Sodium in PDB 5uim: X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N

The structure of X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N, PDB code: 5uim 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)	50.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.236, 58.406, 106.781, 90.00, 96.04, 90.00
R / Rfree (%)	19.5 / 26.4

The structure of X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N (pdb code 5uim). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N, PDB code: 5uim:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N


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 N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.5 occ:1.00 O A:HOH577 2.2 31.8 1.0 O A:HOH592 2.3 31.1 1.0 O A:ILE193 2.4 30.2 1.0 O A:HOH598 2.4 26.0 1.0 O A:LYS190 2.5 34.8 1.0 OH A:TYR105 2.7 27.2 1.0 C A:ILE193 3.6 32.3 1.0 CZ A:TYR105 3.6 26.6 1.0 C A:LYS190 3.7 34.1 1.0 CE2 A:TYR105 3.9 22.8 1.0 CA A:ASP194 4.1 43.2 1.0 N A:TYR195 4.2 40.5 1.0 N A:ASP194 4.3 37.2 1.0 CA A:LYS190 4.4 36.7 1.0 CD2 A:TYR195 4.5 32.9 1.0 CB A:LYS190 4.5 39.7 1.0 N A:LYS191 4.7 34.1 1.0 C A:ASP194 4.7 41.4 1.0 CA A:ILE193 4.8 30.6 1.0 N A:ILE193 4.8 29.8 1.0 CA A:LYS191 4.8 35.4 1.0 CE1 A:TYR105 4.9 23.8 1.0 O A:HOH587 4.9 29.8 1.0 OD2 A:ASP194 5.0 44.9 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N


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 N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:42.1 occ:1.00 O A:SER241 2.2 64.1 1.0 O A:HOH549 2.2 30.9 1.0 O A:HOH506 2.4 35.5 1.0 OG A:SER259 2.5 37.9 1.0 O A:THR260 2.6 48.4 1.0 O A:HOH552 2.7 40.3 1.0 C A:SER241 3.3 63.5 1.0 N A:THR260 3.4 37.1 1.0 CB A:SER259 3.6 42.9 1.0 O A:MET243 3.7 44.5 1.0 C A:THR260 3.7 46.0 1.0 OD2 A:ASP264 3.7 45.0 1.0 CA A:SER259 3.8 44.0 1.0 C A:SER259 3.9 37.0 1.0 O A:ASP262 4.0 48.6 1.0 CA A:SER241 4.0 56.8 1.0 N A:SER241 4.0 47.1 1.0 CA A:THR260 4.2 41.5 1.0 CB A:SER241 4.2 63.5 1.0 C A:ARG240 4.3 48.1 1.0 N A:ILE242 4.4 63.8 1.0 O A:ARG240 4.6 53.5 1.0 OG A:SER241 4.6 80.0 1.0 CA A:ILE242 4.8 73.3 1.0 N A:MET243 4.8 62.9 1.0 C A:MET243 4.8 59.5 1.0 O A:SER259 4.8 32.1 1.0 CD A:PRO245 4.9 64.3 1.0 N A:ILE261 4.9 43.6 1.0 C A:ILE242 4.9 65.2 1.0 O B:HOH607 5.0 33.7 1.0 CG A:ASP264 5.0 44.2 1.0 CG A:PRO245 5.0 62.0 1.0 CA A:ARG240 5.0 47.4 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N


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 N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:26.8 occ:1.00 O B:HOH562 2.2 27.8 1.0 O B:SER241 2.4 35.0 1.0 O B:THR260 2.5 31.6 1.0 O B:HOH540 2.5 26.7 1.0 OG B:SER259 2.6 27.2 1.0 O B:HOH533 2.7 32.2 1.0 O B:MET243 3.4 28.2 1.0 C B:SER241 3.5 32.3 1.0 C B:THR260 3.5 32.6 1.0 CB B:SER259 3.7 28.2 1.0 N B:THR260 3.7 27.4 1.0 C B:SER259 4.1 25.6 1.0 CA B:SER259 4.1 26.3 1.0 CA B:SER241 4.2 27.2 1.0 N B:SER241 4.2 29.9 1.0 O B:ASP262 4.2 25.4 1.0 O B:HOH618 4.2 36.7 1.0 CB B:SER241 4.2 25.1 1.0 CA B:THR260 4.3 27.6 1.0 OG B:SER241 4.5 21.3 1.0 N B:ILE261 4.5 33.0 1.0 C B:ILE261 4.5 26.5 1.0 O B:ILE261 4.6 27.4 1.0 N B:ILE242 4.6 31.2 1.0 C B:MET243 4.6 30.8 1.0 C B:ARG240 4.7 36.0 1.0 OD2 B:ASP264 4.7 30.9 1.0 N B:MET243 4.7 29.7 1.0 C B:ILE242 4.7 28.7 1.0 CA B:ILE261 4.8 32.0 1.0 CA B:ILE242 4.9 31.8 1.0 N B:ASP262 4.9 25.8 1.0 O B:SER259 4.9 26.9 1.0 O B:ARG240 4.9 39.0 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Folinic Acid and Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:33.1 occ:1.00 O B:HOH559 2.1 24.5 1.0 O B:HOH567 2.4 32.1 1.0 O B:ILE193 2.4 26.8 1.0 OH B:TYR105 2.4 22.7 1.0 O B:LYS190 2.5 30.1 1.0 CZ B:TYR105 3.5 21.1 1.0 C B:LYS190 3.6 30.0 1.0 C B:ILE193 3.6 26.1 1.0 CE2 B:TYR105 3.7 19.4 1.0 CA B:ASP194 4.1 28.6 1.0 N B:TYR195 4.2 26.3 1.0 O B:HOH528 4.2 22.5 1.0 CA B:LYS190 4.3 30.7 1.0 N B:ASP194 4.3 31.1 1.0 O B:HOH529 4.4 45.0 1.0 CB B:LYS190 4.4 35.7 1.0 CD2 B:TYR195 4.5 26.0 1.0 N B:LYS191 4.6 31.9 1.0 CA B:ILE193 4.6 26.5 1.0 N B:ILE193 4.6 26.7 1.0 CE1 B:TYR105 4.7 18.2 1.0 C B:ASP194 4.7 28.6 1.0 CA B:LYS191 4.8 31.2 1.0 CG B:LYS190 4.9 44.3 1.0 CB B:ILE193 5.0 28.6 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