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

Protein crystallography data

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

Other elements in 8vil:

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

Sodium Binding Sites:

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 8vil

Go back to Sodium Binding Sites List in 8vil
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 8vil

Go back to Sodium Binding Sites List in 8vil
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

Reference:

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
Page generated: Wed Oct 9 14:02:01 2024

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