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Sodium in PDB 5etm: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 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 1.46 Angstrom Resolution, PDB code: 5etm 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) 34.67 / 1.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.763, 57.631, 38.407, 90.00, 115.49, 90.00
R / Rfree (%) 20.4 / 23.9

Other elements in 5etm:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 2 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 1.46 Angstrom Resolution (pdb code 5etm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution, PDB code: 5etm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5etm

Go back to Sodium Binding Sites List in 5etm
Sodium binding site 1 out of 2 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 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 1.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:9.6
occ:1.00
 O A:HOH348 2.3 25.8 1.0
OD1 A:ASP49 2.5 11.5 1.0
OD2 A:ASP49 2.6 13.6 1.0
OE2 A:GLU87 2.8 29.1 1.0
CG A:ASP49 2.9 11.5 1.0
OE1 A:GLU87 3.1 34.5 1.0
CD A:GLU87 3.3 34.3 1.0
CB A:PRO47 4.2 12.2 1.0
CB A:ASP49 4.4 10.3 1.0
O A:ASP49 4.5 9.9 1.0
CG A:GLU87 4.8 30.9 1.0

Sodium binding site 2 out of 2 in 5etm

Go back to Sodium Binding Sites List in 5etm
Sodium binding site 2 out of 2 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:17.4
occ:1.00
 O A:SER31 2.3 12.5 1.0
O A:ILE28 2.3 13.0 1.0
O A:HOH317 2.8 23.1 1.0
O A:GLY26 2.9 13.8 1.0
C A:SER31 3.4 11.6 1.0
C A:ILE28 3.5 12.1 1.0
C A:GLY26 3.9 10.9 1.0
N A:ILE28 3.9 11.9 1.0
N A:SER31 3.9 11.4 1.0
CA A:SER31 4.1 11.5 1.0
C A:ASP27 4.1 12.8 1.0
CB A:SER31 4.3 11.7 1.0
CA A:ILE28 4.3 12.3 1.0
N A:PRO29 4.4 12.1 1.0
N A:HIS32 4.4 11.5 1.0
CA A:ASP27 4.4 12.2 1.0
CA A:PRO29 4.5 12.4 1.0
N A:ASP27 4.5 10.3 1.0
C A:PRO29 4.6 11.9 1.0
O A:ASP27 4.7 14.9 1.0
CA A:HIS32 4.7 11.7 1.0
N A:GLU30 4.7 13.0 1.0
CA A:GLY26 4.8 9.4 1.0
O A:LEU25 4.8 11.1 1.0
CB A:ILE28 5.0 11.6 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 20:51:05 2024

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