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Sodium in PDB 4uio: Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative

Enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative

All present enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative:
4.2.1.10;

Protein crystallography data

The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative, PDB code: 4uio was solved by J.M.Otero, A.L.Llamas-Saiz, L.Tizon, E.Lence, P.Thompson, A.R.Hawkins, C.Gonzalez-Bello, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.63 / 1.35
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.399, 42.327, 84.828, 90.00, 105.13, 90.00
R / Rfree (%) 17.4 / 21.4

Other elements in 4uio:

The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative (pdb code 4uio). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative, PDB code: 4uio:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4uio

Go back to Sodium Binding Sites List in 4uio
Sodium binding site 1 out of 2 in the Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1256

b:12.4
occ:1.00
 O A:HOH2012 2.7 8.7 1.0
O A:HOH2006 2.7 8.1 1.0
NE A:ARG159 2.9 7.6 1.0
NH2 A:ARG159 3.3 12.1 1.0
CZ A:ARG159 3.6 10.4 1.0
CG A:ARG159 3.8 6.4 1.0
CD A:ARG159 3.9 6.7 1.0
CB A:ARG159 4.0 5.8 1.0
O A:HOH2075 4.1 22.2 1.0
O A:HOH2015 4.5 12.3 1.0
NE2 A:GLN162 4.5 7.1 1.0
O A:TYR195 4.6 7.5 1.0
CD1 A:TYR195 4.7 9.0 1.0
CA A:ARG159 4.8 6.0 1.0
NH1 A:ARG159 4.9 12.5 1.0
CB A:TYR195 4.9 7.2 1.0
O A:ARG159 4.9 5.8 1.0

Sodium binding site 2 out of 2 in 4uio

Go back to Sodium Binding Sites List in 4uio
Sodium binding site 2 out of 2 in the Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Salmonella Typhi Type I Dehydroquinase Covalently Inhibited By A 3-Dehydroquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1257

b:5.2
occ:1.00
 O A:HOH2185 3.0 18.7 1.0
NE A:ARG102 3.2 8.4 1.0
O A:HOH2058 3.2 8.8 1.0
OH A:TYR130 3.7 7.3 1.0
CD A:ARG102 3.8 7.8 1.0
CZ A:TYR130 3.9 6.5 1.0
CB A:ARG102 4.0 7.1 1.0
CZ A:ARG102 4.2 7.8 1.0
NH2 A:ARG102 4.3 9.3 1.0
OD2 A:ASP106 4.3 7.1 1.0
CE1 A:TYR130 4.4 7.6 1.0
CE2 A:TYR130 4.4 5.9 1.0
CG A:ARG102 4.5 7.4 1.0

Reference:

C.Gonzalez-Bello, L.Tizon, E.Lence, J.M.Otero, M.J.Van Raaij, M.Martinez-Guitian, A.Beceiro, P.Thompson, A.R.Hawkins. Chemical Modification of A Dehydratase Enzyme Involved in Bacterial Virulence By An Ammonium Derivative: Evidence of Its Active Site Covalent Adduct. J.Am.Chem.Soc. V. 137 9333 2015.
ISSN: ISSN 0002-7863
PubMed: 26148116
DOI: 10.1021/JACS.5B04080
Page generated: Mon Oct 7 18:40:40 2024

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