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

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca517 b:19.3 occ:1.00 O A:VAL358 2.6 14.6 1.0 O A:GLY356 2.7 16.8 1.0 O A:MET354 2.7 15.2 1.0 O A:GLY399 2.9 19.3 1.0 O A:HOH685 3.0 16.6 1.0 HA3 A:GLY398 3.2 21.1 1.0 OE2 A:GLU360 3.2 14.7 1.0 HG3 A:GLU360 3.4 18.7 1.0 H A:VAL358 3.5 19.2 1.0 C A:MET354 3.5 16.1 1.0 O A:GLN353 3.5 15.2 1.0 O A:GLY398 3.6 18.0 1.0 C A:VAL358 3.6 15.1 1.0 H A:GLY356 3.7 19.6 1.0 C A:GLY398 3.7 17.6 1.0 C A:GLY356 3.8 16.4 1.0 N A:GLY356 3.8 16.4 1.0 CD A:GLU360 3.8 15.3 1.0 HA A:LEU355 3.9 19.9 1.0 CA A:GLY398 3.9 17.6 1.0 HA A:MET354 4.0 19.0 0.5 N A:VAL358 4.0 16.0 1.0 HA A:MET354 4.0 18.9 0.5 C A:GLY399 4.1 18.3 1.0 O A:ARG397 4.1 17.0 1.0 CG A:GLU360 4.1 15.6 1.0 C A:LEU355 4.1 16.8 1.0 HZ2 A:TRP299 4.2 18.7 1.0 HA A:TRP359 4.2 17.7 1.0 N A:GLY399 4.2 17.5 1.0 N A:LEU355 4.2 16.6 1.0 CA A:LEU355 4.3 16.6 1.0 CA A:MET354 4.3 15.9 0.5 HB2 A:ASP357 4.3 19.0 1.0 CA A:MET354 4.4 15.8 0.5 CA A:GLY356 4.4 16.3 1.0 CA A:VAL358 4.4 14.8 1.0 HA2 A:GLY398 4.4 21.1 1.0 HH21 A:ARG428 4.5 19.6 1.0 N A:TRP359 4.5 15.3 1.0 HG23 A:VAL358 4.5 19.4 1.0 C A:GLN353 4.6 15.8 1.0 HA A:SER400 4.6 21.0 1.0 H A:GLY399 4.6 20.9 1.0 OE1 A:GLU360 4.7 15.3 1.0 HG2 A:GLU360 4.7 18.7 1.0 CA A:TRP359 4.7 14.8 1.0 H A:GLU360 4.7 18.4 1.0 CA A:GLY399 4.8 17.0 1.0 HA2 A:GLY356 4.8 19.6 1.0 HG22 A:VAL358 4.8 19.4 1.0 O A:LEU355 4.8 17.6 1.0 N A:ASP357 4.8 15.9 1.0 N A:GLY398 4.9 16.9 1.0 C A:ARG397 4.9 16.3 1.0 HB2 A:GLU360 4.9 18.6 1.0 C A:ASP357 4.9 16.8 1.0 N A:GLU360 4.9 15.4 1.0 N A:MET354 5.0 15.9 1.0 H A:LEU355 5.0 19.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca511 b:31.7 occ:1.00 O B:GLY356 2.6 29.0 1.0 O B:MET354 2.6 29.3 1.0 O B:VAL358 2.7 27.0 1.0 O B:GLY399 2.9 29.5 1.0 O B:HOH626 3.0 29.6 1.0 HA3 B:GLY398 3.1 37.0 1.0 OE2 B:GLU360 3.3 31.7 1.0 H B:VAL358 3.4 34.1 1.0 C B:MET354 3.4 31.7 1.0 O B:GLY398 3.5 31.2 1.0 HG3 B:GLU360 3.5 35.4 1.0 O B:GLN353 3.5 33.1 1.0 H B:GLY356 3.5 38.8 1.0 C B:GLY398 3.6 30.7 1.0 C B:VAL358 3.7 27.5 1.0 C B:GLY356 3.7 30.1 1.0 N B:GLY356 3.7 32.3 1.0 CA B:GLY398 3.8 30.9 1.0 HA B:LEU355 3.9 40.3 1.0 HA B:MET354 3.9 38.6 0.7 CD B:GLU360 3.9 31.4 1.0 HA B:MET354 3.9 38.7 0.3 N B:VAL358 4.0 28.4 1.0 C B:LEU355 4.1 33.7 1.0 HZ2 B:TRP299 4.1 38.4 1.0 O B:ARG397 4.1 29.5 1.0 C B:GLY399 4.1 29.1 1.0 CG B:GLU360 4.2 29.5 1.0 N B:LEU355 4.2 33.9 1.0 HA B:TRP359 4.2 33.5 1.0 N B:GLY399 4.2 30.1 1.0 CA B:MET354 4.2 32.2 0.7 CA B:MET354 4.3 32.3 0.3 CA B:LEU355 4.3 33.6 1.0 CA B:GLY356 4.3 31.0 1.0 HB2 B:ASP357 4.3 36.0 1.0 HA2 B:GLY398 4.3 37.0 1.0 HH21 B:ARG428 4.4 41.0 1.0 CA B:VAL358 4.5 26.5 1.0 C B:GLN353 4.5 34.1 1.0 HG23 B:VAL358 4.5 33.5 1.0 N B:TRP359 4.6 27.4 1.0 H B:GLY399 4.6 36.1 1.0 HA B:SER400 4.6 34.7 1.0 HA2 B:GLY356 4.7 37.2 1.0 H B:GLU360 4.7 32.1 1.0 OE1 B:GLU360 4.8 31.2 1.0 N B:ASP357 4.8 31.0 1.0 CA B:GLY399 4.8 29.0 1.0 HG22 B:VAL358 4.8 33.5 1.0 CA B:TRP359 4.8 27.9 1.0 O B:LEU355 4.8 33.0 1.0 N B:GLY398 4.8 30.5 1.0 HG2 B:GLU360 4.8 35.4 1.0 N B:MET354 4.9 33.2 1.0 C B:ARG397 4.9 29.5 1.0 C B:ASP357 4.9 29.8 1.0 H B:LEU355 5.0 40.6 1.0 HB2 B:GLU360 5.0 34.7 1.0 N B:GLU360 5.0 26.7 1.0 CZ2 B:TRP299 5.0 32.0 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