Manganese in PDB 6f6f: R2-Like Ligand-Binding Oxidase V72I Mutant with Aerobically Reconstituted Mn/Fe Cofactor

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

The structure of R2-Like Ligand-Binding Oxidase V72I Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6f 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)	48.09 / 1.79
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.583, 95.899, 127.877, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.6

The structure of R2-Like Ligand-Binding Oxidase V72I Mutant with Aerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase V72I Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6f). 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 Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6f:
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 Aerobically 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 Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:37.9 occ:1.00 O1 A:PLM401 1.8 51.8 1.0 OE2 A:GLU69 2.1 41.0 1.0 OE2 A:GLU102 2.1 37.0 1.0 O A:HOH512 2.1 44.3 1.0 ND1 A:HIS105 2.2 31.9 1.0 O A:HOH502 2.4 45.0 1.0 C1 A:PLM401 2.7 52.7 1.0 CE1 A:HIS105 3.0 33.5 1.0 HE1 A:HIS105 3.0 40.2 1.0 CD A:GLU69 3.1 44.7 1.0 O2 A:PLM401 3.1 51.3 1.0 CD A:GLU102 3.1 39.0 1.0 CG A:HIS105 3.3 32.0 1.0 OE1 A:GLU69 3.4 46.4 1.0 OE1 A:GLU102 3.4 36.7 1.0 FE A:FE404 3.5 38.6 1.0 HB2 A:HIS105 3.5 42.1 1.0 HB3 A:HIS105 3.6 42.1 1.0 HA A:GLU102 3.7 37.4 1.0 CB A:HIS105 3.7 35.1 1.0 OE1 A:GLU202 4.0 44.5 1.0 C2 A:PLM401 4.1 45.7 1.0 HA A:GLU69 4.1 45.0 1.0 HG A:LEU198 4.1 41.5 1.0 HE1 A:HIS205 4.2 41.1 1.0 NE2 A:HIS105 4.2 34.3 1.0 H31 A:PLM401 4.2 56.3 1.0 H32 A:PLM401 4.3 56.3 1.0 CD2 A:HIS105 4.3 33.4 1.0 HH A:TYR175 4.3 51.3 1.0 OH A:TYR175 4.4 42.7 1.0 CG A:GLU69 4.5 39.0 1.0 CG A:GLU102 4.5 30.9 1.0 C3 A:PLM401 4.5 46.9 1.0 HB3 A:GLU102 4.5 36.6 1.0 H22 A:PLM401 4.5 54.8 1.0 CA A:GLU102 4.6 31.1 1.0 OE2 A:GLU202 4.7 38.0 1.0 HB3 A:GLU69 4.7 40.9 1.0 CG2 A:ILE72 4.7 47.2 1.0 CB A:GLU102 4.7 30.5 1.0 CD A:GLU202 4.7 42.9 1.0 CE1 A:HIS205 4.8 34.2 1.0 H21 A:PLM401 4.8 54.8 1.0 HG3 A:GLU69 4.8 46.8 1.0 ND1 A:HIS205 4.8 35.6 1.0 HD23 A:LEU198 4.9 46.6 1.0 HE2 A:HIS105 4.9 41.2 1.0 CB A:GLU69 4.9 34.1 1.0 CA A:GLU69 4.9 37.5 1.0 HG2 A:GLU102 4.9 37.1 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72I Mutant with Aerobically 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 Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:95.5 occ:0.88 NE2 A:HIS130 2.3 52.5 1.0 CD2 A:HIS130 3.2 55.0 1.0 HD2 A:HIS130 3.3 66.0 1.0 CE1 A:HIS130 3.3 54.4 1.0 HE1 A:HIS130 3.5 65.3 1.0 OD2 A:ASP129 4.2 73.3 1.0 CG A:HIS130 4.3 50.8 1.0 ND1 A:HIS130 4.4 53.8 1.0 OD1 A:ASP129 4.5 61.0 1.0 HA3 A:GLY240 4.7 49.5 1.0 CG A:ASP129 4.8 58.8 1.0 O A:HOH546 4.8 54.2 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