Sodium in PDB 8vik: Egtb-IV From Crocosphaera Subtropica, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis

The structure of Egtb-IV From Crocosphaera Subtropica, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis, PDB code: 8vik 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 / 1.96
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 (%)	19 / 21.9

The structure of Egtb-IV From Crocosphaera Subtropica, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis 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, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis (pdb code 8vik). 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, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis, PDB code: 8vik:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Egtb-IV From Crocosphaera Subtropica, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis


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, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:29.0 occ:1.00 O A:ASP372 2.6 27.6 1.0 O A:VAL377 2.7 23.6 1.0 O A:GLY375 2.8 25.0 1.0 O A:LEU373 2.8 28.4 1.0 OE2 A:GLU379 3.2 35.1 1.0 C A:LEU373 3.4 30.1 1.0 C A:ASP372 3.7 26.8 1.0 C A:VAL377 3.9 25.7 1.0 C A:GLY375 3.9 24.6 1.0 N A:GLY375 4.0 26.5 1.0 CA A:LEU373 4.0 25.6 1.0 O A:GLY415 4.0 24.7 1.0 CG A:GLU379 4.1 33.4 1.0 CD A:GLU379 4.1 35.6 1.0 C A:ARG374 4.1 24.6 1.0 N A:ARG374 4.2 24.4 1.0 O A:LEU413 4.3 26.9 1.0 N A:LEU373 4.4 28.4 1.0 CA A:ARG374 4.4 26.7 1.0 N A:GLU379 4.4 26.2 1.0 N A:VAL377 4.4 25.2 1.0 CD1 A:LEU235 4.4 31.0 1.0 CB A:GLU379 4.5 30.2 1.0 C A:TRP378 4.5 25.9 1.0 CA A:GLY375 4.5 20.4 1.0 CD2 A:LEU235 4.6 26.2 1.0 CA A:TRP378 4.6 23.9 1.0 O A:ARG374 4.6 26.9 1.0 CA A:GLY414 4.7 25.5 1.0 N A:TRP378 4.7 26.5 1.0 C A:GLY414 4.8 24.8 1.0 CA A:ASP372 4.8 26.6 1.0 CA A:VAL377 4.8 25.2 1.0 CB A:ASP372 4.9 27.4 1.0 NH2 A:ARG443 4.9 28.2 1.0 O A:TRP378 5.0 25.1 1.0

Sodium binding site 2 out of 2 in the Egtb-IV From Crocosphaera Subtropica, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis


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, A Type IV Sulfoxide Synthase Involved in Ergothioneine Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:31.1 occ:1.00 O B:VAL377 2.6 26.0 1.0 O B:ASP372 2.7 29.0 1.0 O B:GLY375 2.8 32.1 1.0 O B:LEU373 3.1 31.8 1.0 OE1 B:GLU379 3.4 34.7 1.0 C B:LEU373 3.5 33.0 1.0 C B:ASP372 3.8 29.1 1.0 C B:VAL377 3.8 28.4 1.0 C B:GLY375 4.0 31.6 1.0 N B:GLY375 4.0 27.7 1.0 CA B:LEU373 4.1 28.3 1.0 CG B:GLU379 4.1 36.4 1.0 O B:GLY415 4.1 27.0 1.0 C B:ARG374 4.1 28.3 1.0 N B:ARG374 4.2 27.5 1.0 CD B:GLU379 4.2 31.8 1.0 N B:VAL377 4.3 26.9 1.0 CB B:GLU379 4.3 28.2 1.0 CD1 B:LEU235 4.3 30.3 1.0 CA B:ARG374 4.4 29.5 1.0 N B:LEU373 4.4 26.6 1.0 O B:LEU413 4.5 24.2 1.0 N B:GLU379 4.5 25.5 1.0 C B:TRP378 4.5 25.6 1.0 O B:ARG374 4.6 29.6 1.0 CA B:GLY375 4.6 28.7 1.0 CD2 B:LEU235 4.7 31.7 1.0 CA B:TRP378 4.7 27.9 1.0 N B:TRP378 4.7 22.1 1.0 CA B:VAL377 4.8 25.4 1.0 CA B:GLY414 4.8 25.5 1.0 CA B:ASP372 4.9 27.8 1.0 C B:GLY414 4.9 29.6 1.0 O B:TRP378 4.9 28.1 1.0 CA B:GLU379 4.9 26.9 1.0 CB B:ASP372 4.9 27.5 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