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Magnesium in PDB 8tpy: Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine

Enzymatic activity of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine

All present enzymatic activity of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine:
2.4.2.8;

Protein crystallography data

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

Resolution Low / High (Å) 75.73 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.461, 93.42, 129.32, 90, 90, 90
R / Rfree (%) 20 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine (pdb code 8tpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine, PDB code: 8tpy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8tpy

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Magnesium binding site 1 out of 4 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-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 Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.7
occ:1.00
 OE2 A:GLU133 2.0 54.1 1.0
OD1 A:ASP134 2.4 50.8 1.0
CA A:GLY69 2.8 62.5 1.0
CG A:ASP134 3.1 51.7 1.0
CD A:GLU133 3.2 54.1 1.0
OD2 A:ASP134 3.2 56.6 1.0
N A:GLY69 3.7 73.6 1.0
C A:GLY69 3.9 68.1 1.0
OE1 A:GLU133 3.9 56.9 1.0
N A:GLY70 3.9 68.6 1.0
O26 A:JG6301 4.3 47.8 1.0
CG A:GLU133 4.3 44.6 1.0
O A:VAL66 4.3 57.6 1.0
N A:ASP134 4.4 35.2 1.0
CB A:ASP134 4.5 44.8 1.0
C A:LYS68 4.5 67.3 1.0
O A:LYS68 4.7 73.0 1.0
N A:ILE135 4.8 38.5 1.0
O A:ILE135 4.9 41.5 1.0
CG2 A:ILE135 4.9 36.4 1.0
O A:GLY69 4.9 66.0 1.0

Magnesium binding site 2 out of 4 in 8tpy

Go back to Magnesium Binding Sites List in 8tpy
Magnesium binding site 2 out of 4 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-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 Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:40.5
occ:1.00
 O B:HOH405 2.0 48.3 1.0
O B:HOH410 2.3 62.9 1.0
OE1 B:GLU133 2.4 48.2 1.0
O B:HOH415 2.5 56.7 1.0
OD1 B:ASP134 2.5 56.4 1.0
O B:HOH403 2.6 47.5 1.0
CG B:ASP134 3.3 51.7 1.0
OD2 B:ASP134 3.3 60.0 1.0
CD B:GLU133 3.4 49.4 1.0
O B:LYS68 3.6 66.4 1.0
O26 B:JG6301 3.8 45.5 1.0
OE2 B:GLU133 3.9 44.9 1.0
CG2 B:ILE135 4.4 46.5 1.0
N B:GLY70 4.5 63.0 1.0
CG B:GLU133 4.5 48.8 1.0
O B:VAL66 4.6 63.6 1.0
N B:ASP134 4.6 33.5 1.0
CA B:GLY70 4.6 60.9 1.0
C B:GLY69 4.7 68.6 1.0
C B:LYS68 4.7 69.4 1.0
CB B:ASP134 4.7 41.7 1.0
N B:ILE135 4.7 35.6 1.0
O B:ILE135 4.7 34.9 1.0
O B:GLY69 4.8 70.6 1.0
C07 B:JG6301 4.9 45.8 1.0

Magnesium binding site 3 out of 4 in 8tpy

Go back to Magnesium Binding Sites List in 8tpy
Magnesium binding site 3 out of 4 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-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 3 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:34.0
occ:1.00
 O C:HOH406 2.0 49.3 1.0
OE2 C:GLU133 2.1 39.4 1.0
OD1 C:ASP134 2.4 46.2 1.0
O C:HOH408 2.5 42.9 1.0
O C:HOH418 2.7 49.5 1.0
O C:HOH414 2.7 38.7 1.0
CG C:ASP134 3.2 46.3 1.0
CD C:GLU133 3.4 40.9 1.0
OD2 C:ASP134 3.4 56.7 1.0
CB C:LYS68 3.6 60.6 1.0
N C:GLY69 3.9 64.5 1.0
C C:LYS68 4.0 70.8 1.0
N C:GLY70 4.1 55.7 1.0
OE1 C:GLU133 4.1 48.5 1.0
O26 C:JG6301 4.2 49.7 1.0
CA C:LYS68 4.3 62.4 1.0
O C:LYS68 4.3 78.4 1.0
CG C:GLU133 4.4 43.7 1.0
CA C:GLY69 4.4 59.2 1.0
O C:VAL66 4.5 51.8 1.0
N C:ASP134 4.5 38.9 1.0
CB C:ASP134 4.7 36.5 1.0
CG2 C:ILE135 4.7 36.7 1.0
C C:GLY69 4.7 62.9 1.0
N C:ILE135 4.8 30.5 1.0
N C:LYS68 4.8 67.6 1.0
O C:ILE135 4.8 36.4 1.0
CA C:GLY70 4.9 60.0 1.0

Magnesium binding site 4 out of 4 in 8tpy

Go back to Magnesium Binding Sites List in 8tpy
Magnesium binding site 4 out of 4 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-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 4 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R] 4-Guanin-9-Yl-2-Hydroxymethyl-1-N-(3- Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:47.4
occ:1.00
 O D:HOH416 2.1 55.6 1.0
OD1 D:ASP134 2.2 61.0 1.0
OE2 D:GLU133 2.3 55.0 1.0
O D:HOH411 2.4 58.9 1.0
CA D:GLY69 2.6 63.6 1.0
CD D:GLU133 3.1 53.6 1.0
CG D:ASP134 3.1 53.1 1.0
OD2 D:ASP134 3.4 57.3 1.0
OE1 D:GLU133 3.5 61.0 1.0
N D:GLY70 3.5 65.8 1.0
C D:GLY69 3.6 64.3 1.0
N D:GLY69 3.7 62.4 1.0
O D:LYS68 3.8 72.8 1.0
C D:LYS68 4.1 66.6 1.0
O D:VAL66 4.1 50.3 1.0
CG D:GLU133 4.2 45.7 1.0
N D:ASP134 4.3 39.5 1.0
O D:HOH422 4.4 60.4 1.0
CB D:ASP134 4.4 44.3 1.0
O D:LEU67 4.7 63.1 1.0
O D:GLY69 4.7 60.5 1.0
O26 D:JG6301 4.7 62.2 1.0
N D:ILE135 4.8 44.4 1.0
CA D:GLY70 4.8 57.0 1.0
CA D:ASP134 4.9 43.2 1.0
O D:HOH412 5.0 49.9 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 Aug 15 16:37:04 2025

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