Manganese in PDB 8qfo: Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese

The structure of Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese, PDB code: 8qfo was solved by C.M.Vasseur, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.65 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.684, 59.667, 134.611, 90, 90, 90
R / Rfree (%)	21.3 / 26.1

The structure of Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese (pdb code 8qfo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese, PDB code: 8qfo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:48.1 occ:1.00 NE2 A:HIS88 2.1 48.3 1.0 O A:ACT204 2.1 55.8 1.0 NE2 A:HIS134 2.1 42.7 1.0 O A:HOH302 2.2 51.3 1.0 NE2 A:HIS90 2.2 40.8 1.0 O A:HOH323 2.4 51.7 1.0 CE1 A:HIS134 3.0 42.2 1.0 CE1 A:HIS88 3.0 51.6 1.0 CD2 A:HIS88 3.0 45.5 1.0 CE1 A:HIS90 3.0 39.7 1.0 C A:ACT204 3.1 49.9 1.0 HE1 A:HIS134 3.1 50.6 1.0 HE1 A:HIS88 3.2 61.9 1.0 HD2 A:HIS88 3.2 54.6 1.0 CD2 A:HIS134 3.2 47.5 1.0 CD2 A:HIS90 3.3 38.1 1.0 HD2 A:HIS134 3.5 57.0 1.0 OXT A:ACT204 3.5 52.9 1.0 HE2 A:PHE149 3.9 59.7 1.0 HZ A:PHE128 4.0 61.9 1.0 HZ A:PHE149 4.1 53.1 1.0 HD12 A:LEU136 4.1 52.9 1.0 ND1 A:HIS88 4.1 47.7 1.0 ND1 A:HIS134 4.2 48.1 1.0 CG A:HIS88 4.2 52.9 1.0 ND1 A:HIS90 4.2 50.5 1.0 CG A:HIS134 4.3 46.7 1.0 CG A:HIS90 4.4 47.5 1.0 CH3 A:ACT204 4.4 52.9 1.0 CZ A:PHE128 4.6 51.6 1.0 CE2 A:PHE149 4.6 49.7 1.0 H2 A:ACT204 4.7 63.5 1.0 H1 A:ACT204 4.7 63.5 1.0 CZ A:PHE149 4.7 44.2 1.0 HD11 A:LEU136 4.8 52.9 1.0 CD1 A:LEU136 4.9 44.1 1.0 HD11 A:LEU156 4.9 79.2 1.0 HD1 A:HIS88 4.9 57.3 1.0 HD1 A:HIS134 4.9 57.7 1.0 HG A:LEU136 4.9 52.1 1.0 HE2 A:PHE128 4.9 57.1 1.0

Manganese binding site 2 out of 2 in the Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ergothioneine Dioxygenase, Variant Y128F, From Thermocatellispora Tengchongensis in Complex with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:46.5 occ:1.00 NE2 B:HIS134 2.1 43.6 1.0 NE2 B:HIS88 2.2 61.5 1.0 O B:HOH311 2.2 55.7 1.0 O B:HOH318 2.3 54.4 1.0 NE2 B:HIS90 2.4 43.7 1.0 OXT B:ACT202 2.5 61.0 1.0 CE1 B:HIS134 2.9 46.4 1.0 CE1 B:HIS88 3.0 54.5 1.0 HE1 B:HIS134 3.0 55.6 1.0 HE1 B:HIS88 3.1 65.5 1.0 CD2 B:HIS90 3.2 41.5 1.0 CD2 B:HIS134 3.3 55.3 1.0 CD2 B:HIS88 3.3 51.5 1.0 C B:ACT202 3.3 50.3 1.0 CE1 B:HIS90 3.5 45.0 1.0 HD2 B:HIS134 3.5 66.4 1.0 O B:ACT202 3.5 47.8 1.0 HD2 B:HIS88 3.6 61.8 1.0 HE1 B:PHE149 3.8 56.7 1.0 HZ B:PHE149 4.1 58.4 1.0 ND1 B:HIS134 4.1 43.5 1.0 HZ B:PHE128 4.2 54.6 1.0 ND1 B:HIS88 4.2 51.8 1.0 CG B:HIS134 4.3 48.6 1.0 CG B:HIS88 4.4 54.3 1.0 CG B:HIS90 4.4 48.1 1.0 HD12 B:LEU136 4.4 63.8 1.0 ND1 B:HIS90 4.5 44.3 1.0 CE1 B:PHE149 4.5 47.2 1.0 HG B:LEU136 4.7 66.3 1.0 CZ B:PHE149 4.7 48.7 1.0 CH3 B:ACT202 4.8 51.6 1.0 HD11 B:LEU136 4.8 63.8 1.0 HG21 B:THR85 4.9 76.2 1.0 CZ B:PHE128 4.9 45.5 1.0 HD1 B:HIS134 4.9 52.2 1.0 HD1 B:HIS88 4.9 62.2 1.0 H2 B:ACT202 4.9 62.0 1.0

E.Nalivaiko, C.M.Vasseur, F.P.Seebeck. Enzyme-Catalyzed Oxidative Degradation of Ergothioneine. Angew.Chem.Int.Ed.Engl. 18445 2023.
ISSN: ESSN 1521-3773
PubMed: 38095354
DOI: 10.1002/ANIE.202318445