Sodium in PDB 8vil: Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine

The structure of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine, PDB code: 8vil was solved by K.A.Ireland, K.M.Davis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.197, 94.511, 83.747, 90, 100.16, 90
R / Rfree (%)	20.1 / 21.6

The structure of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine (pdb code 8vil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine, PDB code: 8vil:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:29.8 occ:1.00 O A:ASP372 2.5 24.0 1.0 O A:VAL377 2.7 19.1 1.0 OE2 A:GLU379 2.9 29.2 1.0 O A:LEU373 3.0 22.6 1.0 O A:GLY375 3.1 21.2 1.0 C A:LEU373 3.5 25.0 1.0 C A:ASP372 3.7 25.1 1.0 CD A:GLU379 3.7 29.9 1.0 CG A:GLU379 3.8 27.7 1.0 C A:VAL377 3.9 20.2 1.0 CA A:LEU373 4.0 25.4 1.0 N A:GLY375 4.1 21.3 1.0 CD1 A:LEU235 4.2 27.4 1.0 O A:GLY415 4.2 20.4 1.0 C A:GLY375 4.2 21.1 1.0 N A:ARG374 4.2 25.7 1.0 C A:ARG374 4.3 23.1 1.0 CB A:GLU379 4.3 22.9 1.0 O A:LEU413 4.3 22.9 1.0 N A:LEU373 4.3 23.0 1.0 N A:GLU379 4.4 22.2 1.0 CA A:ARG374 4.5 22.7 1.0 C A:TRP378 4.5 22.3 1.0 N A:VAL377 4.5 18.8 1.0 CD2 A:LEU235 4.6 19.9 1.0 CA A:GLY414 4.6 23.6 1.0 CA A:TRP378 4.7 20.3 1.0 CA A:GLY375 4.7 20.0 1.0 N A:TRP378 4.7 20.3 1.0 NH2 A:ARG443 4.8 21.9 1.0 O A:ARG374 4.8 25.8 1.0 CA A:ASP372 4.9 22.7 1.0 C A:GLY414 4.9 21.4 1.0 CG A:LEU235 4.9 22.8 1.0 CA A:VAL377 4.9 19.1 1.0 CB A:ASP372 4.9 22.3 1.0 OE1 A:GLU379 4.9 26.0 1.0 O A:TRP378 4.9 20.8 1.0 CA A:GLU379 5.0 23.9 1.0

Sodium binding site 2 out of 2 in the Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with N,N-Dimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:26.4 occ:1.00 O B:VAL377 2.6 27.0 1.0 O B:ASP372 2.8 25.3 1.0 O B:GLY375 3.0 25.1 1.0 O B:LEU373 3.1 28.0 1.0 OE2 B:GLU379 3.2 27.8 1.0 C B:LEU373 3.5 28.9 1.0 C B:VAL377 3.8 22.8 1.0 C B:ASP372 3.9 25.0 1.0 CG B:GLU379 3.9 23.8 1.0 CD B:GLU379 4.0 26.9 1.0 N B:GLY375 4.0 24.1 1.0 C B:GLY375 4.1 26.1 1.0 CD1 B:LEU235 4.1 29.4 1.0 CA B:LEU373 4.1 21.5 1.0 C B:ARG374 4.2 23.6 1.0 O B:GLY415 4.2 23.2 1.0 N B:ARG374 4.2 23.1 1.0 N B:VAL377 4.3 26.8 1.0 N B:GLU379 4.3 19.2 1.0 CB B:GLU379 4.4 19.9 1.0 CA B:ARG374 4.4 24.9 1.0 O B:LEU413 4.4 23.4 1.0 C B:TRP378 4.5 22.9 1.0 N B:LEU373 4.5 20.6 1.0 CD2 B:LEU235 4.6 23.0 1.0 CA B:TRP378 4.6 24.5 1.0 CA B:GLY375 4.6 22.8 1.0 N B:TRP378 4.6 19.5 1.0 O B:ARG374 4.7 24.8 1.0 CA B:GLY414 4.7 25.0 1.0 CA B:VAL377 4.7 21.3 1.0 CG B:LEU235 4.9 22.1 1.0 NH2 B:ARG443 5.0 23.1 1.0 CA B:ASP372 5.0 25.9 1.0 O B:TRP378 5.0 25.0 1.0 C B:GLY414 5.0 25.8 1.0 CA B:GLU379 5.0 21.1 1.0 CB B:ASP372 5.0 22.7 1.0

K.A.Ireland, C.M.Kayrouz, M.L.Abbott, M.R.Seyedsayamdost, K.M.Davis. Structural Insights Into the Convergent Evolution of Type IV Sulfoxide Synthase Egtb, An Ergothioneine-Biosynthetic Homolog of Ovothiol Synthase Ovoa Structure 2024.
ISSN: ISSN 0969-2126