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Magnesium in PDB 7tux: Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid

Enzymatic activity of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid

All present enzymatic activity of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid:
2.4.2.22; 2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid, PDB code: 7tux was solved by R.K.Harijan, Y.V.T.Minnow, J.B.Bonanno, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.47 / 1.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.437, 111.199, 173.652, 90, 90, 90
R / Rfree (%) 17 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid (pdb code 7tux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid, PDB code: 7tux:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7tux

Go back to Magnesium Binding Sites List in 7tux
Magnesium binding site 1 out of 4 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid


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 Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:20.7
occ:1.00
 O6 A:POP302 1.9 21.3 1.0
O3 A:POP302 2.0 22.5 1.0
O A:HOH478 2.0 24.5 1.0
OD1 A:ASP204 2.1 19.6 1.0
O A:HOH406 2.2 39.9 1.0
O A:HOH489 2.2 31.9 1.0
CG A:ASP204 3.1 18.9 1.0
P1 A:POP302 3.2 22.3 1.0
P2 A:POP302 3.2 21.4 1.0
O A:POP302 3.4 20.6 1.0
OD2 A:ASP204 3.5 21.3 1.0
O A:HOH407 3.6 40.9 1.0
O2 A:POP302 3.8 21.7 1.0
O A:HOH417 4.1 24.8 1.0
O A:ASP204 4.1 19.7 1.0
O5 A:POP302 4.1 20.7 1.0
NH2 A:ARG210 4.1 19.7 1.0
O4 A:POP302 4.3 19.7 1.0
C10 A:YBM301 4.3 20.5 1.0
NH1 A:ARG210 4.3 19.1 1.0
O1 A:POP302 4.4 24.4 1.0
O A:HOH477 4.4 23.3 1.0
CB A:ASP204 4.4 19.3 1.0
N A:YBM301 4.4 19.1 1.0
N A:ASP204 4.5 18.5 1.0
N3 A:YBM301 4.5 19.0 1.0
O A:HOH418 4.7 35.1 1.0
CZ A:ARG210 4.7 18.8 1.0
C A:ASP204 4.7 18.8 1.0
CA A:ASP204 4.8 19.2 1.0

Magnesium binding site 2 out of 4 in 7tux

Go back to Magnesium Binding Sites List in 7tux
Magnesium binding site 2 out of 4 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid


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 Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:20.1
occ:1.00
 O4 B:POP302 1.9 23.9 1.0
O2 B:POP302 1.9 22.7 1.0
OD1 B:ASP204 2.0 18.4 1.0
O B:HOH456 2.1 22.1 1.0
O B:HOH511 2.1 30.8 1.0
O B:HOH485 2.3 40.1 1.0
CG B:ASP204 3.1 18.4 1.0
P2 B:POP302 3.1 22.0 1.0
P1 B:POP302 3.3 22.6 1.0
O B:POP302 3.4 20.3 1.0
OD2 B:ASP204 3.4 18.6 1.0
O6 B:POP302 3.8 21.8 1.0
NH2 B:ARG210 4.1 17.1 1.0
O B:HOH465 4.1 27.1 1.0
O B:ASP204 4.1 18.6 1.0
O B:HOH423 4.2 33.5 1.0
O1 B:POP302 4.3 22.3 1.0
NH1 B:ARG210 4.3 17.4 1.0
O3 B:POP302 4.3 21.5 1.0
O5 B:POP302 4.4 22.8 1.0
CB B:ASP204 4.4 17.3 1.0
C10 B:YBM301 4.4 19.3 1.0
N B:YBM301 4.4 19.8 1.0
N B:ASP204 4.4 17.8 1.0
O B:HOH444 4.4 23.8 1.0
O B:HOH440 4.5 39.1 1.0
N3 B:YBM301 4.6 18.5 1.0
CZ B:ARG210 4.6 17.7 1.0
C B:ASP204 4.7 17.6 1.0
CA B:ASP204 4.8 18.1 1.0

Magnesium binding site 3 out of 4 in 7tux

Go back to Magnesium Binding Sites List in 7tux
Magnesium binding site 3 out of 4 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:22.1
occ:1.00
 O C:HOH431 1.9 38.8 1.0
O6 C:POP302 2.0 25.4 1.0
O3 C:POP302 2.0 23.2 1.0
OD1 C:ASP204 2.0 20.0 1.0
O C:HOH446 2.1 24.4 1.0
O C:HOH502 2.1 30.9 1.0
CG C:ASP204 3.1 20.1 1.0
P2 C:POP302 3.2 25.2 1.0
P1 C:POP302 3.3 23.6 1.0
O C:POP302 3.4 23.2 1.0
OD2 C:ASP204 3.4 19.9 1.0
O4 C:POP302 3.9 23.1 1.0
O C:HOH437 4.0 35.0 1.0
O C:HOH448 4.0 29.6 1.0
O C:ASP204 4.1 18.9 1.0
NH2 C:ARG210 4.1 18.2 1.0
O2 C:POP302 4.3 24.0 1.0
O1 C:POP302 4.3 23.2 1.0
NH1 C:ARG210 4.3 18.9 1.0
C10 C:YBM301 4.3 23.1 1.0
O5 C:POP302 4.4 24.4 1.0
CB C:ASP204 4.4 19.6 1.0
N C:ASP204 4.4 19.7 1.0
O C:HOH459 4.4 24.3 1.0
N C:YBM301 4.5 22.8 1.0
N3 C:YBM301 4.5 20.6 1.0
CZ C:ARG210 4.7 18.4 1.0
C C:ASP204 4.7 19.8 1.0
CA C:ASP204 4.7 18.9 1.0

Magnesium binding site 4 out of 4 in 7tux

Go back to Magnesium Binding Sites List in 7tux
Magnesium binding site 4 out of 4 in the Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Plasmodium Falciparum Hypoxanthine-Guanine- Xanthine Phosphoribosyltransferase in Complex with [(3S)-4-Hydroxy-3- [({2-Amino-4-Hydroxy-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl}Methyl) Amino]Butyl]Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:29.1
occ:1.00
 O5 D:POP302 2.0 30.3 1.0
O2 D:POP302 2.0 31.6 1.0
OD1 D:ASP204 2.1 23.0 1.0
O D:HOH493 2.2 35.6 1.0
O D:HOH428 2.3 36.0 1.0
O D:HOH446 2.4 53.9 1.0
P1 D:POP302 3.1 33.0 1.0
CG D:ASP204 3.2 23.4 1.0
P2 D:POP302 3.2 33.0 1.0
O D:POP302 3.4 31.7 1.0
OD2 D:ASP204 3.6 26.1 1.0
O3 D:POP302 3.8 34.9 1.0
O D:HOH429 4.1 40.9 1.0
O D:ASP204 4.2 22.0 1.0
O4 D:POP302 4.2 33.3 1.0
O6 D:POP302 4.2 31.1 1.0
NH2 D:ARG210 4.2 24.1 1.0
C10 D:YBM301 4.3 23.8 1.0
N D:YBM301 4.3 23.3 1.0
N3 D:YBM301 4.4 21.5 1.0
O1 D:POP302 4.4 31.5 1.0
NH1 D:ARG210 4.4 24.2 1.0
CB D:ASP204 4.5 23.1 1.0
N D:ASP204 4.5 21.4 1.0
O D:HOH437 4.5 27.5 1.0
O D:HOH413 4.7 38.5 1.0
CZ D:ARG210 4.8 23.9 1.0
C D:ASP204 4.8 22.9 1.0
CA D:ASP204 4.9 22.9 1.0

Reference:

Y.V T Minnow, K.Suthagar, K.Clinch, R.G.Ducati, A.Ghosh, J.N.Buckler, R.K.Harijan, S.M.Cahill, P.C.Tyler, V.L.Schramm. Inhibition and Mechanism of Plasmodium Falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase. Acs Chem.Biol. V. 17 3407 2022.
ISSN: ESSN 1554-8937
PubMed: 36413975
DOI: 10.1021/ACSCHEMBIO.2C00546
Page generated: Thu Oct 3 09:31:08 2024

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