Magnesium in PDB 5w8v: Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid

Enzymatic activity of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid

All present enzymatic activity of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid:
2.4.2.8;

Protein crystallography data

The structure of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid, PDB code: 5w8v was solved by L.W.Guddat, D.T.Keough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.667, 128.399, 65.326, 90.00, 102.98, 90.00
R / Rfree (%) 19.6 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid (pdb code 5w8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid, PDB code: 5w8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5w8v

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Magnesium binding site 1 out of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Human Hgprt in Complex with [(2-[(Guanin-9-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:41.6
occ:1.00
 O A:HOH433 1.9 29.7 1.0
O A:HOH436 2.1 36.1 1.0
OE1 A:GLU133 2.1 43.2 1.0
O A:HOH455 2.1 43.7 1.0
OD1 A:ASP134 2.1 35.9 1.0
O A:HOH476 2.6 42.4 1.0
CD A:GLU133 2.9 41.6 1.0
CG A:ASP134 3.1 37.0 1.0
OE2 A:GLU133 3.2 41.1 1.0
OD2 A:ASP134 3.4 38.0 1.0
O A:HOH493 3.7 54.8 1.0
OAF A:9YP301 4.1 69.2 1.0
N A:ASP134 4.2 33.8 1.0
O A:ILE135 4.3 41.6 1.0
CG A:GLU133 4.3 40.7 1.0
N A:ILE135 4.4 35.3 1.0
CB A:ASP134 4.4 31.4 1.0
CG1 A:VAL66 4.5 31.1 1.0
O A:HOH487 4.7 37.7 1.0
CG2 A:ILE135 4.7 30.9 1.0
CB A:GLU133 4.7 34.0 1.0
CA A:ASP134 4.8 32.2 1.0
O A:VAL66 4.8 32.1 1.0
CAM A:9YP301 4.9 57.2 1.0
O A:HOH439 4.9 36.6 1.0
CB A:VAL66 5.0 34.7 1.0

Magnesium binding site 2 out of 4 in 5w8v

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Magnesium binding site 2 out of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Human Hgprt in Complex with [(2-[(Guanin-9-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:37.2
occ:1.00
 O B:HOH455 2.0 45.4 1.0
OD1 B:ASP134 2.1 39.5 1.0
OE2 B:GLU133 2.1 44.5 1.0
O B:HOH490 2.2 44.7 1.0
O B:HOH452 2.3 26.1 1.0
O B:HOH423 2.4 33.0 1.0
CD B:GLU133 2.9 44.3 1.0
CG B:ASP134 3.0 37.1 1.0
OD2 B:ASP134 3.3 32.8 1.0
OE1 B:GLU133 3.6 44.0 1.0
CG B:GLU133 3.7 47.9 1.0
O B:HOH501 3.8 41.5 1.0
O B:HOH444 3.9 48.8 1.0
N B:ASP134 4.0 28.8 1.0
CAM B:9YP301 4.2 65.9 1.0
CB B:ASP134 4.3 32.0 1.0
N B:ILE135 4.3 29.6 1.0
OAE B:9YP301 4.3 66.3 1.0
O B:ILE135 4.4 44.4 1.0
O B:HOH466 4.6 33.1 1.0
CG1 B:VAL66 4.6 30.1 1.0
CG2 B:ILE135 4.6 40.4 1.0
CA B:ASP134 4.6 28.5 1.0
O B:VAL66 4.8 37.1 1.0
CB B:GLU133 4.9 39.8 1.0
O B:HOH426 5.0 33.8 1.0
CB B:VAL66 5.0 39.4 1.0

Magnesium binding site 3 out of 4 in 5w8v

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Magnesium binding site 3 out of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 3 of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:42.5
occ:1.00
 O C:HOH427 2.0 49.5 1.0
O C:HOH418 2.0 34.4 1.0
O C:HOH410 2.0 27.9 1.0
OD1 C:ASP134 2.1 47.8 1.0
OE1 C:GLU133 2.2 33.9 1.0
O C:HOH453 2.2 38.6 1.0
CD C:GLU133 3.0 39.1 1.0
CG C:ASP134 3.1 42.0 1.0
OE2 C:GLU133 3.2 43.9 1.0
OD2 C:ASP134 3.3 40.0 1.0
OAC C:9YP301 3.9 67.0 1.0
O C:HOH481 4.3 45.4 1.0
N C:ASP134 4.3 34.6 1.0
O C:ILE135 4.3 47.4 1.0
CG C:GLU133 4.4 36.0 1.0
N C:ILE135 4.4 34.7 1.0
CB C:ASP134 4.5 33.8 1.0
CG1 C:VAL66 4.5 35.7 1.0
O C:HOH502 4.5 43.9 1.0
CAM C:9YP301 4.5 62.9 1.0
CG2 C:ILE135 4.7 35.5 1.0
CB C:GLU133 4.8 34.6 1.0
CA C:ASP134 4.9 30.6 1.0
O C:HOH403 5.0 52.7 1.0

Magnesium binding site 4 out of 4 in 5w8v

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Magnesium binding site 4 out of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 4 of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:33.0
occ:1.00
 O D:HOH462 2.0 30.5 1.0
O D:HOH484 2.1 30.9 1.0
OD1 D:ASP134 2.1 37.8 1.0
OE1 D:GLU133 2.1 34.7 1.0
O D:HOH458 2.2 33.3 1.0
O D:HOH446 2.3 29.5 1.0
CD D:GLU133 3.0 37.2 1.0
CG D:ASP134 3.1 40.0 1.0
OE2 D:GLU133 3.3 39.1 1.0
OD2 D:ASP134 3.4 43.1 1.0
O D:HOH416 4.0 38.1 1.0
OAC D:9YP301 4.1 56.8 1.0
N D:ASP134 4.2 36.6 1.0
O D:HOH500 4.3 49.8 1.0
CB D:ASP134 4.4 36.1 1.0
N D:ILE135 4.4 37.9 1.0
CG D:GLU133 4.4 38.1 1.0
CG2 D:ILE135 4.4 43.0 1.0
O D:ILE135 4.5 40.5 1.0
CAM D:9YP301 4.6 57.6 1.0
CG1 D:VAL66 4.6 34.8 1.0
O D:HOH443 4.7 39.9 1.0
O D:VAL66 4.8 33.6 1.0
CA D:ASP134 4.8 37.2 1.0
CB D:GLU133 4.8 35.8 1.0

Reference:

P.Spacek, D.T.Keough, M.Chavchich, M.Dracinsky, Z.Janeba, L.Naesens, M.D.Edstein, L.W.Guddat, D.Hockova. Synthesis and Evaluation of Asymmetric Acyclic Nucleoside Bisphosphonates As Inhibitors of Plasmodium Falciparum and Human Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase. J. Med. Chem. V. 60 7539 2017.
ISSN: ISSN 1520-4804
PubMed: 28813147
DOI: 10.1021/ACS.JMEDCHEM.7B00926
Page generated: Mon Dec 14 21:20:39 2020

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