Magnesium in PDB 8ts4: Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine

Enzymatic activity of Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine

All present enzymatic activity of Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine, PDB code: 8ts4 was solved by L.W.Guddat, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 2.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.031, 93.031, 105.701, 90, 90, 90
R / Rfree (%) 17.1 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine (pdb code 8ts4). 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 T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine, PDB code: 8ts4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8ts4

Go back to Magnesium Binding Sites List in 8ts4
Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine


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 T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:40.4
occ:1.00
 O A:HOH515 1.9 39.5 1.0
O04 A:KFF302 1.9 28.9 1.0
O A:HOH415 2.1 42.2 1.0
H061 A:KFF302 2.6 44.6 1.0
O A:HOH505 3.1 35.4 1.0
P02 A:KFF302 3.1 38.0 1.0
C06 A:KFF302 3.3 37.1 1.0
H062 A:KFF302 3.4 44.6 1.0
C05 A:KFF302 3.6 38.5 1.0
N A:LYS54 3.7 24.9 1.0
NH2 A:ARG179 3.8 26.1 1.0
O03 A:KFF302 3.8 36.4 1.0
H052 A:KFF302 3.8 46.2 1.0
CB A:LYS54 3.9 30.0 1.0
N A:GLY55 3.9 24.6 1.0
NH1 A:ARG179 4.0 25.0 1.0
O A:HOH485 4.1 37.7 1.0
CA A:LYS54 4.2 28.6 1.0
O01 A:KFF302 4.3 28.7 1.0
CZ A:ARG179 4.3 26.9 1.0
OD1 A:ASP173 4.5 29.3 1.0
CB A:LEU53 4.5 26.2 1.0
C A:LEU53 4.5 27.9 1.0
O07 A:KFF302 4.6 35.8 1.0
C A:LYS54 4.6 25.9 1.0
H051 A:KFF302 4.6 46.2 1.0
CA A:LEU53 4.8 27.8 1.0
H082 A:KFF302 4.8 45.8 1.0
CA A:GLY55 4.8 22.3 1.0

Magnesium binding site 2 out of 2 in 8ts4

Go back to Magnesium Binding Sites List in 8ts4
Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine


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 T. Brucei Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [2S,4S]-4-Guanin-9-Yl-2-(2- Phosphonoethoxymethyl)-1-N-(3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:40.2
occ:1.00
 O04 B:KFF302 2.2 28.0 1.0
O B:HOH413 2.5 33.6 1.0
H061 B:KFF302 2.9 39.0 1.0
P02 B:KFF302 3.4 32.2 1.0
O B:HOH491 3.4 35.5 1.0
N B:LYS54 3.5 19.0 1.0
O B:HOH499 3.5 34.5 1.0
H062 B:KFF302 3.5 39.0 1.0
C06 B:KFF302 3.6 32.5 1.0
O03 B:KFF302 3.8 34.0 1.0
CB B:LYS54 3.9 25.8 1.0
O B:HOH510 3.9 46.0 1.0
C05 B:KFF302 3.9 32.5 1.0
N B:GLY55 4.1 21.5 1.0
H052 B:KFF302 4.1 39.0 1.0
CA B:LYS54 4.2 26.5 1.0
CB B:LEU53 4.2 20.0 1.0
NH2 B:ARG179 4.3 22.6 1.0
C B:LEU53 4.3 23.7 1.0
CA B:LEU53 4.4 26.9 1.0
CD2 B:LEU53 4.6 26.2 1.0
NH1 B:ARG179 4.6 20.4 1.0
O B:HOH524 4.6 46.6 1.0
O01 B:KFF302 4.7 26.8 1.0
C B:LYS54 4.7 22.6 1.0
O07 B:KFF302 4.8 34.8 1.0
H082 B:KFF302 4.9 33.7 1.0
CG B:LEU53 4.9 26.1 1.0
CZ B:ARG179 4.9 23.8 1.0
H051 B:KFF302 4.9 39.0 1.0

Reference:

D.T.Keough, M.Petrova, G.King, M.Kratochvil, R.Pohl, E.Dolezelova, A.Zikova, L.W.Guddat, D.Rejman. Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38651522
DOI: 10.1021/ACS.JMEDCHEM.4C00021
Page generated: Fri Oct 4 20:56:17 2024

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