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Chlorine 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
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5etm

Go back to Chlorine Binding Sites List in 5etm
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl207

b:21.2
occ:1.00
 N A:THR93 3.3 8.3 1.0
N A:VAL83 3.4 20.2 1.0
CA A:ARG92 3.5 9.9 1.0
O A:GLY81 3.6 26.4 1.0
CA A:ARG82 3.7 17.9 1.0
OG1 A:THR93 3.8 11.1 1.0
O A:VAL83 3.8 27.9 1.0
CG2 A:THR93 3.8 10.2 1.0
CB A:ARG92 3.9 11.6 1.0
C A:ARG92 4.0 9.6 1.0
C A:ARG82 4.0 18.2 1.0
O A:PRO91 4.2 10.6 1.0
CD1 A:LEU11 4.3 11.8 1.0
CB A:THR93 4.3 9.7 1.0
CA A:VAL83 4.4 22.1 1.0
NZ A:LYS85 4.4 33.8 1.0
C A:GLY81 4.4 19.1 1.0
CA A:THR93 4.4 7.9 1.0
N A:ARG82 4.4 16.9 1.0
CG A:ARG82 4.4 19.5 1.0
CB A:ARG82 4.5 18.5 1.0
CB A:VAL83 4.5 24.3 1.0
C A:VAL83 4.5 21.4 1.0
N A:ARG92 4.7 8.8 1.0
C A:PRO91 4.9 9.9 1.0
CE A:LYS85 4.9 31.0 1.0

Chlorine binding site 2 out of 2 in 5etm

Go back to Chlorine Binding Sites List in 5etm
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl208

b:36.0
occ:1.00
 N A:LYS85 3.3 19.0 1.0
O A:HOH322 3.4 25.6 1.0
O A:VAL83 4.0 27.9 1.0
O A:LYS85 4.0 24.3 1.0
CA A:LYS85 4.1 23.2 1.0
CB A:LYS85 4.1 25.4 1.0
O A:GLU87 4.2 22.1 1.0
CA A:ARG84 4.2 18.5 1.0
C A:ARG84 4.3 20.2 1.0
CE A:LYS85 4.3 31.0 1.0
C A:LYS85 4.4 23.8 1.0
O A:PRO91 4.4 10.6 1.0
CD A:ARG84 4.5 19.5 1.0
NH1 A:ARG84 4.5 24.3 1.0
CA A:GLY90 4.5 13.1 1.0
N A:GLY90 4.6 12.8 1.0
C A:GLY90 4.7 11.7 1.0
O A:GLY90 4.8 10.9 1.0
C A:VAL83 4.9 21.4 1.0
NE A:ARG84 4.9 20.3 1.0
CZ A:ARG84 5.0 22.9 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: Sat Jul 12 01:49:41 2025

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