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Calcium in PDB 5etn: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 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 1.40 Angstrom Resolution, PDB code: 5etn 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) 34.96 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.880, 57.890, 38.610, 90.00, 115.12, 90.00
R / Rfree (%) 18.2 / 21.9

Other elements in 5etn:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
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 1.40 Angstrom Resolution (pdb code 5etn). 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 1.40 Angstrom Resolution, PDB code: 5etn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5etn

Go back to Calcium Binding Sites List in 5etn
Calcium binding site 1 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 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 1.40 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:7.3
occ:1.00
 OD1 A:ASP97 2.2 10.5 1.0
O A:HOH368 2.3 11.1 1.0
O A:HOH353 2.3 10.5 1.0
O1A A:ATP205 2.3 8.8 1.0
O1B A:ATP205 2.4 10.7 1.0
OD1 A:ASP95 2.4 8.9 1.0
CG A:ASP95 3.2 8.0 1.0
CG A:ASP97 3.3 8.3 1.0
PA A:ATP205 3.4 10.0 1.0
PB A:ATP205 3.5 9.7 1.0
OD2 A:ASP95 3.5 9.9 1.0
OD2 A:ASP97 3.7 13.7 1.0
O3A A:ATP205 3.7 14.0 1.0
CA A:CA202 3.8 10.6 1.0
O5' A:ATP205 3.8 11.5 1.0
O A:HOH306 4.3 15.1 1.0
NH2 A:ARG82 4.3 30.7 1.0
OE2 A:GLU77 4.3 9.2 1.0
O2B A:ATP205 4.3 16.6 1.0
O A:HOH350 4.5 7.7 1.0
NH1 A:ARG82 4.5 18.1 1.0
O A:LEU96 4.5 8.8 1.0
CB A:ASP97 4.6 9.4 1.0
CB A:ASP95 4.6 7.5 1.0
O2A A:ATP205 4.7 14.1 1.0
CZ A:ARG82 4.7 24.0 1.0
O3B A:ATP205 4.8 9.2 1.0
C2 A:ATP205 4.8 6.5 1.0
C A:LEU96 4.8 5.7 1.0
N3 A:ATP205 4.8 8.2 1.0
CA A:ASP97 4.8 7.6 1.0
O1G A:ATP205 4.9 11.6 1.0
N A:LEU96 4.9 6.6 1.0
NH2 A:ARG92 4.9 34.6 1.0
O2G A:ATP205 4.9 9.7 1.0
N A:ASP97 5.0 5.2 1.0

Calcium binding site 2 out of 4 in 5etn

Go back to Calcium Binding Sites List in 5etn
Calcium binding site 2 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 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 1.40 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:10.6
occ:1.00
 O A:HOH397 2.2 25.1 1.0
OD2 A:ASP97 2.2 13.7 1.0
O2G A:ATP205 2.3 9.7 1.0
O A:HOH314 2.3 19.4 1.0
O1B A:ATP205 2.4 10.7 1.0
OD2 A:ASP95 2.4 9.9 1.0
CG A:ASP97 3.2 8.3 1.0
PB A:ATP205 3.5 9.7 1.0
CG A:ASP95 3.5 8.0 1.0
OD1 A:ASP97 3.5 10.5 1.0
PG A:ATP205 3.5 9.2 1.0
O3B A:ATP205 3.7 9.2 1.0
CA A:CA201 3.8 7.3 1.0
OD1 A:ASP95 4.0 8.9 1.0
NH2 A:ARG92 4.0 34.6 1.0
O2B A:ATP205 4.1 16.6 1.0
O A:HOH364 4.1 15.6 1.0
NH1 A:ARG121 4.1 6.5 1.0
O1G A:ATP205 4.2 11.6 1.0
O A:HOH318 4.2 16.0 1.0
CB A:ASP97 4.5 9.4 1.0
N16 A:5RX206 4.6 15.1 1.0
O A:HOH399 4.6 28.8 1.0
O3G A:ATP205 4.7 9.7 1.0
CB A:ASP95 4.8 7.5 1.0
NE2 A:HIS115 4.8 8.1 1.0
O3A A:ATP205 4.9 14.0 1.0
O A:HOH368 5.0 11.1 1.0

Calcium binding site 3 out of 4 in 5etn

Go back to Calcium Binding Sites List in 5etn
Calcium binding site 3 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 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 1.40 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:12.9
occ:1.00
 O A:ILE28 2.2 9.4 1.0
O A:SER31 2.3 12.4 1.0
O A:HOH394 2.3 27.5 1.0
O A:HOH385 2.4 25.0 1.0
O A:GLY26 2.5 13.9 1.0
O A:HOH316 3.2 30.1 1.0
C A:ILE28 3.4 7.7 1.0
C A:SER31 3.5 10.8 1.0
C A:GLY26 3.7 11.6 1.0
N A:SER31 4.0 8.2 1.0
N A:ILE28 4.0 8.0 1.0
C A:ASP27 4.1 9.4 1.0
CA A:SER31 4.2 10.0 1.0
CA A:ILE28 4.3 7.2 1.0
N A:PRO29 4.3 9.7 1.0
CA A:PRO29 4.3 12.3 1.0
CA A:ASP27 4.3 11.6 1.0
O A:HOH367 4.4 35.4 1.0
CB A:SER31 4.5 8.8 1.0
N A:ASP27 4.5 9.1 1.0
C A:PRO29 4.5 9.3 1.0
N A:HIS32 4.5 9.9 1.0
O A:ASP27 4.5 12.1 1.0
N A:GLU30 4.6 10.8 1.0
CA A:GLY26 4.8 11.6 1.0
CA A:HIS32 4.8 10.4 1.0
CD2 A:HIS32 4.8 31.4 1.0
O A:LEU25 4.9 10.5 1.0

Calcium binding site 4 out of 4 in 5etn

Go back to Calcium Binding Sites List in 5etn
Calcium binding site 4 out of 4 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.40 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 1.40 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:19.9
occ:1.00
 O A:HOH348 2.1 12.0 1.0
O A:HOH309 2.2 28.2 1.0
OD1 A:ASP49 2.5 11.8 1.0
O A:HOH391 2.5 34.3 1.0
OD2 A:ASP49 2.6 15.2 1.0
OE2 A:GLU87 2.7 17.2 1.0
CG A:ASP49 2.9 10.5 1.0
OE1 A:GLU87 3.1 43.2 1.0
CD A:GLU87 3.3 24.2 1.0
CB A:PRO47 4.2 14.7 1.0
CB A:ASP49 4.4 8.0 1.0
O A:ASP49 4.6 9.0 1.0
CG A:GLU87 4.8 29.0 1.0
CG A:PRO47 5.0 14.6 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: Sun Jul 14 18:50:36 2024

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