Magnesium in PDB 5brn: Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate

All present enzymatic activity of Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate:
2.4.2.8;

The structure of Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate, PDB code: 5brn was solved by D.T.Keough, L.W.Guddat, M.M.Kaiser, D.Hockova, T.-H.Wang, Z.Janeba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.33 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.530, 94.310, 139.270, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 29.2

The binding sites of Magnesium atom in the Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate (pdb code 5brn). 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 (S)-Hpephx, An Acyclic Nucleoside Phosphonate, PDB code: 5brn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate


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 (S)-Hpephx, An Acyclic Nucleoside Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:21.8 occ:1.00 O A:HOH427 2.0 41.3 1.0 O A:HOH456 2.1 20.9 1.0 O A:HOH469 2.3 34.5 1.0 OE1 A:GLU133 2.4 30.8 1.0 O A:HOH447 2.4 28.8 1.0 OD1 A:ASP134 2.5 27.3 1.0 OE2 A:GLU133 2.6 32.8 1.0 CD A:GLU133 2.6 31.6 1.0 CG A:ASP134 3.4 27.7 1.0 O10 A:4X2302 3.7 43.7 1.0 OD2 A:ASP134 3.7 29.4 1.0 O A:HOH463 3.8 42.5 1.0 CG A:GLU133 3.9 30.4 1.0 CG1 A:VAL66 4.1 24.4 1.0 O A:HOH466 4.2 39.4 1.0 O A:HOH405 4.2 30.1 1.0 N A:ASP134 4.5 25.7 1.0 C09 A:4X2302 4.6 41.2 1.0 O A:ILE135 4.6 30.7 1.0 CB A:VAL66 4.7 27.7 1.0 N A:ILE135 4.7 27.6 1.0 CB A:ASP134 4.8 26.2 1.0 O A:VAL66 4.9 26.6 1.0 CG2 A:ILE135 5.0 27.3 1.0

Magnesium binding site 2 out of 4 in the Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate


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 (S)-Hpephx, An Acyclic Nucleoside Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:22.1 occ:1.00 O B:HOH428 2.0 47.8 1.0 O B:HOH411 2.1 33.7 1.0 O B:HOH424 2.1 47.8 1.0 O B:HOH402 2.1 42.7 1.0 OE2 B:GLU133 2.2 42.0 1.0 OE1 B:GLU133 2.2 40.2 1.0 CD B:GLU133 2.4 41.0 1.0 OD1 B:ASP134 2.4 41.7 1.0 CG B:ASP134 3.3 40.7 1.0 O10 B:4X2302 3.6 63.0 1.0 OD2 B:ASP134 3.7 41.9 1.0 CG B:GLU133 3.7 40.5 1.0 CG1 B:VAL66 4.2 34.8 1.0 N B:ASP134 4.3 36.2 1.0 O B:HOH436 4.3 43.6 1.0 C09 B:4X2302 4.5 61.9 1.0 O B:ILE135 4.6 40.7 1.0 CB B:ASP134 4.6 37.6 1.0 N B:ILE135 4.7 34.9 1.0 CG2 B:THR141 4.8 44.1 1.0 CB B:GLU133 4.8 39.2 1.0 O B:HOH438 4.8 46.5 1.0 CB B:VAL66 4.8 35.4 1.0 O B:VAL66 4.9 34.0 1.0 O07 B:4X2302 5.0 59.7 1.0 CA B:ASP134 5.0 35.7 1.0

Magnesium binding site 3 out of 4 in the Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate


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 (S)-Hpephx, An Acyclic Nucleoside Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:25.7 occ:1.00 O10 C:4X2302 2.2 49.6 1.0 O C:HOH463 2.3 49.2 1.0 O C:HOH460 2.4 42.1 1.0 OD1 C:ASP134 2.4 36.7 1.0 OE1 C:GLU133 2.5 35.2 1.0 O C:HOH407 2.5 41.2 1.0 OE2 C:GLU133 2.7 37.1 1.0 CD C:GLU133 2.7 35.5 1.0 CG C:ASP134 3.3 37.4 1.0 C09 C:4X2302 3.5 48.2 1.0 OD2 C:ASP134 3.5 40.0 1.0 CG C:GLU133 3.9 34.7 1.0 CG1 C:VAL66 4.2 30.2 1.0 C08 C:4X2302 4.4 44.9 1.0 O C:ILE135 4.5 39.9 1.0 O C:HOH456 4.5 28.4 1.0 N C:ASP134 4.5 33.6 1.0 CB C:ASP134 4.6 35.1 1.0 N C:ILE135 4.7 35.5 1.0 O07 C:4X2302 4.8 42.9 1.0 O C:HOH441 4.9 46.2 1.0

Magnesium binding site 4 out of 4 in the Human Hgprt in Complex with (S)-Hpephx, An Acyclic Nucleoside Phosphonate


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 (S)-Hpephx, An Acyclic Nucleoside Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:27.3 occ:1.00 O D:HOH402 2.1 42.5 1.0 O D:HOH429 2.2 40.3 1.0 OE1 D:GLU133 2.3 34.0 1.0 O10 D:4X2302 2.4 54.7 1.0 OD1 D:ASP134 2.5 37.5 1.0 CD D:GLU133 2.6 34.8 1.0 OE2 D:GLU133 2.6 37.4 1.0 CG D:ASP134 3.5 35.9 1.0 C09 D:4X2302 3.6 53.5 1.0 OD2 D:ASP134 3.8 36.6 1.0 CG D:GLU133 3.8 35.0 1.0 CG1 D:VAL66 4.1 33.9 1.0 O D:ILE135 4.4 46.4 1.0 N D:ASP134 4.5 32.8 1.0 N D:ILE135 4.7 39.0 1.0 O D:HOH433 4.7 34.9 1.0 C08 D:4X2302 4.7 50.8 1.0 CB D:ASP134 4.8 33.6 1.0 CB D:VAL66 4.8 34.6 1.0 O D:VAL66 4.9 35.9 1.0 CB D:GLU133 5.0 34.6 1.0

M.M.Kaiser, D.Hockova, T.H.Wang, M.Dracinsky, L.Postova-Slavetinska, E.Prochazkova, M.D.Edstein, M.Chavchich, D.T.Keough, L.W.Guddat, Z.Janeba. Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates As Inhibitors of Plasmodium Falciparum and Human 6-Oxopurine Phosphoribosyltransferases. Chemmedchem V. 10 1707 2015.
ISSN: ESSN 1860-7187
PubMed: 26368337
DOI: 10.1002/CMDC.201500322