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Sodium in PDB 5uin: X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60

Protein crystallography data

The structure of X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60, PDB code: 5uin 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 (°) 72.467, 59.457, 107.599, 90.00, 96.25, 90.00
R / Rfree (%) 18.8 / 25.2

Other elements in 5uin:

The structure of X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 (pdb code 5uin). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60, PDB code: 5uin:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5uin

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Sodium binding site 1 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


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 W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.5
occ:1.00
 O A:HOH557 2.4 20.0 1.0
O A:PHE85 2.5 20.8 1.0
O A:SER83 2.6 23.8 1.0
C A:PHE85 3.4 19.9 1.0
C A:SER83 3.5 24.9 1.0
CA A:ASN86 4.0 21.2 1.0
N A:ASN86 4.0 21.8 1.0
CA A:SER83 4.1 28.2 1.0
N A:PHE85 4.3 18.0 1.0
C A:LYS84 4.4 21.1 1.0
N A:LYS84 4.4 22.3 1.0
CA A:PHE85 4.5 19.7 1.0
OD1 A:ASN86 4.6 25.2 1.0
CA A:LYS84 4.6 22.8 1.0
CB A:ASN86 4.8 23.0 1.0
O A:PRO82 4.8 27.6 1.0
O A:LYS84 4.8 21.9 1.0
CB A:SER83 4.9 32.7 1.0

Sodium binding site 2 out of 6 in 5uin

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Sodium binding site 2 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


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 W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:28.1
occ:1.00
 O A:HOH522 2.2 18.8 1.0
O A:HOH565 2.3 26.7 1.0
O A:THR260 2.4 16.4 1.0
O A:HOH551 2.4 13.1 1.0
OG A:SER259 2.6 17.3 1.0
O A:SER241 2.6 26.1 1.0
C A:THR260 3.5 16.3 1.0
N A:THR260 3.6 15.2 1.0
O A:MET243 3.6 26.4 1.0
C A:SER241 3.7 25.7 1.0
CB A:SER259 3.8 17.1 1.0
O A:ASP262 3.8 17.8 1.0
N A:SER241 4.0 23.5 1.0
CA A:SER259 4.1 16.1 1.0
C A:SER259 4.2 14.7 1.0
CA A:SER241 4.2 23.2 1.0
CA A:THR260 4.2 14.9 1.0
CB A:SER241 4.3 23.2 1.0
OD2 A:ASP264 4.4 18.9 1.0
C A:ARG240 4.6 22.8 1.0
N A:ILE261 4.6 16.4 1.0
C A:ILE261 4.8 18.1 1.0
C A:MET243 4.8 28.9 1.0
C A:ASP262 4.8 16.5 1.0
N A:ILE242 4.8 27.0 1.0
N A:MET243 4.9 29.7 1.0
O A:ILE261 4.9 18.7 1.0
OG A:SER241 4.9 22.2 1.0
CA A:ILE261 5.0 19.1 1.0
C A:ILE242 5.0 30.9 1.0

Sodium binding site 3 out of 6 in 5uin

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Sodium binding site 3 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


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 W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:33.0
occ:1.00
 O A:HOH650 2.1 18.7 1.0
O A:HOH651 2.4 25.4 1.0
O A:HOH664 2.4 31.3 1.0
O A:LYS190 2.5 25.5 1.0
OH A:TYR105 2.5 18.1 1.0
O A:ILE193 2.5 19.6 1.0
CZ A:TYR105 3.6 16.4 1.0
C A:LYS190 3.6 24.6 1.0
C A:ILE193 3.7 19.6 1.0
CE2 A:TYR105 3.9 15.7 1.0
CA A:ASP194 4.3 23.0 1.0
CA A:LYS190 4.4 24.2 1.0
CB A:LYS190 4.4 26.2 1.0
N A:ASP194 4.4 21.5 1.0
N A:TYR195 4.5 22.9 1.0
CD2 A:TYR195 4.6 21.4 1.0
N A:LYS191 4.6 26.9 1.0
CE1 A:TYR105 4.8 14.3 1.0
CA A:LYS191 4.9 29.6 1.0
CG A:LYS190 4.9 31.1 1.0
CA A:ILE193 4.9 18.7 1.0
N A:ILE193 5.0 18.2 1.0
C A:ASP194 5.0 22.9 1.0

Sodium binding site 4 out of 6 in 5uin

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Sodium binding site 4 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


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 W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:5.3
occ:1.00
 O B:HOH573 1.6 41.2 1.0
O B:HOH623 2.2 17.2 1.0
O B:HOH590 2.2 13.4 1.0
O B:ILE57 2.2 18.8 1.0
O B:HOH567 2.4 12.8 1.0
O B:HOH661 2.6 12.2 1.0
C B:ILE57 3.4 17.2 1.0
O B:HOH638 4.0 22.4 1.0
CA B:ILE58 4.1 16.4 1.0
N B:ILE58 4.2 16.7 1.0
OE2 B:GLU62 4.5 16.6 1.0
OE1 B:GLU62 4.5 15.8 1.0
CA B:ILE57 4.6 17.0 1.0
CB B:ILE57 4.9 16.5 1.0
C B:ILE58 4.9 17.0 1.0
N B:ILE57 5.0 17.8 1.0
CD B:GLU62 5.0 16.2 1.0

Sodium binding site 5 out of 6 in 5uin

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Sodium binding site 5 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


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 W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:26.9
occ:1.00
 O B:THR260 2.2 17.8 1.0
O B:SER241 2.4 20.7 1.0
O B:HOH552 2.4 11.9 1.0
O B:HOH598 2.5 14.2 1.0
OG B:SER259 2.5 19.8 1.0
O B:HOH541 2.6 20.8 1.0
C B:THR260 3.4 18.8 1.0
C B:SER241 3.5 20.9 1.0
N B:THR260 3.6 18.4 1.0
O B:MET243 3.8 20.8 1.0
CB B:SER259 3.8 21.6 1.0
O B:ASP262 3.9 17.7 1.0
N B:SER241 3.9 23.1 1.0
CA B:SER241 4.1 19.5 1.0
CA B:THR260 4.2 17.7 1.0
CB B:SER241 4.2 17.6 1.0
CA B:SER259 4.2 22.4 1.0
C B:SER259 4.3 19.2 1.0
N B:ILE261 4.5 19.9 1.0
C B:ILE261 4.5 19.7 1.0
OD2 B:ASP264 4.5 21.4 1.0
NE2 A:HIS127 4.5 59.5 1.0
O B:ILE261 4.6 21.7 1.0
N B:ILE242 4.6 21.5 1.0
C B:ARG240 4.6 25.5 1.0
N B:ASP262 4.7 20.1 1.0
C B:ASP262 4.7 16.7 1.0
CA B:ILE261 4.8 19.0 1.0
OG B:SER241 4.8 16.0 1.0
N B:MET243 4.9 20.7 1.0
CD2 A:HIS127 4.9 52.2 1.0
C B:MET243 4.9 21.0 1.0
C B:ILE242 5.0 21.8 1.0

Sodium binding site 6 out of 6 in 5uin

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Sodium binding site 6 out of 6 in the X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the W305A Variant of the Fdtf N-Formyltransferase From Salmonella Enteric O60 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:25.9
occ:1.00
 O B:HOH634 2.1 21.9 1.0
O B:HOH631 2.3 25.0 1.0
O B:ILE193 2.3 17.6 1.0
O B:HOH666 2.4 31.3 1.0
O B:LYS190 2.4 24.5 1.0
OH B:TYR105 2.5 18.4 1.0
C B:ILE193 3.5 18.8 1.0
C B:LYS190 3.6 23.4 1.0
CZ B:TYR105 3.7 15.6 1.0
CA B:ASP194 4.0 23.2 1.0
CE2 B:TYR105 4.0 15.4 1.0
N B:ASP194 4.2 20.6 1.0
N B:TYR195 4.4 21.6 1.0
CA B:LYS190 4.4 26.8 1.0
CB B:LYS190 4.5 30.5 1.0
N B:LYS191 4.6 20.8 1.0
CA B:LYS191 4.7 20.0 1.0
CD2 B:TYR195 4.7 20.7 1.0
CG B:LYS190 4.7 40.4 1.0
CA B:ILE193 4.7 17.0 1.0
N B:ILE193 4.8 17.6 1.0
O B:HOH528 4.8 29.3 1.0
C B:ASP194 4.8 21.5 1.0
CE1 B:TYR105 4.9 15.2 1.0
O B:HOH650 4.9 35.1 1.0
OD1 B:ASP194 5.0 27.0 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 00:32:28 2024

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