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Sodium in PDB 5uil: X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate

Protein crystallography data

The structure of X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate, PDB code: 5uil 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.671, 72.812, 191.738, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 27

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate (pdb code 5uil). 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 Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate, PDB code: 5uil:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5uil

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Sodium binding site 1 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate


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 Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:18.5
occ:1.00
 O A:SER241 2.4 16.1 1.0
O A:HOH555 2.4 10.2 1.0
O A:THR260 2.4 15.0 1.0
O A:HOH560 2.4 15.3 1.0
OG A:SER259 2.6 23.7 1.0
O A:HOH520 2.6 13.8 1.0
C A:SER241 3.4 20.6 1.0
C A:THR260 3.6 14.3 1.0
O A:ASP262 3.7 16.9 1.0
N A:SER241 3.7 24.8 1.0
N A:THR260 3.7 14.2 1.0
NE2 B:HIS127 3.8 30.1 1.0
O A:MET243 3.9 23.4 1.0
CB A:SER259 3.9 21.5 1.0
CA A:SER241 4.0 22.0 1.0
O A:ILE261 4.2 12.8 1.0
CB A:SER241 4.3 19.8 1.0
CA A:SER259 4.3 18.8 1.0
CA A:THR260 4.4 13.9 1.0
C A:ILE261 4.4 14.5 1.0
C A:SER259 4.4 15.9 1.0
C A:ARG240 4.5 22.8 1.0
OD2 A:ASP264 4.5 15.7 1.0
N A:ILE242 4.6 21.9 1.0
C A:ASP262 4.6 15.8 1.0
CE1 B:HIS127 4.6 30.0 1.0
N A:ILE261 4.6 15.2 1.0
N A:ASP262 4.7 13.8 1.0
CD2 B:HIS127 4.8 27.4 1.0
CA A:ILE261 4.8 14.3 1.0
OG A:SER241 4.9 19.7 1.0
O A:HOH652 5.0 18.4 1.0

Sodium binding site 2 out of 4 in 5uil

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Sodium binding site 2 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate


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 Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:39.0
occ:1.00
 O A:HOH609 2.1 21.1 1.0
O A:ILE193 2.3 18.6 1.0
O A:HOH633 2.4 15.4 1.0
O A:HOH639 2.4 25.2 1.0
O A:LYS190 2.4 30.9 1.0
OH A:TYR105 2.6 18.3 1.0
C A:LYS190 3.5 31.3 1.0
C A:ILE193 3.5 20.5 1.0
CZ A:TYR105 3.6 17.5 1.0
CE2 A:TYR105 3.8 16.7 1.0
CA A:ASP194 4.1 25.8 1.0
CA A:LYS190 4.2 33.1 1.0
N A:ASP194 4.3 23.5 1.0
CB A:LYS190 4.3 37.4 1.0
N A:TYR195 4.4 28.5 1.0
O A:HOH570 4.4 28.6 1.0
N A:LYS191 4.5 33.7 1.0
CA A:ILE193 4.6 20.5 1.0
CD2 A:TYR195 4.7 25.6 1.0
N A:ILE193 4.7 20.4 1.0
CA A:LYS191 4.7 35.4 1.0
OD2 A:ASP194 4.7 27.5 1.0
CE1 A:TYR105 4.8 17.6 1.0
C A:ASP194 4.8 25.6 1.0
O A:HOH607 4.9 22.8 1.0
C A:LYS191 4.9 28.3 1.0
CG A:LYS190 4.9 45.8 1.0

Sodium binding site 3 out of 4 in 5uil

Go back to Sodium Binding Sites List in 5uil
Sodium binding site 3 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate


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 Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:23.6
occ:1.00
 O B:THR260 2.3 18.5 1.0
O B:HOH513 2.4 25.7 1.0
O B:HOH563 2.4 14.1 1.0
O B:SER241 2.5 27.8 1.0
O B:HOH521 2.6 20.6 1.0
OG B:SER259 2.6 27.4 1.0
C B:THR260 3.5 19.4 1.0
C B:SER241 3.6 29.4 1.0
NE2 A:HIS127 3.7 46.5 1.0
N B:THR260 3.7 20.8 1.0
O B:ASP262 3.7 21.2 1.0
CB B:SER259 3.9 27.3 1.0
O B:MET243 4.0 30.9 1.0
N B:SER241 4.1 29.3 1.0
CA B:SER241 4.3 27.3 1.0
CA B:THR260 4.3 20.0 1.0
C B:ILE261 4.3 19.5 1.0
C B:SER259 4.4 22.4 1.0
O B:ILE261 4.4 17.1 1.0
CA B:SER259 4.4 26.0 1.0
C B:ARG240 4.4 29.8 1.0
CE1 A:HIS127 4.5 43.6 1.0
N B:ILE261 4.5 20.0 1.0
CB B:SER241 4.6 26.6 1.0
N B:ILE242 4.6 32.1 1.0
OD2 B:ASP264 4.6 24.5 1.0
C B:ASP262 4.6 19.3 1.0
N B:ASP262 4.6 19.2 1.0
CD2 A:HIS127 4.7 44.0 1.0
CA B:ILE261 4.7 19.4 1.0
O B:ARG240 4.7 31.6 1.0
OG B:SER241 4.9 26.7 1.0
CA B:ILE242 5.0 33.5 1.0
CA B:ARG240 5.0 29.2 1.0
CA B:ASP262 5.0 18.2 1.0
OG1 B:THR260 5.0 16.4 1.0

Sodium binding site 4 out of 4 in 5uil

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Sodium binding site 4 out of 4 in the X-Ray Structure of the Fdtf N-Formyltransferase From Salmonella Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate


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 Enterica O60 in Complex with Tdp-FUC3N and Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:30.6
occ:1.00
 O B:HOH622 2.3 15.7 1.0
O B:HOH632 2.3 19.7 1.0
O B:HOH647 2.4 15.3 1.0
O B:ILE193 2.4 21.7 1.0
O B:LYS190 2.5 27.6 1.0
OH B:TYR105 2.7 16.6 1.0
C B:LYS190 3.6 27.7 1.0
C B:ILE193 3.6 21.3 1.0
CZ B:TYR105 3.8 15.2 1.0
O B:HOH503 3.8 22.1 1.0
CE2 B:TYR105 4.1 14.4 1.0
CA B:ASP194 4.1 24.8 1.0
N B:ASP194 4.3 24.2 1.0
CA B:LYS190 4.3 25.3 1.0
O B:HOH531 4.4 19.7 1.0
CB B:LYS190 4.4 31.7 1.0
N B:TYR195 4.4 25.1 1.0
N B:LYS191 4.5 27.4 1.0
CA B:LYS191 4.7 27.7 1.0
CD2 B:TYR195 4.7 22.6 1.0
CA B:ILE193 4.7 21.2 1.0
N B:ILE193 4.8 22.8 1.0
O B:HOH588 4.9 21.3 1.0
C B:ASP194 4.9 25.4 1.0
CE1 B:TYR105 5.0 14.8 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 Dec 15 11:42:11 2020

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