Sodium in PDB 8vig: Egtb-IV From Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine

The structure of Egtb-IV From Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine, PDB code: 8vig 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)	47.82 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.177, 95.639, 101.392, 90, 90, 90
R / Rfree (%)	18.6 / 20.7

The structure of Egtb-IV From Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the Egtb-IV From Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine (pdb code 8vig). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Egtb-IV From Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine, PDB code: 8vig:

Sodium binding site 1 out of 1 in the Egtb-IV From Geminocystis Sp. Isolate SKYG4, 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 Geminocystis Sp. Isolate SKYG4, An Ergothioneine- Biosynthetic Type IV Sulfoxide Synthase in Complex with Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:19.6 occ:1.00 O A:ASP367 2.6 14.6 1.0 O A:VAL372 2.8 12.4 1.0 O A:GLY370 2.8 13.1 1.0 OE2 A:GLU374 3.0 21.3 1.0 O A:CYS368 3.1 15.2 1.0 C A:CYS368 3.5 14.2 1.0 C A:ASP367 3.7 14.0 1.0 CD A:GLU374 3.9 21.1 1.0 CG A:GLU374 3.9 20.2 1.0 C A:GLY370 3.9 12.6 1.0 C A:VAL372 4.0 14.0 1.0 N A:GLY370 4.0 12.3 1.0 O A:GLY410 4.0 12.8 1.0 CA A:CYS368 4.0 14.9 1.0 C A:ARG369 4.1 13.2 1.0 N A:ARG369 4.2 12.4 1.0 CD1 A:LEU232 4.3 12.8 1.0 N A:CYS368 4.4 13.9 1.0 N A:VAL372 4.4 11.6 1.0 CA A:ARG369 4.4 11.2 1.0 N A:GLU374 4.4 16.0 1.0 CB A:GLU374 4.5 18.4 1.0 C A:TRP373 4.5 14.8 1.0 O A:ILE408 4.5 14.0 1.0 NH2 A:ARG438 4.5 15.3 1.0 CA A:GLY370 4.5 12.6 1.0 CD2 A:LEU232 4.6 14.3 1.0 O A:ARG369 4.6 13.5 1.0 CB A:ASP367 4.7 14.2 1.0 CA A:TRP373 4.7 13.2 1.0 N A:TRP373 4.8 13.5 1.0 CA A:ASP367 4.8 14.9 1.0 C A:GLY409 4.9 12.6 1.0 O A:GLY409 4.9 12.4 1.0 CG A:LEU232 4.9 12.9 1.0 CA A:VAL372 4.9 13.2 1.0 O A:TRP373 4.9 16.4 1.0 CA A:GLY409 5.0 11.6 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