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Sodium in PDB 5etk: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution:
2.7.6.3;

Protein crystallography data

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution, PDB code: 5etk was solved by M.L.Dennis, T.S.Peat, J.D.Swarbrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.68 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.790, 57.690, 38.450, 90.00, 115.57, 90.00
R / Rfree (%) 11.6 / 13.6

Other elements in 5etk:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution (pdb code 5etk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution, PDB code: 5etk:

Sodium binding site 1 out of 1 in 5etk

Go back to Sodium Binding Sites List in 5etk
Sodium binding site 1 out of 1 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:25.8
occ:1.00
 O A:HOH303 1.8 18.6 1.0
OD2 A:ASP139 2.2 11.9 1.0
O A:HOH443 2.3 36.0 1.0
O A:HOH373 2.6 28.7 1.0
CG A:ASP139 3.2 9.1 1.0
CB A:ASP139 3.8 8.6 1.0
O A:HOH357 4.1 31.9 1.0
OD1 A:ASP139 4.1 8.8 1.0
O A:HOH370 4.3 32.2 1.0
NZ A:LYS119 4.4 10.5 1.0
OE1 A:GLU141 4.4 11.6 1.0
O A:ASP139 4.8 7.3 1.0
O A:HOH419 4.9 41.8 1.0

Reference:

M.L.Dennis, N.P.Pitcher, M.D.Lee, A.J.Debono, Z.C.Wang, J.R.Harjani, R.Rahmani, B.Cleary, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002
Page generated: Mon Oct 7 20:50:58 2024

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