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Magnesium in PDB 6cck: Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile

Enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile

All present enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile, PDB code: 6cck was solved by M.Mamo, B.A.Appleton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.71 / 1.61
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 135.050, 135.050, 135.050, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.8

Other elements in 6cck:

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile (pdb code 6cck). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile, PDB code: 6cck:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6cck

Go back to Magnesium Binding Sites List in 6cck
Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:44.2
occ:1.00
 O1B A:ATP202 1.9 34.7 1.0
O1A A:ATP202 2.1 29.2 1.0
O A:HOH361 2.2 41.6 1.0
O2G A:ATP202 2.3 41.3 1.0
PB A:ATP202 2.8 32.9 1.0
O3B A:ATP202 3.0 36.9 1.0
PG A:ATP202 3.1 37.6 1.0
PA A:ATP202 3.3 24.9 1.0
O3A A:ATP202 3.3 27.8 1.0
O5' A:ATP202 3.9 23.3 1.0
O3G A:ATP202 4.1 28.3 1.0
NH1 A:ARG91 4.1 40.1 1.0
O A:HOH331 4.1 49.7 1.0
O2B A:ATP202 4.2 31.0 1.0
O1G A:ATP202 4.2 40.6 1.0
O2A A:ATP202 4.5 28.7 1.0
NZ A:LYS42 4.6 99.5 1.0
C2' A:ATP202 4.9 23.8 1.0
O A:HOH370 5.0 37.4 1.0

Magnesium binding site 2 out of 2 in 6cck

Go back to Magnesium Binding Sites List in 6cck
Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with (R)-3-(3-Chlorophenyl)-3-((5-Methyl-7- Oxo-4,7-Dihydro-[1,2,4]Triazolo[1,5-A]Pyrimidin-2-Yl)Amino) Propanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:50.8
occ:1.00
 O2B B:ATP202 1.9 39.5 1.0
O1A B:ATP202 2.0 34.6 1.0
O2G B:ATP202 2.5 50.6 1.0
O3B B:ATP202 2.5 43.1 1.0
O B:HOH400 2.6 63.4 1.0
PB B:ATP202 2.7 38.6 1.0
PG B:ATP202 3.1 46.1 1.0
PA B:ATP202 3.2 24.8 1.0
O3A B:ATP202 3.3 30.7 1.0
O B:HOH339 3.6 50.0 1.0
O5' B:ATP202 3.9 23.1 1.0
O1B B:ATP202 4.0 35.1 1.0
O3G B:ATP202 4.1 47.6 1.0
O1G B:ATP202 4.2 34.4 1.0
O B:HOH399 4.2 35.9 1.0
NH1 B:ARG91 4.3 30.3 1.0
O2A B:ATP202 4.4 30.8 1.0
OG1 B:THR10 4.9 20.0 0.5
C2' B:ATP202 5.0 23.8 1.0

Reference:

R.J.Moreau, C.K.Skepper, B.A.Appleton, A.Blechschmidt, C.J.Balibar, B.M.Benton, J.E.Drumm, B.Y.Feng, M.Geng, C.Li, M.K.Lindvall, A.Lingel, Y.Lu, M.Mamo, W.Mergo, V.Polyakov, T.M.Smith, K.Takeoka, K.Uehara, L.Wang, J.R.Wei, A.H.Weiss, L.Xie, W.Xu, Q.Zhang, J.De Vicente. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase From Gram-Negative Bacteria. J. Med. Chem. V. 61 3309 2018.
ISSN: ISSN 1520-4804
PubMed: 29498517
DOI: 10.1021/ACS.JMEDCHEM.7B01691
Page generated: Mon Sep 30 20:30:47 2024

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