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

The structure of Egtb-IV From Crocosphaera Subtropica, An Ergothioneine-Biosynthetic Type IV Sulfoxide Synthase in Complex with Cysteine and Hercynine, PDB code: 8vii 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 / 1.62
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 (%)	16.6 / 19.3

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

Manganese

(Mn)

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 Cysteine and Hercynine (pdb code 8vii). 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 Cysteine and Hercynine, PDB code: 8vii:
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 Cysteine and 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 Cysteine and Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:22.4 occ:1.00 O A:VAL377 2.7 12.6 1.0 O A:ASP372 2.7 17.8 1.0 O A:LEU373 2.9 16.7 1.0 O A:GLY375 2.9 13.9 1.0 OE2 A:GLU379 3.2 19.7 1.0 C A:LEU373 3.5 16.5 1.0 C A:ASP372 3.8 16.2 1.0 C A:VAL377 3.9 13.4 1.0 N A:GLY375 4.0 13.5 1.0 CA A:LEU373 4.0 14.1 1.0 C A:GLY375 4.0 14.7 1.0 CD A:GLU379 4.1 20.4 1.0 CG A:GLU379 4.1 18.9 1.0 O A:GLY415 4.1 12.2 1.0 C A:ARG374 4.2 14.4 1.0 N A:ARG374 4.2 15.1 1.0 N A:GLU379 4.3 14.1 1.0 O A:LEU413 4.3 13.3 1.0 CB A:GLU379 4.3 19.1 1.0 C A:TRP378 4.4 14.5 1.0 CD1 A:LEU235 4.4 17.4 1.0 N A:LEU373 4.4 15.3 1.0 N A:VAL377 4.4 13.7 1.0 CA A:ARG374 4.4 13.5 1.0 CA A:TRP378 4.5 15.0 1.0 CD2 A:LEU235 4.6 17.2 1.0 CA A:GLY375 4.6 15.3 1.0 N A:TRP378 4.7 12.9 1.0 O A:ARG374 4.7 14.3 1.0 CA A:GLY414 4.8 14.4 1.0 O A:TRP378 4.9 16.0 1.0 NH2 A:ARG443 4.9 16.6 1.0 C A:GLY414 4.9 16.1 1.0 CA A:VAL377 4.9 14.1 1.0 CA A:ASP372 4.9 15.4 1.0 CB A:ASP372 4.9 15.1 1.0 CA A:GLU379 4.9 15.7 1.0 CG A:LEU235 5.0 16.9 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 Cysteine and 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 Cysteine and Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:20.3 occ:1.00 O B:HOH773 2.3 25.7 1.0 O B:ASP372 2.6 17.9 1.0 O B:VAL377 2.7 15.1 1.0 O B:GLY375 2.9 17.4 1.0 O B:LEU373 3.0 18.6 1.0 OE2 B:GLU379 3.2 21.5 1.0 C B:LEU373 3.5 15.9 1.0 C B:ASP372 3.7 19.6 1.0 CG B:GLU379 3.8 22.9 1.0 C B:VAL377 3.9 12.1 1.0 CD B:GLU379 3.9 20.5 1.0 CA B:LEU373 4.0 19.1 1.0 N B:GLY375 4.1 14.8 1.0 C B:GLY375 4.1 14.8 1.0 C B:ARG374 4.2 18.4 1.0 N B:ARG374 4.2 16.0 1.0 N B:GLU379 4.3 15.3 1.0 O B:GLY415 4.3 15.8 1.0 N B:LEU373 4.4 16.1 1.0 CD1 B:LEU235 4.4 17.4 1.0 N B:VAL377 4.4 14.4 1.0 C B:TRP378 4.4 17.3 1.0 CD2 B:LEU235 4.5 15.2 1.0 CA B:ARG374 4.5 13.3 1.0 CB B:GLU379 4.5 18.1 1.0 O B:LEU413 4.5 16.7 1.0 O B:ARG374 4.6 17.0 1.0 CA B:GLY375 4.7 14.3 1.0 CA B:TRP378 4.7 14.1 1.0 N B:TRP378 4.8 14.2 1.0 NH2 B:ARG443 4.8 16.1 1.0 CB B:ASP372 4.8 20.4 1.0 CA B:ASP372 4.9 18.8 1.0 CA B:VAL377 4.9 15.4 1.0 CG B:LEU235 4.9 15.0 1.0 O B:TRP378 4.9 15.5 1.0 CA B:GLU379 4.9 15.5 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