Manganese in PDB 4x8d: Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine, PDB code: 4x8d was solved by A.Vit, K.V.Goncharenko, W.Blankenfeldt, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.83 / 1.98
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.292, 135.292, 141.293, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.3

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	12 atoms

The binding sites of Manganese atom in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine (pdb code 4x8d). 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-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine, PDB code: 4x8d:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:24.6 occ:1.00 HKL A:AVI502 1.4 25.9 1.0 NE2 A:HIS134 2.1 19.4 1.0 NE2 A:AVI502 2.2 21.6 1.0 NE2 A:HIS138 2.3 17.3 1.0 NE2 A:HIS51 2.3 18.9 1.0 O A:HOH1087 2.4 16.9 1.0 SG2 A:3GC501 2.5 19.5 1.0 HG2 A:3GC501 2.7 23.4 1.0 CE1 A:HIS134 3.1 18.7 1.0 CD2 A:HIS134 3.1 18.4 1.0 CD2 A:HIS138 3.2 17.2 1.0 CE1 A:AVI502 3.2 20.6 1.0 CD2 A:HIS51 3.2 17.6 1.0 CD2 A:AVI502 3.2 19.7 1.0 HE1 A:HIS134 3.2 22.5 1.0 CE1 A:HIS138 3.2 17.9 1.0 HD2 A:HIS138 3.3 20.6 1.0 CE1 A:HIS51 3.3 19.9 1.0 HD2 A:HIS134 3.3 22.0 1.0 HD2 A:HIS51 3.3 21.1 1.0 HD2 A:AVI502 3.4 23.7 1.0 HE1 A:AVI502 3.4 24.7 1.0 HB21 A:3GC501 3.4 25.5 1.0 HE1 A:HIS138 3.4 21.5 1.0 HE1 A:HIS51 3.5 23.9 1.0 CB2 A:3GC501 3.5 21.2 1.0 HG3 A:GLN55 3.7 27.2 1.0 HB22 A:3GC501 3.7 25.5 1.0 ND1 A:HIS134 4.2 20.1 1.0 CG A:HIS134 4.2 19.2 1.0 CG A:HIS138 4.3 17.8 1.0 ND1 A:AVI502 4.3 18.7 1.0 ND1 A:HIS138 4.3 18.2 1.0 CG A:AVI502 4.4 18.8 1.0 CG A:HIS51 4.4 17.5 1.0 ND1 A:HIS51 4.4 19.1 1.0 CG A:GLN55 4.6 22.7 1.0 HE2 A:TYR377 4.6 26.2 1.0 OE1 A:GLN55 4.6 24.3 1.0 OH A:TYR377 4.7 22.3 1.0 CD A:GLN55 4.9 24.2 1.0 CL A:CL510 4.9 37.0 1.0 CA2 A:3GC501 4.9 22.6 1.0 HD1 A:HIS134 4.9 24.1 1.0 O A:HOH1102 5.0 39.5 1.0

Manganese binding site 2 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb in Complex with N, N-Dimethyl-Histidine and Gamma-Glutamyl-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:27.0 occ:1.00 HKL B:AVI502 1.4 31.9 1.0 HG2 B:3GC501 1.5 41.2 1.0 NE2 B:HIS138 2.1 36.2 1.0 NE2 B:HIS134 2.1 36.9 1.0 NE2 B:HIS51 2.2 34.4 1.0 NE2 B:AVI502 2.2 26.6 1.0 O B:HOH886 2.3 29.4 1.0 SG2 B:3GC501 2.6 34.4 1.0 CE1 B:HIS138 3.0 35.8 1.0 CE1 B:HIS51 3.1 36.1 1.0 CE1 B:HIS134 3.1 37.0 1.0 CE1 B:AVI502 3.1 25.9 1.0 CD2 B:HIS134 3.1 36.3 1.0 CD2 B:HIS138 3.1 35.2 1.0 CD2 B:HIS51 3.2 34.1 1.0 HE1 B:HIS138 3.2 42.9 1.0 HE1 B:AVI502 3.2 31.1 1.0 HE1 B:HIS51 3.2 43.3 1.0 HE1 B:HIS134 3.3 44.4 1.0 HD2 B:HIS134 3.3 43.5 1.0 CD2 B:AVI502 3.3 26.7 1.0 HD2 B:HIS138 3.3 42.3 1.0 HD2 B:HIS51 3.3 40.9 1.0 HB22 B:3GC501 3.5 44.4 1.0 HD2 B:AVI502 3.5 32.0 1.0 CB2 B:3GC501 3.5 37.0 1.0 HG3 B:GLN55 3.6 45.8 1.0 HB21 B:3GC501 3.7 44.4 1.0 ND1 B:HIS138 4.1 34.3 1.0 ND1 B:HIS134 4.2 36.7 1.0 ND1 B:HIS51 4.2 36.6 1.0 CG B:HIS138 4.2 34.0 1.0 CG B:HIS134 4.2 36.4 1.0 ND1 B:AVI502 4.2 26.1 1.0 CG B:HIS51 4.3 35.5 1.0 CG B:AVI502 4.4 26.6 1.0 CG B:GLN55 4.5 38.2 1.0 HE2 B:TYR377 4.6 48.4 1.0 OH B:TYR377 4.7 38.0 1.0 OE1 B:GLN55 4.7 40.6 1.0 HG2 B:GLN55 4.9 45.8 1.0 CD B:GLN55 4.9 40.1 1.0 HD1 B:HIS138 4.9 41.2 1.0 CA2 B:3GC501 4.9 36.2 1.0 HD1 B:HIS134 5.0 44.1 1.0 HD1 B:HIS51 5.0 43.9 1.0

K.V.Goncharenko, A.Vit, W.Blankenfeldt, F.P.Seebeck. Structure of the Sulfoxide Synthase Egtb From the Ergothioneine Biosynthetic Pathway. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25597398
DOI: 10.1002/ANIE.201410045