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Magnesium in PDB 4crj: Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor

Enzymatic activity of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor

All present enzymatic activity of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor:
2.7.6.3;

Protein crystallography data

The structure of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor, PDB code: 4crj was solved by M.L.Dennis, J.D.Swarbrick, T.S.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.17 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 82.480, 82.480, 52.173, 90.00, 90.00, 120.00
R / Rfree (%) 16.269 / 19.961

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor (pdb code 4crj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor, PDB code: 4crj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4crj

Go back to Magnesium Binding Sites List in 4crj
Magnesium binding site 1 out of 2 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1160

b:18.9
occ:1.00
O1B A:APC1159 2.1 17.9 1.0
O A:HOH2047 2.1 14.2 1.0
O1A A:APC1159 2.1 20.7 1.0
O A:HOH2034 2.1 19.2 1.0
OD1 A:ASP97 2.1 16.2 1.0
OD1 A:ASP95 2.1 17.2 1.0
CG A:ASP95 3.1 18.4 1.0
CG A:ASP97 3.2 17.1 1.0
PB A:APC1159 3.2 20.6 1.0
PA A:APC1159 3.3 20.9 1.0
OD2 A:ASP95 3.3 19.1 1.0
MG A:MG1161 3.5 18.8 1.0
C3A A:APC1159 3.5 19.7 1.0
OD2 A:ASP97 3.6 17.5 1.0
O3G A:APC1159 3.9 21.2 1.0
C5' A:APC1159 4.0 25.5 1.0
O5' A:APC1159 4.1 23.5 1.0
OE2 A:GLU78 4.2 30.9 1.0
O A:HOH2033 4.2 37.9 1.0
O2B A:APC1159 4.2 19.2 1.0
O A:VAL96 4.3 19.0 1.0
NH1 A:ARG83 4.4 26.0 1.0
O3B A:APC1159 4.4 19.9 1.0
CB A:ASP95 4.5 18.3 1.0
CB A:ASP97 4.5 18.0 1.0
O2A A:APC1159 4.5 20.2 1.0
PG A:APC1159 4.6 19.1 1.0
N3 A:APC1159 4.6 22.3 1.0
C2 A:APC1159 4.6 20.8 1.0
O1G A:APC1159 4.6 19.4 1.0
C A:VAL96 4.6 18.1 1.0
N A:VAL96 4.7 18.1 1.0
CA A:ASP97 4.7 18.0 1.0
O A:HOH2045 4.8 19.9 1.0
N A:ASP97 4.9 18.1 1.0
NH1 A:ARG92 4.9 23.1 1.0
CA A:ASP95 4.9 18.9 1.0

Magnesium binding site 2 out of 2 in 4crj

Go back to Magnesium Binding Sites List in 4crj
Magnesium binding site 2 out of 2 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1161

b:18.8
occ:1.00
OD2 A:ASP97 2.0 17.5 1.0
O1G A:APC1159 2.1 19.4 1.0
O A:HOH2045 2.1 19.9 1.0
O A:HOH2046 2.1 20.0 1.0
OD2 A:ASP95 2.2 19.1 1.0
O1B A:APC1159 2.2 17.9 1.0
CG A:ASP97 3.1 17.1 1.0
PG A:APC1159 3.2 19.1 1.0
PB A:APC1159 3.2 20.6 1.0
CG A:ASP95 3.3 18.4 1.0
OD1 A:ASP97 3.3 16.2 1.0
O3B A:APC1159 3.4 19.9 1.0
MG A:MG1160 3.5 18.9 1.0
O3G A:APC1159 3.6 21.2 1.0
OD1 A:ASP95 3.7 17.2 1.0
O2B A:APC1159 3.7 19.2 1.0
O A:HOH2048 3.9 21.8 1.0
O A:HOH2007 4.0 24.6 1.0
O A:HOH2044 4.0 24.3 1.0
NH1 A:ARG121 4.2 20.1 1.0
NH1 A:ARG92 4.2 23.1 1.0
O A:HOH2047 4.3 14.2 1.0
CB A:ASP97 4.4 18.0 1.0
N1 A:YH51163 4.5 22.2 1.0
O2G A:APC1159 4.5 19.1 1.0
CB A:ASP95 4.5 18.3 1.0
C3A A:APC1159 4.8 19.7 1.0
O1 A:YH51163 4.9 19.6 1.0
NE2 A:HIS115 4.9 21.9 1.0
O1A A:APC1159 4.9 20.7 1.0
C6 A:YH51163 5.0 34.1 1.0

Reference:

M.L.Dennis, S.Chhabra, Z.Wang, A.Debono, O.Dolezal, J.Newman, N.P.Pitcher, R.Rahmani, B.Cleary, N.Barlow, M.Hattarki, B.Graham, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives As Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase From Staphylococcus Aureus. J.Med.Chem. V. 57 9612 2014.
ISSN: ISSN 0022-2623
PubMed: 25357262
DOI: 10.1021/JM501417F
Page generated: Mon Dec 14 11:41:42 2020

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