Magnesium in PDB 6aps: Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid

Enzymatic activity of Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid

All present enzymatic activity of Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid:
2.4.2.8;

Protein crystallography data

The structure of Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid, PDB code: 6aps was solved by D.Teran, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.58 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.013, 93.885, 44.715, 90.00, 107.80, 90.00
R / Rfree (%) 15.8 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid (pdb code 6aps). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid, PDB code: 6aps:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6aps

Go back to Magnesium Binding Sites List in 6aps
Magnesium binding site 1 out of 2 in the Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.1
occ:1.00
 O A:HOH516 2.3 53.2 1.0
OAH A:SV2301 2.3 47.8 1.0
O A:HOH526 2.3 40.9 1.0
O A:HOH416 2.5 47.6 1.0
OD1 A:ASP173 2.7 20.9 1.0
O A:HOH405 3.0 51.9 1.0
O A:HOH536 3.0 43.6 1.0
PBA A:SV2301 3.3 42.3 1.0
OAD A:SV2301 3.4 45.7 1.0
OAS A:SV2301 3.5 29.9 1.0
CG A:ASP173 3.6 23.8 1.0
OD2 A:ASP173 3.7 20.3 1.0
CAM A:SV2301 3.9 35.7 1.0
NH1 A:ARG179 4.4 14.6 1.0
OAG A:SV2301 4.7 42.0 1.0
NH2 A:ARG179 4.7 11.7 1.0
CAK A:SV2301 4.7 25.6 1.0
N3 A:SV2301 4.8 15.0 1.0
O A:ASP173 5.0 16.3 1.0
O A:HOH472 5.0 33.7 1.0

Magnesium binding site 2 out of 2 in 6aps

Go back to Magnesium Binding Sites List in 6aps
Magnesium binding site 2 out of 2 in the Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypanosoma Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3 Diyl)Bis(Oxy) ]Bis(Methylene))Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:40.5
occ:1.00
 O B:HOH409 2.0 36.3 1.0
O B:HOH510 2.2 35.5 1.0
OAG B:SV2301 2.2 38.1 1.0
OD1 B:ASP173 2.2 17.9 1.0
O B:HOH416 2.8 98.8 1.0
CG B:ASP173 3.1 21.2 1.0
OD2 B:ASP173 3.2 17.5 1.0
PBA B:SV2301 3.4 34.9 1.0
O B:HOH447 3.6 20.7 0.4
O B:HOH536 3.8 41.1 1.0
OAD B:SV2301 3.8 38.4 1.0
OAS B:SV2301 3.8 26.8 1.0
NH2 B:ARG179 3.9 14.9 1.0
CAM B:SV2301 4.1 29.8 1.0
NH1 B:ARG179 4.3 14.1 1.0
CB B:ASP173 4.5 10.9 1.0
CZ B:ARG179 4.6 13.5 1.0
O B:ASP173 4.6 14.7 1.0
OAH B:SV2301 4.7 31.9 1.0
N3 B:SV2301 4.8 14.8 1.0
O B:HOH447 4.8 20.0 0.6
N2 B:SV2301 4.8 14.5 1.0
N B:ASP173 4.8 10.6 1.0
NE2 B:GLN176 4.8 20.4 1.0

Reference:

E.Dolezelova, D.Teran, O.Gahura, Z.Kotrbova, M.Prochazkova, D.Keough, P.Spacek, D.Hockova, L.Guddat, A.Zikova. Evaluation of the Trypanosoma Brucei 6-Oxopurine Salvage Pathway As A Potential Target For Drug Discovery. Plos Negl Trop Dis V. 12 06301 2018.
ISSN: ESSN 1935-2735
PubMed: 29481567
DOI: 10.1371/JOURNAL.PNTD.0006301
Page generated: Mon Dec 14 22:21:02 2020

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