Magnesium in PDB 6ar9: Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid

The structure of Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid, PDB code: 6ar9 was solved by D.Teran, L.W.Gudday, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.76 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.309, 107.338, 117.354, 90.00, 96.61, 90.00
R / Rfree (%)	17.6 / 21.8

The binding sites of Magnesium atom in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid (pdb code 6ar9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid, PDB code: 6ar9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]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 Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:42.3 occ:1.00 OD2 A:ASP76 2.5 28.7 1.0 OH D:TYR216 2.7 25.7 1.0 O D:HOH455 3.0 25.4 1.0 O D:HOH500 3.2 49.2 1.0 CG A:ASP76 3.3 30.1 1.0 OD1 A:ASP76 3.3 31.1 1.0 O A:HOH490 3.3 32.9 1.0 CZ D:TYR216 3.5 24.9 1.0 CE1 D:TYR216 3.6 26.3 1.0 O A:HOH430 3.8 25.1 1.0 CB A:PRO106 4.1 22.9 1.0 CA A:PRO106 4.1 20.5 1.0 CG A:PRO106 4.4 23.5 1.0 CD1 D:TYR213 4.7 21.7 1.0 CB A:ASP76 4.7 27.4 1.0 CE2 D:TYR216 4.8 25.6 1.0 N A:PRO106 4.9 19.9 1.0 NH2 D:ARG25 4.9 66.6 1.0 CD1 D:TYR216 5.0 26.7 1.0 CE1 D:TYR213 5.0 24.9 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]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 Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:37.4 occ:0.66 MG A:MG303 0.0 37.4 0.7 MG A:MG303 2.6 17.5 0.3 OE1 A:GLU147 2.9 36.9 1.0 OE2 A:GLU147 2.9 38.9 1.0 OD1 A:ASP148 2.9 38.8 1.0 CD A:GLU147 3.1 34.6 1.0 NAY A:3L4301 3.3 50.5 1.0 CAJ A:3L4301 3.6 46.8 1.0 CG A:ASP148 3.7 35.6 1.0 OD2 A:ASP148 3.7 40.0 1.0 OAF A:3L4301 3.7 83.3 1.0 OAE A:3L4301 3.7 90.0 1.0 CAK A:3L4301 3.9 44.8 1.0 CAM A:3L4301 3.9 62.5 1.0 CAL A:3L4301 4.1 44.5 1.0 PBA A:3L4301 4.1 87.0 1.0 CG A:GLU147 4.3 31.0 1.0 CAO A:3L4301 4.5 76.4 1.0 O A:HOH426 4.5 11.2 0.4 CG1 A:VAL85 4.6 27.3 1.0 OAT A:3L4301 4.9 40.9 1.0 OG A:SER89 4.9 25.8 0.4 O A:ILE149 4.9 30.8 1.0 N A:ASP148 5.0 24.2 1.0 CG2 A:ILE149 5.0 24.1 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]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 Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:17.5 occ:0.34 MG A:MG303 0.0 17.5 0.3 OE2 A:GLU147 2.4 38.9 1.0 MG A:MG303 2.6 37.4 0.7 OG A:SER89 2.7 25.8 0.4 O A:VAL85 2.9 32.1 1.0 OD1 A:ASP148 3.1 38.8 1.0 CG A:ASP148 3.3 35.6 1.0 OD2 A:ASP148 3.3 40.0 1.0 N A:SER89 3.5 25.2 0.6 N A:SER89 3.5 25.5 0.4 N A:GLY88 3.5 31.6 1.0 CD A:GLU147 3.5 34.6 1.0 OAE A:3L4301 3.7 90.0 1.0 CA A:GLY88 3.8 31.5 1.0 C A:VAL85 3.8 29.1 1.0 C A:GLY88 3.9 28.2 1.0 CB A:SER89 3.9 22.2 0.6 OAF A:3L4301 3.9 83.3 1.0 CB A:SER89 3.9 22.6 0.4 CG1 A:VAL85 4.0 27.3 1.0 CB A:VAL85 4.0 35.0 1.0 OE1 A:GLU147 4.0 36.9 1.0 N A:ASP148 4.2 24.2 1.0 CB A:ASP148 4.3 28.6 1.0 C A:LEU86 4.3 33.5 1.0 CA A:SER89 4.3 24.0 0.6 O A:LEU86 4.3 37.0 1.0 CA A:SER89 4.3 23.9 0.4 N A:LYS87 4.4 31.7 1.0 PBA A:3L4301 4.5 87.0 1.0 C A:LYS87 4.5 30.8 1.0 CA A:VAL85 4.5 29.3 1.0 N A:LEU86 4.7 26.3 1.0 CG A:GLU147 4.7 31.0 1.0 CA A:LEU86 4.8 31.0 1.0 O A:GLY88 4.8 36.2 1.0 CA A:ASP148 4.9 24.6 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]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 Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:76.7 occ:1.00 CAJ C:3L4301 2.5 90.5 1.0 OE1 C:GLU147 2.6 46.7 1.0 OE2 C:GLU147 2.8 42.6 1.0 OAT C:3L4301 2.8 0.5 1.0 O C:HOH429 2.9 34.6 1.0 CD C:GLU147 3.0 40.9 1.0 CAK C:3L4301 3.1 75.1 1.0 CG1 C:VAL85 3.4 30.2 1.0 OD1 C:ASP148 3.6 33.9 1.0 OAD C:3L4301 4.2 0.8 1.0 CAP C:3L4301 4.2 0.7 1.0 O C:HOH404 4.3 22.4 0.6 CB C:VAL85 4.3 31.7 1.0 CG2 C:THR155 4.4 25.6 1.0 CG C:GLU147 4.5 33.2 1.0 NAY C:3L4301 4.5 62.9 1.0 CG C:ASP148 4.6 37.1 1.0 OD2 C:ASP148 4.9 40.5 1.0 PBB C:3L4301 4.9 0.2 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:82.9 occ:1.00 OAE D:3L4301 2.2 89.5 1.0 O D:HOH481 2.6 62.0 1.0 OE1 D:GLU208 2.6 38.2 1.0 O D:HOH474 2.9 42.5 1.0 O D:HOH491 3.1 42.1 1.0 PBA D:3L4301 3.3 90.5 1.0 CD D:GLU208 3.4 34.0 1.0 OE2 D:GLU208 3.4 36.8 1.0 CAO D:3L4301 3.5 80.9 1.0 O D:HOH402 3.6 46.2 1.0 OH D:TYR201 4.1 35.0 1.0 CAM D:3L4301 4.2 68.5 1.0 OAC D:3L4301 4.3 88.4 1.0 OAF D:3L4301 4.4 90.2 1.0 O D:GLU208 4.5 23.5 1.0 MG D:MG303 4.6 71.2 1.0 CG D:GLU208 4.8 25.4 1.0 O D:HOH494 4.9 50.9 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:71.2 occ:1.00 NH1 D:ARG214 2.9 31.1 1.0 NH2 D:ARG214 3.0 35.4 1.0 OE1 D:GLU208 3.2 38.2 1.0 O D:HOH494 3.2 50.9 1.0 CZ D:ARG214 3.4 32.3 1.0 N D:GLY88 3.8 19.0 1.0 OAF D:3L4301 3.8 90.2 1.0 CAO D:3L4301 3.8 80.9 1.0 O D:HOH488 3.8 40.0 1.0 CA D:GLY88 3.8 19.7 1.0 CD D:GLU208 3.9 34.0 1.0 CG D:GLU208 4.2 25.4 1.0 PBA D:3L4301 4.2 90.5 1.0 O D:HOH402 4.2 46.2 1.0 OAE D:3L4301 4.3 89.5 1.0 C D:LYS87 4.5 24.8 1.0 MG D:MG302 4.6 82.9 1.0 O D:GLY206 4.6 26.1 1.0 CB D:LYS87 4.7 29.9 1.0 N D:LYS87 4.7 27.8 1.0 NE D:ARG214 4.7 32.4 1.0 CA D:LYS87 4.9 27.8 1.0 OE2 D:GLU208 4.9 36.8 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:67.8 occ:1.00 OE2 E:GLU208 2.5 40.6 1.0 OAE E:3L4301 2.6 1.0 1.0 O E:HOH495 2.7 49.4 1.0 CD E:GLU208 3.3 34.9 1.0 OE1 E:GLU208 3.5 38.6 1.0 CAO E:3L4301 3.6 93.1 1.0 PBA E:3L4301 3.6 0.1 1.0 OH E:TYR201 3.6 39.7 1.0 O E:HOH493 3.7 44.6 1.0 O E:GLU208 4.0 35.2 1.0 OAF E:3L4301 4.4 0.7 1.0 O E:HOH476 4.6 45.6 1.0 CG E:GLU208 4.7 26.8 1.0 C E:GLU208 4.8 37.1 1.0 OAC E:3L4301 4.8 0.6 1.0 N3 E:3L4301 4.8 29.4 1.0 N2 E:3L4301 4.9 36.1 1.0 CZ E:TYR201 5.0 35.8 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Hypoxanthine-Guanine-Xanthine Phosphorybosyltranferase in Complex with [(2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl][(E)-2-Phosphonoethenyl]Amino}Ethoxy) Methyl]Phosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:64.5 occ:1.00 OE2 E:GLU147 2.5 45.5 1.0 O E:VAL85 2.8 33.5 1.0 CG1 E:VAL85 3.3 27.0 1.0 OD1 E:ASP148 3.4 42.1 1.0 CG E:ASP148 3.4 37.9 1.0 O E:HOH487 3.4 48.1 1.0 OD2 E:ASP148 3.5 41.1 1.0 CB E:VAL85 3.5 28.6 1.0 N E:SER89 3.5 24.1 1.0 C E:VAL85 3.6 30.6 1.0 N E:GLY88 3.6 28.2 1.0 CD E:GLU147 3.7 45.7 1.0 CA E:GLY88 3.7 28.2 1.0 CB E:SER89 3.9 32.5 1.0 C E:GLY88 3.9 27.9 1.0 N E:ASP148 3.9 32.5 1.0 CB E:ASP148 4.1 30.5 1.0 CA E:VAL85 4.2 29.6 1.0 CA E:SER89 4.3 26.4 1.0 OE1 E:GLU147 4.4 47.2 1.0 C E:LEU86 4.5 39.2 1.0 N E:LEU86 4.6 27.6 1.0 O E:LEU86 4.6 41.9 1.0 C E:LYS87 4.6 27.0 1.0 CA E:ASP148 4.7 30.1 1.0 N E:LYS87 4.7 26.8 1.0 CA E:GLU147 4.7 31.9 1.0 CG E:GLU147 4.8 43.0 1.0 CG2 E:VAL85 4.8 28.3 1.0 C E:GLU147 4.8 30.6 1.0 CA E:LEU86 4.9 24.5 1.0 O E:GLY88 4.9 30.4 1.0 N E:VAL85 4.9 25.1 1.0

E.Dolezelova, D.Teran, O.Gahura, Z.Kotrbova, M.Prochazkova, D.Keough, P.Spacek, D.Hockova, L.Guddat, A.Zikova. Evaluation of the Trypanosoma Brucei 6-Oxopurine Salvage Pathway As A Potential Target For Drug Discovery. Plos Negl Trop Dis V. 12 06301 2018.
ISSN: ESSN 1935-2735
PubMed: 29481567
DOI: 10.1371/JOURNAL.PNTD.0006301