 44.9 1.0 HG21 A:ILE72 4.1 52.8 1.0 H31 A:PLM404 4.1 59.1 1.0 CG A:GLU202 4.1 37.5 1.0 NE2 A:HIS105 4.2 27.8 1.0 HG2 A:GLU202 4.2 44.9 1.0 HE1 A:HIS205 4.2 36.0 1.0 H21 A:PLM404 4.3 65.2 1.0 HD11 A:LEU198 4.3 41.7 1.0 CD2 A:HIS105 4.3 38.9 1.0 H32 A:PLM404 4.3 59.1 1.0 HA A:GLU69 4.4 39.2 1.0 C3 A:PLM404 4.4 49.2 1.0 CG A:GLU102 4.5 27.5 1.0 CG A:GLU69 4.5 41.1 1.0 CA A:GLU102 4.5 24.7 1.0 HB3 A:GLU69 4.5 36.8 1.0 HD21 A:LEU198 4.6 57.8 1.0 HB3 A:GLU102 4.6 32.5 1.0 CG A:LEU198 4.7 42.5 1.0 CB A:GLU102 4.8 27.1 1.0 ND1 A:HIS205 4.8 29.0 1.0 CE1 A:HIS205 4.8 30.0 1.0 HG3 A:GLU69 4.8 49.3 1.0 CG2 A:ILE72 4.8 44.0 1.0 CD1 A:LEU198 4.8 34.8 1.0 H22 A:PLM404 4.8 65.2 1.0 OH A:TYR175 4.9 62.2 1.0 HE2 A:HIS105 4.9 33.4 1.0 CB A:GLU69 4.9 30.7 1.0 HG23 A:ILE72 4.9 52.8 1.0 HD12 A:LEU198 4.9 41.7 1.0 HG2 A:GLU167 5.0 62.6 1.0 HG2 A:GLU102 5.0 33.0 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:31.8 occ:1.00 O2 B:PLM404 1.7 56.4 1.0 OE2 B:GLU69 2.1 34.7 1.0 OE2 B:GLU102 2.1 35.1 1.0 ND1 B:HIS105 2.2 28.4 1.0 OE1 B:GLU202 2.2 41.9 1.0 O B:HOH501 2.2 48.2 1.0 C1 B:PLM404 2.7 54.8 1.0 CE1 B:HIS105 3.0 31.6 1.0 CD B:GLU69 3.1 44.5 1.0 HE1 B:HIS105 3.1 38.0 1.0 O1 B:PLM404 3.1 46.8 1.0 CD B:GLU102 3.2 32.9 1.0 CG B:HIS105 3.3 28.3 1.0 CD B:GLU202 3.3 40.9 1.0 OE1 B:GLU69 3.4 57.5 1.0 HB2 B:HIS105 3.5 30.2 1.0 OE1 B:GLU102 3.5 34.7 1.0 HA B:GLU102 3.6 29.8 1.0 FE B:FE2402 3.6 32.2 1.0 HB3 B:HIS105 3.6 30.2 1.0 CB B:HIS105 3.7 25.2 1.0 HD12 B:ILE72 3.7 57.0 0.4 H32 B:PLM404 3.8 54.9 1.0 HG B:LEU198 3.8 58.7 1.0 HD11 B:LEU198 4.0 43.2 1.0 OE2 B:GLU202 4.1 37.6 1.0 C2 B:PLM404 4.1 60.2 1.0 HE1 B:HIS205 4.1 39.0 1.0 HD21 B:LEU198 4.2 53.1 1.0 NE2 B:HIS105 4.2 36.0 1.0 HG2 B:GLU202 4.2 48.6 1.0 CG B:GLU202 4.2 40.5 1.0 HH B:TYR162 4.3 74.4 0.6 HG3 B:GLU202 4.3 48.6 1.0 HG21 B:ILE72 4.3 49.7 0.6 CD2 B:HIS105 4.3 30.1 1.0 C3 B:PLM404 4.4 45.8 1.0 HB3 B:GLU69 4.4 42.3 1.0 CG B:GLU69 4.4 39.3 1.0 CD1 B:ILE72 4.4 47.5 0.4 HA B:GLU69 4.4 47.0 1.0 CA B:GLU102 4.5 24.9 1.0 CG B:GLU102 4.5 38.3 1.0 HD11 B:ILE72 4.5 57.0 0.4 H31 B:PLM404 4.5 54.9 1.0 HB3 B:GLU102 4.5 34.3 1.0 CG B:LEU198 4.5 48.9 1.0 HD13 B:ILE72 4.6 57.0 0.4 CD1 B:LEU198 4.7 36.0 1.0 CB B:GLU102 4.7 28.6 1.0 H21 B:PLM404 4.7 72.2 1.0 CE1 B:HIS205 4.7 32.5 1.0 ND1 B:HIS205 4.7 27.0 1.0 H22 B:PLM404 4.8 72.2 1.0 CD2 B:LEU198 4.8 44.2 1.0 HG3 B:GLU69 4.8 47.1 1.0 OH B:TYR162 4.8 62.0 0.6 CB B:GLU69 4.9 35.3 1.0 HD12 B:LEU198 4.9 43.2 1.0 HG2 B:GLU102 4.9 45.9 1.0 HE2 B:HIS105 5.0 43.2 1.0 OE2 B:GLU167 5.0 36.0 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