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Calcium 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
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 5etm

Go back to Calcium Binding Sites List in 5etm
Calcium 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 Calcium with other atoms in the Ca 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:Ca203

b:7.9
occ:1.00
 O A:HOH363 2.3 9.3 1.0
OD1 A:ASP97 2.3 9.9 1.0
O1A A:APC202 2.3 8.8 1.0
OD1 A:ASP95 2.3 8.3 1.0
O A:HOH332 2.3 7.8 1.0
O1B A:APC202 2.3 9.9 1.0
CG A:ASP95 3.3 8.4 1.0
OD2 A:ASP95 3.4 9.0 1.0
PA A:APC202 3.5 10.2 1.0
CG A:ASP97 3.5 9.1 1.0
PB A:APC202 3.5 11.1 1.0
C3A A:APC202 3.7 10.0 1.0
CA A:CA204 3.8 9.4 1.0
O5' A:APC202 3.8 10.6 1.0
OD2 A:ASP97 4.0 10.3 1.0
NH1 A:ARG82 4.2 20.4 1.0
O2B A:APC202 4.4 11.9 1.0
OE2 A:GLU77 4.4 11.0 1.0
O A:HOH302 4.4 18.6 1.0
O A:LEU96 4.4 7.4 1.0
O A:HOH357 4.5 9.4 1.0
NH2 A:ARG82 4.5 24.1 1.0
CB A:ASP95 4.7 7.2 1.0
CB A:ASP97 4.7 8.1 1.0
N3 A:APC202 4.7 7.6 1.0
C A:LEU96 4.7 7.1 1.0
O3B A:APC202 4.7 10.8 1.0
C2 A:APC202 4.8 7.5 1.0
O2A A:APC202 4.8 11.7 1.0
N A:LEU96 4.8 7.0 1.0
CA A:ASP97 4.8 7.7 1.0
CZ A:ARG82 4.8 21.8 1.0
O1G A:APC202 4.8 13.9 1.0
N A:ASP97 5.0 7.2 1.0

Calcium binding site 2 out of 2 in 5etm

Go back to Calcium Binding Sites List in 5etm
Calcium 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 Calcium with other atoms in the Ca 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:Ca204

b:9.4
occ:1.00
 OD2 A:ASP95 2.3 9.0 1.0
OD2 A:ASP97 2.3 10.3 1.0
O2G A:APC202 2.3 12.8 1.0
O A:HOH370 2.4 17.2 1.0
O A:HOH309 2.4 16.9 1.0
O1B A:APC202 2.4 9.9 1.0
CG A:ASP97 3.1 9.1 1.0
OD1 A:ASP97 3.3 9.9 1.0
PB A:APC202 3.4 11.1 1.0
CG A:ASP95 3.4 8.4 1.0
PG A:APC202 3.5 10.5 1.0
O3B A:APC202 3.6 10.8 1.0
CA A:CA203 3.8 7.9 1.0
OD1 A:ASP95 3.9 8.3 1.0
O A:HOH347 4.0 12.4 1.0
O2B A:APC202 4.1 11.9 1.0
NH1 A:ARG121 4.2 8.5 1.0
O1G A:APC202 4.2 13.9 1.0
NH1 A:ARG92 4.2 23.1 1.0
O A:HOH340 4.2 13.6 1.0
CB A:ASP97 4.5 8.1 1.0
N13 A:5RW201 4.5 13.2 1.0
CE A:MET124 4.7 11.9 1.0
CB A:ASP95 4.7 7.2 1.0
NE2 A:HIS115 4.7 13.1 1.0
O3G A:APC202 4.8 10.4 1.0
O A:HOH377 4.8 17.8 1.0
C3A A:APC202 4.9 10.0 1.0
O A:HOH363 4.9 9.3 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: Wed Jul 9 05:44:38 2025

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