Manganese in PDB 6i90: R2-Like Ligand-Binding Oxidase G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6i90 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)	39.22 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.073, 96.770, 128.704, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.3

The structure of R2-Like Ligand-Binding Oxidase G68F 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 G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6i90). 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 G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6i90:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase G68F 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 G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:30.5 occ:1.00 O1 A:PLM401 1.9 50.5 1.0 O A:HOH527 2.0 37.4 1.0 OE2 A:GLU69 2.1 33.2 1.0 OE2 A:GLU102 2.1 30.4 1.0 ND1 A:HIS105 2.2 30.3 1.0 O A:HOH508 2.2 36.4 1.0 C1 A:PLM401 2.9 47.1 1.0 CE1 A:HIS105 3.1 30.2 1.0 CD A:GLU69 3.1 41.6 1.0 CD A:GLU102 3.1 32.4 1.0 HE1 A:HIS105 3.2 36.2 1.0 O2 A:PLM401 3.2 45.1 1.0 CG A:HIS105 3.3 28.4 1.0 OE1 A:GLU69 3.4 42.7 1.0 HB2 A:HIS105 3.5 36.7 1.0 OE1 A:GLU102 3.5 31.4 1.0 HB3 A:HIS105 3.5 36.7 1.0 FE A:FE404 3.5 31.6 1.0 CB A:HIS105 3.6 30.6 1.0 HA A:GLU102 3.7 31.4 1.0 HG21 A:VAL72 4.0 42.6 1.0 HG A:LEU198 4.0 39.4 1.0 OE1 A:GLU202 4.1 39.3 1.0 HE1 A:HIS205 4.1 35.7 1.0 HA A:GLU69 4.1 39.4 1.0 NE2 A:HIS105 4.3 30.2 1.0 C2 A:PLM401 4.3 35.7 1.0 H31 A:PLM401 4.3 52.3 1.0 CD2 A:HIS105 4.3 32.7 1.0 HH A:TYR175 4.5 45.4 1.0 OH A:TYR175 4.5 37.8 1.0 CG A:GLU102 4.5 29.5 1.0 CG A:GLU69 4.5 34.0 1.0 H32 A:PLM401 4.6 52.3 1.0 HB3 A:GLU69 4.6 42.3 1.0 CA A:GLU102 4.6 26.2 1.0 HB3 A:GLU102 4.6 36.7 1.0 C3 A:PLM401 4.7 43.6 1.0 CG2 A:VAL72 4.7 35.5 1.0 HD23 A:LEU198 4.7 43.6 1.0 OE2 A:GLU202 4.7 31.8 1.0 HG22 A:VAL72 4.8 42.6 1.0 HG23 A:VAL72 4.8 42.6 1.0 CE1 A:HIS205 4.8 29.8 1.0 CD A:GLU202 4.8 39.3 1.0 CB A:GLU102 4.8 30.6 1.0 H21 A:PLM401 4.9 42.8 1.0 ND1 A:HIS205 4.9 30.8 1.0 CB A:GLU69 4.9 35.2 1.0 CG A:LEU198 4.9 32.8 1.0 H22 A:PLM401 4.9 42.8 1.0 CA A:GLU69 5.0 32.8 1.0 HG2 A:GLU102 5.0 35.5 1.0 HG3 A:GLU69 5.0 40.8 1.0

Manganese binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase G68F 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 G68F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:92.2 occ:0.98 NE2 A:HIS130 2.3 62.3 1.0 CD2 A:HIS130 3.2 59.3 1.0 HD2 A:HIS130 3.2 71.1 1.0 CE1 A:HIS130 3.3 59.1 1.0 HE1 A:HIS130 3.6 71.0 1.0 OD2 A:ASP129 4.0 66.9 1.0 CG A:HIS130 4.4 57.1 1.0 ND1 A:HIS130 4.4 56.5 1.0 O A:HOH518 4.6 53.1 1.0 HA3 A:GLY240 4.7 54.5 1.0 CG A:ASP129 4.9 70.9 1.0 OD1 A:ASP129 4.9 68.3 1.0

Y.Kutin, R.Kositzki, R.M.M.Branca, V.Srinivas, D.Lundin, M.Haumann, M.Hogbom, N.Cox, J.J.Griese. Chemical Flexibility of Heterobimetallic Mn/Fe Cofactors: R2LOX and R2C Proteins. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31591267
DOI: 10.1074/JBC.RA119.010570