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Calcium 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
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

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 1.09 Angstrom Resolution (pdb code 5etk). 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 1.09 Angstrom Resolution, PDB code: 5etk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5etk

Go back to Calcium Binding Sites List in 5etk
Calcium binding site 1 out of 4 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:10.0
occ:1.00
 OE2 A:GLU87 2.4 13.3 1.0
O A:HOH380 2.4 23.8 1.0
OD2 A:ASP49 2.5 9.4 1.0
OD1 A:ASP49 2.5 7.2 1.0
OE1 A:GLU87 2.7 31.4 1.0
CG A:ASP49 2.9 6.7 1.0
CD A:GLU87 2.9 19.6 1.0
O A:HOH329 4.4 23.1 1.0
CB A:ASP49 4.4 6.7 1.0
CB A:PRO47 4.4 9.4 1.0
CG A:GLU87 4.4 20.9 1.0
O A:ASP49 4.6 5.7 1.0
O A:HOH311 4.7 27.3 1.0

Calcium binding site 2 out of 4 in 5etk

Go back to Calcium Binding Sites List in 5etk
Calcium binding site 2 out of 4 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:5.4
occ:1.00
 OD1 A:ASP97 2.3 7.4 1.0
OD1 A:ASP95 2.3 6.7 1.0
O A:HOH316 2.3 7.5 1.0
O2A A:APC201 2.3 7.1 1.0
O A:HOH394 2.3 7.6 1.0
O2B A:APC201 2.3 6.9 1.0
CG A:ASP95 3.2 5.3 1.0
PA A:APC201 3.4 7.9 1.0
CG A:ASP97 3.4 5.8 1.0
PB A:APC201 3.5 7.7 1.0
OD2 A:ASP95 3.5 6.9 1.0
C3A A:APC201 3.7 8.5 1.0
CA A:CA205 3.8 7.1 1.0
O5' A:APC201 3.8 8.8 1.0
OD2 A:ASP97 4.0 8.4 1.0
NH1 A:ARG82 4.3 11.9 1.0
O A:HOH309 4.3 15.2 1.0
O1B A:APC201 4.3 10.5 1.0
OE2 A:GLU77 4.4 6.5 0.7
O A:LEU96 4.5 5.8 1.0
OE2 A:GLU77 4.6 5.5 0.3
CB A:ASP95 4.6 4.9 1.0
NH2 A:ARG82 4.6 19.4 1.0
CB A:ASP97 4.6 5.5 1.0
O3B A:APC201 4.7 8.2 1.0
N3 A:APC201 4.7 5.2 1.0
C2 A:APC201 4.7 5.1 1.0
O1A A:APC201 4.8 9.7 1.0
CA A:ASP97 4.8 5.0 1.0
C A:LEU96 4.8 4.4 1.0
O3G A:APC201 4.8 9.0 1.0
N A:ASP97 4.9 4.8 1.0
N A:LEU96 4.9 4.7 1.0
CZ A:ARG82 4.9 12.8 1.0
O2G A:APC201 4.9 9.1 1.0

Calcium binding site 3 out of 4 in 5etk

Go back to Calcium Binding Sites List in 5etk
Calcium binding site 3 out of 4 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:7.1
occ:1.00
 OD2 A:ASP97 2.3 8.4 1.0
O A:HOH366 2.3 14.7 1.0
O2G A:APC201 2.4 9.1 1.0
O2B A:APC201 2.4 6.9 1.0
OD2 A:ASP95 2.4 6.9 1.0
O A:HOH418 2.4 13.4 1.0
CG A:ASP97 3.1 5.8 1.0
OD1 A:ASP97 3.3 7.4 1.0
PB A:APC201 3.4 7.7 1.0
CG A:ASP95 3.5 5.3 1.0
PG A:APC201 3.5 6.8 1.0
O3B A:APC201 3.6 8.2 1.0
CA A:CA204 3.8 5.4 1.0
OD1 A:ASP95 3.9 6.7 1.0
O1B A:APC201 4.1 10.5 1.0
NH1 A:ARG121 4.1 6.7 1.0
O A:HOH405 4.2 8.5 1.0
O3G A:APC201 4.2 9.0 1.0
NH1 A:ARG92 4.2 36.4 1.0
O A:HOH363 4.2 9.9 1.0
CB A:ASP97 4.5 5.5 1.0
N16 A:5RU202 4.6 10.9 1.0
NE2 A:HIS115 4.6 7.8 1.0
CE A:MET124 4.7 11.2 1.0
O1G A:APC201 4.7 7.8 1.0
CB A:ASP95 4.7 4.9 1.0
O A:HOH428 4.8 12.3 1.0
C3A A:APC201 5.0 8.5 1.0

Calcium binding site 4 out of 4 in 5etk

Go back to Calcium Binding Sites List in 5etk
Calcium binding site 4 out of 4 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 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 1.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:10.5
occ:1.00
 O A:ILE28 2.3 7.9 1.0
O A:HOH422 2.3 19.0 1.0
O A:HOH377 2.3 20.2 1.0
O A:SER31 2.4 9.9 1.0
O A:GLY26 2.6 12.1 1.0
O A:HOH330 2.7 11.8 1.0
C A:ILE28 3.4 7.7 1.0
C A:SER31 3.4 7.7 1.0
C A:GLY26 3.7 9.6 1.0
N A:SER31 3.9 7.6 1.0
N A:ILE28 4.0 7.6 1.0
CA A:SER31 4.1 7.5 1.0
C A:ASP27 4.1 7.8 1.0
CB A:SER31 4.3 7.8 1.0
CA A:ILE28 4.3 7.5 1.0
N A:PRO29 4.3 8.5 1.0
CA A:PRO29 4.4 9.5 1.0
CA A:ASP27 4.4 8.4 1.0
O A:HOH355 4.4 29.6 1.0
N A:ASP27 4.4 8.3 1.0
N A:HIS32 4.5 7.2 1.0
C A:PRO29 4.6 8.6 1.0
O A:ASP27 4.6 10.0 1.0
CA A:GLY26 4.7 10.4 1.0
O A:LEU25 4.7 8.7 1.0
O A:HOH429 4.7 21.8 1.0
N A:GLU30 4.8 8.9 1.0
CA A:HIS32 4.8 7.8 1.0
CB A:ILE28 5.0 7.0 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 05:40:54 2025

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