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Calcium in PDB 5etp: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 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 1.05 Angstrom Resolution, PDB code: 5etp 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) 34.70 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.950, 57.770, 38.640, 90.00, 116.11, 90.00
R / Rfree (%) 10.7 / 12.5

Other elements in 5etp:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 3 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 1.05 Angstrom Resolution (pdb code 5etp). 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 1.05 Angstrom Resolution, PDB code: 5etp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5etp

Go back to Calcium Binding Sites List in 5etp
Calcium binding site 1 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 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 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:4.3
occ:1.00
 O A:HOH434 2.3 6.8 1.0
O A:ILE28 2.3 4.6 1.0
O A:HOH396 2.4 5.0 1.0
O A:SER31 2.4 4.8 1.0
O A:HOH361 2.5 4.7 1.0
O A:GLY26 2.6 4.8 1.0
C A:SER31 3.5 4.3 1.0
C A:ILE28 3.5 4.6 1.0
C A:GLY26 3.7 4.0 1.0
N A:ILE28 4.0 4.3 1.0
N A:SER31 4.1 4.5 1.0
CA A:SER31 4.2 4.6 1.0
C A:ASP27 4.2 4.8 1.0
CB A:SER31 4.3 4.7 1.0
CA A:ILE28 4.4 4.7 1.0
N A:PRO29 4.4 5.6 1.0
CA A:PRO29 4.4 5.5 1.0
N A:ASP27 4.4 4.0 1.0
CA A:ASP27 4.5 4.7 1.0
N A:HIS32 4.5 4.8 1.0
O A:LEU25 4.5 4.2 1.0
O A:HOH473 4.6 14.4 1.0
CA A:GLY26 4.6 4.0 1.0
C A:PRO29 4.6 5.1 1.0
O A:ASP27 4.7 6.5 1.0
CA A:HIS32 4.7 4.4 1.0
N A:GLU30 4.9 5.0 1.0
CB A:ILE28 5.0 4.4 1.0

Calcium binding site 2 out of 4 in 5etp

Go back to Calcium Binding Sites List in 5etp
Calcium binding site 2 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 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 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:6.0
occ:1.00
 OD2 A:ASP49 2.4 6.0 1.0
OE2 A:GLU87 2.4 8.8 1.0
O A:HOH448 2.4 10.9 1.0
O A:HOH405 2.5 13.2 1.0
OE1 A:GLU87 2.6 11.2 1.0
OD1 A:ASP49 2.6 5.0 1.0
CG A:ASP49 2.8 4.6 1.0
CD A:GLU87 2.9 9.0 1.0
O A:HOH303 3.9 12.1 1.0
O A:HOH423 4.1 18.5 1.0
CB A:ASP49 4.4 4.2 1.0
O A:HOH486 4.4 18.4 1.0
CG A:GLU87 4.4 9.0 1.0
CB A:PRO47 4.6 9.5 1.0
O A:ASP49 4.6 3.8 1.0
O A:HOH312 4.7 12.0 1.0

Calcium binding site 3 out of 4 in 5etp

Go back to Calcium Binding Sites List in 5etp
Calcium binding site 3 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 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 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:4.4
occ:1.00
 OD2 A:ASP97 2.3 8.0 1.0
O A:HOH356 2.3 7.8 1.0
O2B A:APC201 2.3 4.2 0.5
O2G A:APC201 2.4 5.1 0.5
O2B A:APC201 2.4 4.4 0.5
O2G A:APC201 2.4 5.1 0.5
OD2 A:ASP95 2.4 5.2 1.0
O A:HOH471 2.5 8.3 1.0
CG A:ASP97 3.1 5.2 1.0
OD1 A:ASP97 3.4 6.1 1.0
PB A:APC201 3.4 4.9 0.5
PB A:APC201 3.5 5.0 0.5
CG A:ASP95 3.5 4.0 1.0
O3B A:APC201 3.5 5.1 0.5
PG A:APC201 3.5 4.8 0.5
PG A:APC201 3.5 4.7 0.5
O3B A:APC201 3.6 5.4 0.5
CA A:CA205 3.8 3.8 1.0
OD1 A:ASP95 3.9 4.9 1.0
O1B A:APC201 4.0 6.0 0.5
O A:HOH438 4.1 6.5 1.0
NH1 A:ARG121 4.2 4.9 1.0
O1B A:APC201 4.2 6.4 0.5
O A:HOH407 4.2 6.9 1.0
O3G A:APC201 4.3 6.0 0.5
O3G A:APC201 4.3 6.0 0.5
NH1 A:ARG92 4.3 10.1 1.0
NE2 A:HIS115 4.5 5.8 1.0
CB A:ASP97 4.5 4.1 1.0
CE A:MET124 4.6 4.6 1.0
O1G A:APC201 4.7 5.3 0.5
N17 A:5RZ209 4.7 6.5 1.0
CB A:ASP95 4.7 3.6 1.0
O1G A:APC201 4.7 5.3 0.5
O A:HOH478 4.8 9.7 1.0
C13 A:5RZ209 4.8 13.2 1.0
C3A A:APC201 4.9 5.7 0.5
C3A A:APC201 4.9 5.6 0.5
O19 A:5RZ209 5.0 15.3 1.0

Calcium binding site 4 out of 4 in 5etp

Go back to Calcium Binding Sites List in 5etp
Calcium binding site 4 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 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 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:3.8
occ:1.00
 OD1 A:ASP97 2.3 6.1 1.0
OD1 A:ASP95 2.3 4.9 1.0
O2A A:APC201 2.3 4.9 0.5
O2A A:APC201 2.3 5.0 0.5
O A:HOH428 2.4 5.8 1.0
O2B A:APC201 2.4 4.4 0.5
O2B A:APC201 2.4 4.2 0.5
CG A:ASP95 3.3 4.0 1.0
CG A:ASP97 3.4 5.2 1.0
PA A:APC201 3.4 5.5 0.5
PA A:APC201 3.5 5.1 0.5
PB A:APC201 3.5 5.0 0.5
PB A:APC201 3.5 4.9 0.5
OD2 A:ASP95 3.6 5.2 1.0
C3A A:APC201 3.6 5.7 0.5
O5' A:APC201 3.7 6.3 0.5
C3A A:APC201 3.8 5.6 0.5
CA A:CA204 3.8 4.4 1.0
OD2 A:ASP97 4.0 8.0 1.0
O5' A:APC201 4.0 5.1 0.5
NH1 A:ARG82 4.2 8.5 1.0
O1B A:APC201 4.3 6.0 0.5
O1B A:APC201 4.3 6.4 0.5
O A:HOH316 4.4 16.7 1.0
C5' A:APC201 4.4 4.2 0.5
OE2 A:GLU77 4.4 5.3 1.0
O A:LEU96 4.5 4.4 1.0
NH2 A:ARG82 4.6 11.0 1.0
CB A:ASP95 4.6 3.6 1.0
CB A:ASP97 4.6 4.1 1.0
N3 A:APC201 4.7 3.7 0.5
C2 A:APC201 4.7 3.7 0.5
O3B A:APC201 4.7 5.1 0.5
N3 A:APC201 4.7 3.8 0.5
O3B A:APC201 4.8 5.4 0.5
O1A A:APC201 4.8 6.5 0.5
C2 A:APC201 4.8 3.7 0.5
O1A A:APC201 4.8 6.3 0.5
C A:LEU96 4.8 3.2 1.0
CA A:ASP97 4.8 3.4 1.0
O3G A:APC201 4.8 6.0 0.5
O3G A:APC201 4.8 6.0 0.5
N A:LEU96 4.9 2.8 1.0
CZ A:ARG82 4.9 7.4 1.0
N A:ASP97 4.9 3.3 1.0
O2G A:APC201 4.9 5.1 0.5
O2G A:APC201 4.9 5.1 0.5

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: Sun Jul 14 18:52:29 2024

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