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Chlorine 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
Sodium (Na) 1 atom

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 1.09 Angstrom Resolution (pdb code 5etk). 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 1.09 Angstrom Resolution, PDB code: 5etk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5etk

Go back to Chlorine Binding Sites List in 5etk
Chlorine binding site 1 out of 2 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:14.7
occ:1.00
 O A:HOH441 3.0 24.6 1.0
O A:HOH440 3.0 25.6 1.0
CG A:ASP139 3.4 9.1 1.0
OD1 A:ASP139 3.4 8.8 1.0
NZ A:LYS119 3.5 10.5 1.0
N A:ASP139 3.6 6.6 1.0
CD A:PRO138 3.6 7.1 1.0
CB A:ASP139 3.7 8.6 1.0
CB A:PHE137 3.7 6.1 1.0
OD2 A:ASP139 3.8 11.9 1.0
CG A:PRO114 3.8 7.7 1.0
CE A:LYS119 3.9 9.2 1.0
N A:PRO138 3.9 6.2 1.0
O A:HOH357 4.0 31.9 1.0
CD2 A:PHE137 4.2 6.9 1.0
CB A:PRO138 4.3 7.5 1.0
CA A:ASP139 4.3 7.3 1.0
CG A:PRO138 4.3 7.6 1.0
CG A:PHE137 4.4 6.0 1.0
C A:PRO138 4.5 6.4 1.0
CA A:PRO138 4.5 6.8 1.0
C A:PHE137 4.6 6.2 1.0
CB A:PRO114 4.6 6.8 1.0
CD A:PRO114 4.6 7.8 1.0
CA A:PHE137 4.7 5.9 1.0

Chlorine binding site 2 out of 2 in 5etk

Go back to Chlorine Binding Sites List in 5etk
Chlorine binding site 2 out of 2 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:16.5
occ:1.00
 O A:HOH408 3.0 35.3 1.0
N A:THR93 3.3 6.5 1.0
N A:VAL83 3.3 11.1 1.0
CA A:ARG92 3.6 7.1 1.0
CA A:ARG82 3.6 9.4 1.0
CG2 A:THR93 3.7 9.9 1.0
OG1 A:THR93 3.8 9.6 1.0
O A:VAL83 3.9 19.5 1.0
C A:ARG92 3.9 6.3 1.0
O A:GLY81 3.9 14.1 1.0
CG A:ARG82 4.0 11.7 1.0
C A:ARG82 4.0 10.2 1.0
CB A:ARG92 4.0 7.8 1.0
CD1 A:LEU11 4.1 9.9 1.0
CB A:THR93 4.1 8.6 1.0
O A:PRO91 4.3 8.4 1.0
CA A:THR93 4.3 6.7 1.0
CA A:VAL83 4.3 12.5 1.0
CB A:ARG82 4.3 10.4 1.0
N A:ARG82 4.5 9.0 1.0
CB A:VAL83 4.5 16.4 1.0
C A:VAL83 4.5 12.4 1.0
C A:GLY81 4.5 11.1 1.0
N A:ARG92 4.7 6.5 1.0
C A:PRO91 4.9 6.4 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 01:49:19 2025

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