Sodium in PDB 5uik: X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid

The structure of X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid, PDB code: 5uik was solved by C.R.Woodford, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.09 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.237, 69.199, 200.641, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 27.1

The binding sites of Sodium atom in the X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid (pdb code 5uik). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid, PDB code: 5uik:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:25.5 occ:1.00 O A:SER241 2.4 26.9 1.0 O A:HOH568 2.4 14.5 1.0 O A:HOH543 2.5 20.9 1.0 OG A:SER259 2.6 25.9 1.0 O A:THR260 2.6 26.8 1.0 O A:HOH551 2.6 25.2 1.0 C A:SER241 3.5 28.8 1.0 C A:THR260 3.7 25.2 1.0 N A:THR260 3.7 22.9 1.0 N A:SER241 3.8 28.3 1.0 O A:ASP262 3.8 22.3 1.0 CB A:SER259 3.9 26.0 1.0 CA A:SER241 4.0 28.6 1.0 O A:HOH617 4.0 35.8 1.0 O A:MET243 4.0 35.5 1.0 CB A:SER241 4.1 27.5 1.0 CA A:SER259 4.3 25.3 1.0 CA A:THR260 4.3 24.4 1.0 C A:SER259 4.3 25.1 1.0 C A:ARG240 4.4 28.7 1.0 OD2 A:ASP264 4.6 21.5 1.0 N A:ILE242 4.6 29.7 1.0 N A:ILE261 4.7 26.8 1.0 C A:ASP262 4.7 22.4 1.0 C A:ILE261 4.7 25.4 1.0 N A:ASP262 4.8 23.7 1.0 OG A:SER241 4.9 27.6 1.0 O A:HOH523 4.9 27.3 1.0 CA A:ARG240 4.9 29.9 1.0 CA A:ILE261 4.9 27.1 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:24.0 occ:1.00 O B:SER241 2.3 36.0 1.0 O B:HOH616 2.3 22.5 1.0 OG B:SER259 2.5 29.2 1.0 O B:HOH564 2.5 19.6 1.0 O B:THR260 2.5 25.4 1.0 O B:HOH550 2.6 12.2 1.0 C B:SER241 3.4 34.1 1.0 O B:MET243 3.5 29.8 1.0 C B:THR260 3.7 23.7 1.0 CB B:SER259 3.8 27.8 1.0 N B:THR260 3.8 24.7 1.0 N B:SER241 4.0 27.9 1.0 O B:ASP262 4.1 18.9 1.0 CA B:SER241 4.1 29.6 1.0 O B:HOH637 4.3 28.0 1.0 CA B:SER259 4.3 26.6 1.0 CB B:SER241 4.4 28.9 1.0 C B:SER259 4.4 24.7 1.0 CA B:THR260 4.5 23.0 1.0 N B:ILE242 4.5 35.9 1.0 C B:ARG240 4.5 28.7 1.0 C B:MET243 4.7 33.3 1.0 OD2 B:ASP264 4.7 27.8 1.0 C B:ILE261 4.8 21.8 1.0 C B:ILE242 4.8 35.8 1.0 N B:ILE261 4.8 24.1 1.0 CA B:ILE242 4.8 38.9 1.0 N B:MET243 4.8 34.6 1.0 O B:ILE261 4.8 23.0 1.0 O A:HOH632 4.9 18.6 1.0 CA B:ILE261 4.9 24.4 1.0 O B:ARG240 4.9 25.7 1.0 OG B:SER241 5.0 26.7 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Fdtf Formyltransferase From Salmonella Enteric O60 in Complex with Tdp-FUC3N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:38.4 occ:1.00 O B:HOH611 2.3 27.7 1.0 O B:HOH635 2.3 27.7 1.0 O B:ILE193 2.4 27.6 1.0 OH B:TYR105 2.4 26.6 1.0 O B:LYS190 2.5 30.8 1.0 O B:HOH652 2.5 38.9 1.0 CZ B:TYR105 3.4 24.2 1.0 C B:ILE193 3.6 26.6 1.0 C B:LYS190 3.6 31.6 1.0 CE2 B:TYR105 3.8 23.4 1.0 CA B:ASP194 3.9 29.7 1.0 N B:ASP194 4.2 29.0 1.0 O B:HOH609 4.3 23.8 1.0 CA B:LYS190 4.3 33.1 1.0 N B:TYR195 4.5 27.0 1.0 N B:LYS191 4.5 30.5 1.0 CB B:LYS190 4.5 37.4 1.0 CE1 B:TYR105 4.6 22.7 1.0 CA B:LYS191 4.6 29.7 1.0 OD1 B:ASP194 4.7 27.5 1.0 O B:HOH639 4.7 24.7 1.0 CA B:ILE193 4.7 25.9 1.0 N B:ILE193 4.7 24.8 1.0 CB B:ASP194 4.8 31.4 1.0 C B:ASP194 4.8 28.1 1.0 CD2 B:TYR195 5.0 24.8 1.0

C.R.Woodford, J.B.Thoden, H.M.Holden. Molecular Architecture of An N-Formyltransferase From Salmonella Enterica O60. J. Struct. Biol. V. 200 267 2017.
ISSN: ESSN 1095-8657
PubMed: 28263875
DOI: 10.1016/J.JSB.2017.03.002