Magnesium 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:

Manganese	(Mn)	2 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	12 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 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 Magnesium with other atoms in the Mg 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:Mg505 b:28.6 occ:0.50 O A:HOH668 2.1 33.3 1.0 O A:HOH602 2.3 30.7 1.0 O A:HOH604 2.4 38.5 1.0 OD2 A:ASP271 4.0 25.0 1.0 HB3 A:PRO166 4.0 28.0 1.0 O A:HOH1095 4.4 35.7 1.0 HA A:PRO166 4.4 25.8 1.0 OD1 A:ASP271 4.5 24.5 1.0 CG A:ASP271 4.7 24.3 1.0 O A:HOH653 4.9 18.4 1.0 CB A:PRO166 4.9 23.3 1.0

Magnesium binding site 2 out of 7 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 Magnesium with other atoms in the Mg 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 A:Mg506 b:43.8 occ:1.00 O A:HOH622 2.2 31.8 1.0 O A:HOH639 2.4 27.4 1.0 O A:HOH629 2.4 54.8 1.0 H A:LEU174 3.8 23.0 1.0 HB3 A:LEU174 4.1 25.4 1.0 O A:HOH637 4.2 18.9 1.0 HB A:VAL173 4.2 21.3 1.0 O A:CYS349 4.3 21.8 1.0 HG12 A:VAL173 4.6 23.4 1.0 N A:LEU174 4.6 19.2 1.0 O A:HOH627 4.7 33.7 1.0 HA A:VAL173 4.7 21.5 1.0 O A:LEU174 4.9 21.7 1.0 CB A:LEU174 5.0 21.2 1.0 CB A:VAL173 5.0 17.7 1.0

Magnesium binding site 3 out of 7 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg507 b:53.1 occ:1.00 O A:HOH662 2.3 35.2 1.0 O A:HOH1008 2.4 54.0 1.0 O A:HOH1190 2.4 67.3 1.0 O A:HOH614 4.1 24.0 1.0 O A:HOH1175 4.6 47.8 1.0

Magnesium binding site 4 out of 7 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg508 b:30.7 occ:1.00 O A:HOH636 1.9 31.7 1.0 O A:HOH664 2.0 31.6 1.0 O A:HOH1218 2.1 30.7 1.0 O A:HOH677 2.1 32.0 1.0 OD2 A:ASP188 3.6 44.5 1.0 O A:HOH1091 4.1 56.0 1.0 OD1 A:ASP188 4.2 41.7 1.0 CG A:ASP188 4.3 40.4 1.0 O A:HOH660 4.3 47.1 1.0 O A:HOH743 4.4 26.9 1.0 O A:HOH678 4.5 63.3 1.0 HB3 A:ALA199 4.5 31.8 1.0 HG11 A:VAL181 4.5 27.9 1.0 HB1 A:ALA199 4.6 31.8 1.0 OD2 A:ASP185 4.6 33.3 1.0 O A:HOH1113 4.6 62.0 1.0 HB2 A:ALA199 4.7 31.8 1.0 CB A:ALA199 4.8 26.5 1.0

Magnesium binding site 5 out of 7 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg509 b:35.4 occ:1.00 OE2 A:GLU11 2.7 45.7 1.0 HG2 A:GLN15 3.2 34.0 1.0 HE21 A:GLN15 3.3 41.5 1.0 OD1 A:ASP406 3.4 41.1 1.0 OD2 A:ASP406 3.5 44.6 1.0 CD A:GLU11 3.7 45.7 1.0 HG3 A:GLN15 3.7 34.0 1.0 CG A:ASP406 3.9 40.4 1.0 CG A:GLN15 3.9 28.3 1.0 NE2 A:GLN15 4.0 34.6 1.0 OE1 A:GLU11 4.1 46.0 1.0 CD A:GLN15 4.4 32.3 1.0 HE22 A:GLN15 4.6 41.5 1.0 OD2 A:ASP18 4.7 34.5 0.7 HA A:GLN15 4.8 30.6 1.0 HB3 A:ARG14 4.9 40.4 1.0 HE A:ARG14 4.9 60.6 1.0 HG3 A:GLU11 4.9 52.8 1.0 CG A:GLU11 5.0 44.0 1.0

Magnesium binding site 6 out of 7 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg504 b:37.6 occ:1.00 O A:HOH998 2.1 45.2 1.0 O A:HOH1200 2.1 63.7 1.0 OD1 B:ASP267 2.1 38.1 1.0 O B:HOH974 2.1 74.3 1.0 O B:HOH994 2.2 31.7 1.0 O A:HOH1007 2.3 49.6 1.0 CG B:ASP267 3.0 39.5 1.0 OD2 B:ASP267 3.3 43.5 1.0 OD2 A:ASP117 3.3 73.9 0.5 HB3 A:LEU113 3.6 37.3 1.0 H B:ILE268 3.7 41.7 1.0 O A:HOH806 4.2 36.2 1.0 O B:ILE268 4.3 35.5 1.0 O B:GLY257 4.3 34.4 1.0 N B:ILE268 4.3 34.8 1.0 CG A:ASP117 4.4 64.7 0.5 CB B:ASP267 4.4 37.3 1.0 HB2 A:LEU113 4.4 37.3 1.0 HB B:ILE268 4.4 40.0 1.0 O B:HOH857 4.4 43.5 1.0 HD13 A:LEU113 4.4 36.9 1.0 CB A:LEU113 4.5 31.1 1.0 OD1 A:ASP114 4.5 54.4 1.0 HA B:ASP267 4.5 41.4 1.0 O A:LEU113 4.7 34.7 1.0 HB2 A:ASP117 4.7 69.6 0.5 HB3 B:ASP267 4.8 44.7 1.0 HA A:ASP114 4.8 44.6 1.0 CA B:ASP267 4.8 34.5 1.0 OD1 A:ASP117 4.8 68.8 0.5 C A:LEU113 4.9 32.6 1.0 C B:ASP267 5.0 35.0 1.0

Magnesium binding site 7 out of 7 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg505 b:34.6 occ:1.00 OE1 B:GLU73 2.5 62.9 1.0 O B:HOH601 3.0 62.5 1.0 HD2 B:PRO74 3.3 70.2 1.0 CD B:GLU73 3.5 60.7 1.0 O B:HOH613 3.7 68.4 1.0 OE2 B:GLU73 3.7 61.9 1.0 HD3 B:PRO74 3.9 70.2 1.0 CD B:PRO74 3.9 58.5 1.0 HG2 B:PRO74 4.0 68.3 1.0 HA B:GLU73 4.4 65.7 1.0 CG B:PRO74 4.5 56.9 1.0 CL B:CL507 4.6 58.3 1.0 HB3 B:GLU73 4.7 65.6 1.0 CG B:GLU73 4.8 57.0 1.0 HG3 B:PRO74 5.0 68.3 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