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Calcium in PDB 5eto: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 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 1.07 Angstrom Resolution, PDB code: 5eto 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) 34.69 / 1.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.770, 57.750, 38.420, 90.00, 115.46, 90.00
R / Rfree (%) 12.9 / 15

Other elements in 5eto:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 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 1.07 Angstrom Resolution (pdb code 5eto). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution, PDB code: 5eto:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5eto

Go back to Calcium Binding Sites List in 5eto
Calcium binding site 1 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 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 1.07 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:5.0
occ:1.00
 OD1 A:ASP97 2.3 6.8 1.0
O2A A:APC202 2.3 6.5 1.0
OD1 A:ASP95 2.3 6.6 1.0
O A:HOH325 2.3 6.5 1.0
O2B A:APC202 2.4 6.6 1.0
O A:HOH396 2.4 7.0 1.0
CG A:ASP95 3.2 5.4 1.0
PA A:APC202 3.4 7.1 1.0
CG A:ASP97 3.4 5.5 1.0
PB A:APC202 3.5 7.6 1.0
OD2 A:ASP95 3.5 7.0 1.0
C3A A:APC202 3.7 7.8 1.0
CA A:CA204 3.8 7.0 1.0
O5' A:APC202 3.8 8.3 1.0
OD2 A:ASP97 4.0 8.3 1.0
NH1 A:ARG82 4.2 11.6 1.0
O A:HOH311 4.3 13.6 1.0
O1B A:APC202 4.3 10.4 1.0
OE2 A:GLU77 4.4 7.5 1.0
O A:LEU96 4.5 5.7 1.0
O A:HOH369 4.5 5.3 1.0
NH2 A:ARG82 4.6 20.6 1.0
CB A:ASP95 4.6 5.2 1.0
CB A:ASP97 4.6 5.7 1.0
N3 A:APC202 4.7 5.1 1.0
O3B A:APC202 4.7 8.0 1.0
C2 A:APC202 4.7 5.0 1.0
CA A:ASP97 4.8 5.3 1.0
O1A A:APC202 4.8 8.2 1.0
C A:LEU96 4.8 4.3 1.0
O2G A:APC202 4.9 8.9 1.0
N A:LEU96 4.9 4.7 1.0
N A:ASP97 4.9 4.8 1.0
CZ A:ARG82 4.9 13.6 1.0
O1G A:APC202 5.0 9.8 1.0
NH1 A:ARG92 5.0 24.7 1.0

Calcium binding site 2 out of 4 in 5eto

Go back to Calcium Binding Sites List in 5eto
Calcium binding site 2 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 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 1.07 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:7.0
occ:1.00
 OD2 A:ASP97 2.3 8.3 1.0
O A:HOH373 2.3 14.4 1.0
O1G A:APC202 2.3 9.8 1.0
O2B A:APC202 2.4 6.6 1.0
OD2 A:ASP95 2.4 7.0 1.0
O A:HOH413 2.5 13.3 1.0
CG A:ASP97 3.1 5.5 1.0
OD1 A:ASP97 3.3 6.8 1.0
CG A:ASP95 3.4 5.4 1.0
PB A:APC202 3.5 7.6 1.0
PG A:APC202 3.5 6.8 1.0
O3B A:APC202 3.6 8.0 1.0
CA A:CA203 3.8 5.0 1.0
OD1 A:ASP95 3.9 6.6 1.0
O1B A:APC202 4.1 10.4 1.0
NH1 A:ARG121 4.2 6.5 1.0
O2G A:APC202 4.2 8.9 1.0
O A:HOH401 4.2 8.8 1.0
NH1 A:ARG92 4.2 24.7 1.0
O A:HOH361 4.2 10.4 1.0
CB A:ASP97 4.5 5.7 1.0
N18 A:5RY201 4.5 10.4 1.0
NE2 A:HIS115 4.6 7.3 1.0
CB A:ASP95 4.7 5.2 1.0
CE A:MET124 4.7 10.8 1.0
O3G A:APC202 4.7 7.6 1.0
O A:HOH420 4.8 12.3 1.0
C3A A:APC202 5.0 7.8 1.0

Calcium binding site 3 out of 4 in 5eto

Go back to Calcium Binding Sites List in 5eto
Calcium binding site 3 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:9.2
occ:1.00
 OE2 A:GLU109 2.3 10.6 1.0
O A:HOH407 2.3 18.4 1.0
O A:HOH422 2.3 22.5 1.0
CD A:GLU109 3.4 11.3 1.0
CG A:GLU109 3.9 10.6 1.0
OE1 A:GLU109 4.5 14.8 1.0

Calcium binding site 4 out of 4 in 5eto

Go back to Calcium Binding Sites List in 5eto
Calcium binding site 4 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.07 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:11.0
occ:1.00
 O A:HOH375 2.1 19.2 1.0
OE2 A:GLU87 2.4 14.3 1.0
O A:HOH348 2.4 21.3 1.0
O A:HOH404 2.4 26.0 1.0
OD2 A:ASP49 2.5 9.9 1.0
OD1 A:ASP49 2.5 7.8 1.0
CG A:ASP49 2.9 7.2 1.0
CD A:GLU87 3.1 21.9 1.0
OE1 A:GLU87 3.2 37.5 1.0
CB A:PRO47 4.4 9.7 1.0
O A:HOH335 4.4 23.0 1.0
CB A:ASP49 4.4 7.0 1.0
CG A:GLU87 4.5 22.2 1.0
O A:ASP49 4.6 5.8 1.0
O A:HOH316 4.7 28.8 1.0
O A:HOH367 4.9 13.7 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 05:45:11 2025

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