Sodium in PDB 8vih: Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine

The structure of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine, PDB code: 8vih 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)	47.26 / 1.55
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 (%)	18 / 19.8

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

Chlorine	(Cl)	2 atoms
Iron	(Fe)	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 Hercynine (pdb code 8vih). 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 Hercynine, PDB code: 8vih:
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 Hercynine


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 Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:23.3 occ:1.00 O A:ASP372 2.7 15.1 1.0 O A:VAL377 2.7 11.5 1.0 O A:LEU373 2.9 12.7 1.0 OE2 A:GLU379 3.0 16.8 1.0 O A:GLY375 3.1 10.8 1.0 C A:LEU373 3.5 14.0 1.0 C A:ASP372 3.8 15.7 1.0 CG A:GLU379 3.8 13.9 1.0 CD A:GLU379 3.9 17.5 1.0 C A:VAL377 3.9 12.4 1.0 CA A:LEU373 4.0 12.7 1.0 N A:GLU379 4.1 11.0 1.0 O A:LEU413 4.2 12.7 1.0 CB A:GLU379 4.2 16.9 1.0 O A:GLY415 4.2 12.1 1.0 N A:GLY375 4.2 10.9 1.0 C A:GLY375 4.2 10.7 1.0 C A:TRP378 4.3 11.6 1.0 N A:ARG374 4.3 12.2 1.0 C A:ARG374 4.3 12.0 1.0 CD1 A:LEU235 4.4 12.5 1.0 N A:LEU373 4.4 13.8 1.0 CD2 A:LEU235 4.5 13.4 1.0 CA A:TRP378 4.5 10.8 1.0 N A:VAL377 4.6 10.1 1.0 CA A:ARG374 4.6 10.8 1.0 N A:TRP378 4.7 9.3 1.0 CA A:GLU379 4.7 11.9 1.0 O A:TRP378 4.8 13.1 1.0 NH2 A:ARG443 4.8 14.5 1.0 CA A:GLY414 4.8 10.8 1.0 CA A:GLY375 4.8 9.4 1.0 O A:ARG374 4.9 11.6 1.0 CG A:LEU235 4.9 10.5 1.0 CA A:ASP372 5.0 12.3 1.0 C A:GLY414 5.0 11.9 1.0 CB A:ASP372 5.0 11.9 1.0 CA A:VAL377 5.0 11.5 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 Hercynine


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 Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:19.9 occ:1.00 O B:HOH753 2.2 25.3 1.0 O B:ASP372 2.7 14.1 1.0 O B:VAL377 2.8 13.5 1.0 O B:LEU373 3.0 15.4 1.0 O B:GLY375 3.0 13.1 1.0 OE2 B:GLU379 3.1 17.6 1.0 C B:LEU373 3.5 15.0 1.0 C B:ASP372 3.8 14.1 1.0 C B:VAL377 4.0 11.6 1.0 CD B:GLU379 4.0 19.6 1.0 CA B:LEU373 4.0 14.0 1.0 CG B:GLU379 4.0 14.6 1.0 N B:GLY375 4.0 11.3 1.0 C B:GLY375 4.1 14.0 1.0 N B:ARG374 4.2 13.2 1.0 C B:ARG374 4.2 14.3 1.0 N B:GLU379 4.3 12.0 1.0 O B:GLY415 4.3 12.8 1.0 CB B:GLU379 4.3 16.2 1.0 CD1 B:LEU235 4.4 14.9 1.0 O B:LEU413 4.4 13.4 1.0 C B:TRP378 4.4 14.2 1.0 N B:LEU373 4.4 13.3 1.0 CA B:ARG374 4.5 12.9 1.0 N B:VAL377 4.5 12.4 1.0 CD2 B:LEU235 4.6 15.0 1.0 CA B:GLY375 4.7 13.8 1.0 CA B:TRP378 4.7 13.0 1.0 O B:ARG374 4.7 14.3 1.0 N B:TRP378 4.8 11.0 1.0 NH2 B:ARG443 4.8 14.7 1.0 O B:TRP378 4.9 14.6 1.0 CA B:GLU379 4.9 13.5 1.0 CA B:VAL377 5.0 12.0 1.0 CA B:ASP372 5.0 14.0 1.0 CG B:LEU235 5.0 12.9 1.0 CB B:ASP372 5.0 16.8 1.0 CA B:GLY414 5.0 12.5 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