Atomistry » Calcium » PDB 5egt-5eyg » 5etp
Atomistry »
  Calcium »
    PDB 5egt-5eyg »
      5etp »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy