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Sodium in PDB 5uij: X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp

Protein crystallography data

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

Resolution Low / High (Å) 97.75 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.910, 64.757, 97.757, 90.00, 90.54, 90.00
R / Rfree (%) 18.1 / 23.1

Sodium Binding Sites:

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

Sodium binding site 1 out of 5 in 5uij

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Sodium binding site 1 out of 5 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.0
occ:1.00
 O A:HOH597 2.3 22.3 1.0
O A:HOH588 2.3 19.2 1.0
O A:SER241 2.4 29.6 1.0
O A:THR260 2.4 19.0 1.0
OG A:SER259 2.4 23.7 1.0
O A:HOH637 2.5 20.1 1.0
C A:THR260 3.5 21.9 1.0
C A:SER241 3.5 33.1 1.0
N A:THR260 3.5 24.6 1.0
O A:MET243 3.7 22.7 1.0
CB A:SER259 3.7 21.9 1.0
O A:ASP262 3.9 20.7 1.0
N A:SER241 3.9 24.9 1.0
CA A:THR260 4.1 20.6 1.0
O A:HOH723 4.1 33.5 1.0
C A:SER259 4.1 21.5 1.0
CA A:SER241 4.1 27.9 1.0
CA A:SER259 4.1 24.4 1.0
O A:HOH638 4.2 31.8 1.0
OD2 A:ASP264 4.3 21.6 1.0
O A:HOH737 4.4 28.8 1.0
C A:ARG240 4.4 31.6 1.0
CB A:SER241 4.4 24.9 1.0
N A:ILE242 4.5 28.4 1.0
N A:ILE261 4.6 22.8 1.0
C A:ILE261 4.7 20.2 1.0
O A:ARG240 4.8 34.5 1.0
C A:ASP262 4.8 20.6 1.0
O A:ILE261 4.8 23.7 1.0
OG A:SER241 4.8 27.7 1.0
CA A:ILE242 4.8 28.5 1.0
C A:MET243 4.9 23.8 1.0
N A:ASP262 4.9 19.8 1.0
CA A:ILE261 4.9 21.8 1.0

Sodium binding site 2 out of 5 in 5uij

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Sodium binding site 2 out of 5 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:27.7
occ:1.00
 O A:ILE193 2.3 20.3 1.0
O A:LYS190 2.3 18.9 1.0
O A:HOH697 2.3 18.6 1.0
OH A:TYR105 2.4 23.3 1.0
O A:HOH714 2.4 30.6 1.0
O A:HOH729 2.5 22.5 1.0
C A:LYS190 3.4 18.7 1.0
CZ A:TYR105 3.4 20.4 1.0
C A:ILE193 3.5 19.4 1.0
CE2 A:TYR105 3.7 23.1 1.0
CA A:LYS190 4.1 19.5 1.0
CA A:ASP194 4.1 23.6 1.0
CB A:LYS190 4.2 23.1 1.0
O A:HOH547 4.2 31.4 1.0
O A:HOH747 4.2 35.8 1.0
O A:HOH756 4.2 32.0 1.0
N A:ASP194 4.3 20.3 1.0
O A:HOH611 4.3 32.6 1.0
N A:LYS191 4.4 18.5 1.0
N A:ILE193 4.5 14.8 1.0
N A:TYR195 4.5 18.3 1.0
CA A:ILE193 4.5 15.7 1.0
CA A:LYS191 4.6 25.6 1.0
CD2 A:TYR195 4.7 25.3 1.0
CE1 A:TYR105 4.7 18.1 1.0
CG A:LYS190 4.7 28.6 1.0
C A:LYS191 4.8 24.4 1.0
C A:ASP194 4.9 20.9 1.0

Sodium binding site 3 out of 5 in 5uij

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Sodium binding site 3 out of 5 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:32.2
occ:1.00
 O A:PHE85 2.3 22.3 1.0
O A:SER83 2.6 31.2 1.0
C A:PHE85 3.2 21.4 1.0
C A:SER83 3.8 31.1 1.0
CA A:ASN86 3.8 30.7 1.0
N A:ASN86 3.9 29.1 1.0
O A:HOH609 4.2 33.6 1.0
N A:PHE85 4.2 21.3 1.0
C A:LYS84 4.3 22.5 1.0
CA A:PHE85 4.3 21.1 1.0
O A:LYS84 4.5 19.8 1.0
N A:LYS84 4.7 27.7 1.0
CA A:LYS84 4.7 24.9 1.0
CA A:SER83 4.7 27.1 0.5
CA A:SER83 4.7 28.3 0.5
OG A:SER83 4.8 25.3 0.5
CB A:ASN86 4.8 36.2 1.0
C A:ASN86 4.8 34.3 1.0
OD1 A:ASN86 4.9 54.0 1.0

Sodium binding site 4 out of 5 in 5uij

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Sodium binding site 4 out of 5 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:30.0
occ:1.00
 O B:ILE193 2.2 21.2 1.0
O B:HOH719 2.3 36.0 1.0
O B:LYS190 2.3 27.5 1.0
O B:HOH733 2.4 30.7 1.0
O B:HOH687 2.4 25.7 1.0
OH B:TYR105 2.6 27.7 1.0
C B:ILE193 3.4 20.9 1.0
C B:LYS190 3.5 26.3 1.0
CZ B:TYR105 3.6 26.0 1.0
CE2 B:TYR105 3.8 22.5 1.0
CA B:ASP194 4.1 25.7 1.0
N B:ASP194 4.2 24.8 1.0
CA B:LYS190 4.3 27.8 1.0
N B:TYR195 4.4 20.2 1.0
N B:ILE193 4.4 16.7 1.0
CB B:LYS190 4.4 35.0 1.0
CA B:ILE193 4.5 19.5 1.0
N B:LYS191 4.5 22.8 1.0
CA B:LYS191 4.6 27.4 1.0
CD2 B:TYR195 4.6 19.6 1.0
CE1 B:TYR105 4.8 22.7 1.0
C B:LYS191 4.8 26.9 1.0
C B:ASP194 4.9 22.9 1.0
CB B:ILE193 4.9 18.1 1.0

Sodium binding site 5 out of 5 in 5uij

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Sodium binding site 5 out of 5 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enteric O60 in Complex with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:23.3
occ:1.00
 O B:HOH654 2.3 29.1 1.0
O B:THR260 2.3 18.5 1.0
O B:HOH603 2.4 18.4 1.0
O B:HOH543 2.4 20.2 1.0
O B:SER241 2.5 26.6 1.0
OG B:SER259 2.5 20.2 1.0
C B:THR260 3.5 17.5 1.0
N B:THR260 3.5 17.9 1.0
C B:SER241 3.6 27.8 1.0
O B:MET243 3.8 22.6 1.0
CB B:SER259 3.8 21.1 1.0
O B:ASP262 3.9 23.1 1.0
N B:SER241 3.9 25.5 1.0
CA B:THR260 4.1 16.8 1.0
CA B:SER241 4.2 27.0 1.0
C B:SER259 4.2 16.2 1.0
CA B:SER259 4.2 17.8 1.0
CB B:SER241 4.4 23.5 1.0
C B:ILE261 4.5 19.6 1.0
OD2 B:ASP264 4.5 22.8 1.0
N B:ILE261 4.5 18.1 1.0
C B:ARG240 4.6 29.9 1.0
O B:ILE261 4.6 20.8 1.0
N B:ILE242 4.7 29.1 1.0
C B:ASP262 4.7 22.8 1.0
N B:ASP262 4.8 16.9 1.0
CA B:ILE261 4.8 18.8 1.0
OG B:SER241 4.8 24.1 1.0
OG1 B:THR260 4.9 18.0 1.0
CG B:PRO245 4.9 25.3 1.0
O B:HOH778 4.9 23.3 1.0
N B:MET243 5.0 24.2 1.0

Reference:

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
Page generated: Tue Oct 8 00:32:04 2024

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