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Magnesium in PDB 4ijq: Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid

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

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

Protein crystallography data

The structure of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid, PDB code: 4ijq was solved by L.W.Guddat, D.T.Keough, D.Hockova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.505, 127.741, 64.756, 90.00, 102.01, 90.00
R / Rfree (%) 17.3 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid (pdb code 4ijq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid, PDB code: 4ijq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ijq

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Magnesium binding site 1 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:33.0
occ:1.00
 O A:HOH401 2.1 33.4 1.0
O A:HOH402 2.1 25.2 1.0
O A:HOH404 2.1 36.4 1.0
OD1 A:ASP134 2.1 23.7 1.0
OE1 A:GLU133 2.1 36.0 1.0
O A:HOH403 2.1 28.9 1.0
CD A:GLU133 2.7 37.5 1.0
OE2 A:GLU133 3.0 37.7 1.0
CG A:ASP134 3.1 26.7 1.0
OD2 A:ASP134 3.4 33.5 1.0
CG A:GLU133 3.8 37.4 1.0
O A:HOH429 3.8 43.8 1.0
O1 A:SO4302 4.1 36.3 1.0
O A:HOH409 4.1 48.6 1.0
N A:ASP134 4.2 19.5 1.0
CB A:ASP134 4.4 22.9 1.0
N A:ILE135 4.4 20.9 1.0
O A:ILE135 4.5 20.6 1.0
O A:VAL66 4.5 20.2 1.0
CG1 A:VAL66 4.6 29.5 1.0
CAJ A:SV2301 4.7 30.8 1.0
O2 A:SO4302 4.7 45.2 1.0
CA A:ASP134 4.8 17.2 1.0
O A:HOH437 4.8 30.1 1.0
CB A:VAL66 4.9 28.4 1.0
CG2 A:ILE135 4.9 27.1 1.0
N A:GLY70 5.0 20.1 1.0
CB A:GLU133 5.0 27.6 1.0

Magnesium binding site 2 out of 8 in 4ijq

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Magnesium binding site 2 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:42.7
occ:1.00
 OD1 A:ASP193 2.1 21.6 1.0
OAE A:SV2301 2.1 47.9 1.0
O A:HOH406 2.1 35.9 1.0
O A:HOH405 2.1 30.4 1.0
O A:HOH407 2.2 35.1 1.0
O4 A:SO4302 2.2 33.2 1.0
CG A:ASP193 3.0 22.4 1.0
OD2 A:ASP193 3.3 25.2 1.0
PAZ A:SV2301 3.4 40.2 1.0
S A:SO4302 3.5 37.0 1.0
O A:HOH411 3.7 30.0 1.0
O2 A:SO4302 3.7 45.2 1.0
CAL A:SV2301 3.8 37.9 1.0
NH2 A:ARG199 4.0 20.9 1.0
OAR A:SV2301 4.0 30.6 1.0
O A:HOH408 4.1 29.8 1.0
O A:ASP193 4.2 24.3 1.0
OAC A:SV2301 4.2 45.3 1.0
O1 A:SO4302 4.3 36.3 1.0
CB A:ASP193 4.4 16.7 1.0
NH1 A:ARG199 4.5 16.6 1.0
O A:HOH436 4.5 38.8 1.0
O3 A:SO4302 4.5 34.3 1.0
OAF A:SV2301 4.5 40.7 1.0
N A:ASP193 4.6 18.0 1.0
CZ A:ARG199 4.6 20.3 1.0
C A:ASP193 4.7 24.8 1.0
CE A:LYS102 4.7 77.6 1.0
N2 A:SV2301 4.8 26.2 1.0
CA A:ASP193 4.8 15.0 1.0

Magnesium binding site 3 out of 8 in 4ijq

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Magnesium binding site 3 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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:29.7
occ:1.00
 OE1 B:GLU133 2.0 31.9 1.0
O B:HOH470 2.1 28.3 1.0
O B:HOH404 2.1 25.9 1.0
O B:HOH405 2.1 26.7 1.0
OD1 B:ASP134 2.1 26.1 1.0
O B:HOH403 2.1 25.2 1.0
CD B:GLU133 2.8 34.9 1.0
CG B:ASP134 3.0 22.9 1.0
OE2 B:GLU133 3.2 35.9 1.0
OD2 B:ASP134 3.3 28.4 1.0
CG B:GLU133 3.8 37.2 1.0
O B:HOH466 4.0 46.3 1.0
O4 B:SO4303 4.1 35.0 1.0
N B:ASP134 4.2 20.3 1.0
O B:HOH436 4.3 50.8 1.0
CB B:ASP134 4.4 19.6 1.0
N B:ILE135 4.4 20.5 1.0
O B:ILE135 4.4 23.3 1.0
CG1 B:VAL66 4.7 19.7 1.0
O B:VAL66 4.7 19.1 1.0
O2 B:SO4303 4.7 42.1 1.0
CA B:ASP134 4.8 20.1 1.0
CG2 B:ILE135 4.8 24.1 1.0
CB B:GLU133 4.9 27.6 1.0
CB B:VAL66 5.0 22.8 1.0
CA B:GLU133 5.0 22.0 1.0

Magnesium binding site 4 out of 8 in 4ijq

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Magnesium binding site 4 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:49.6
occ:1.00
 OAE B:SV2301 2.0 78.3 1.0
OD1 B:ASP193 2.1 22.5 1.0
O B:HOH450 2.1 37.0 1.0
O B:HOH423 2.2 40.0 1.0
O B:HOH415 2.2 29.1 1.0
O1 B:SO4303 2.4 37.0 1.0
CG B:ASP193 3.0 23.9 1.0
OD2 B:ASP193 3.3 25.6 1.0
PAZ B:SV2301 3.4 51.4 1.0
O2 B:SO4303 3.4 42.1 1.0
S B:SO4303 3.5 39.5 1.0
O B:HOH421 3.7 32.9 1.0
NH2 B:ARG199 3.9 21.3 1.0
CAL B:SV2301 4.0 50.9 1.0
OAC B:SV2301 4.0 55.2 1.0
O B:HOH458 4.1 41.9 1.0
O B:ASP193 4.4 22.4 1.0
O3 B:SO4303 4.4 36.7 1.0
CB B:ASP193 4.4 16.2 1.0
O4 B:SO4303 4.5 35.0 1.0
NH1 B:ARG199 4.5 21.4 1.0
O B:HOH443 4.6 38.8 1.0
OAF B:SV2301 4.6 0.0 1.0
CZ B:ARG199 4.6 23.5 1.0
CAJ B:SV2301 4.6 43.3 1.0
OAR B:SV2301 4.8 53.7 1.0
N B:ASP193 4.8 23.4 1.0
C B:ASP193 4.8 21.1 1.0
N2 B:SV2301 4.9 36.5 1.0
CA B:ASP193 5.0 18.9 1.0
O B:HOH437 5.0 42.5 1.0

Magnesium binding site 5 out of 8 in 4ijq

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Magnesium binding site 5 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 5 of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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:40.5
occ:1.00
 OE1 C:GLU133 2.0 36.9 1.0
O C:HOH403 2.1 40.4 1.0
OD1 C:ASP134 2.1 28.2 1.0
O C:HOH467 2.1 34.3 1.0
O C:HOH401 2.1 31.3 1.0
O C:HOH402 2.1 27.5 1.0
CD C:GLU133 2.7 37.1 1.0
CG C:ASP134 3.1 32.3 1.0
OE2 C:GLU133 3.2 39.4 1.0
OD2 C:ASP134 3.4 34.7 1.0
CG C:GLU133 3.7 42.3 1.0
N C:ASP134 4.1 22.4 1.0
O C:ILE135 4.2 33.5 1.0
O4 C:SO4304 4.2 56.9 1.0
N C:ILE135 4.4 21.1 1.0
CB C:ASP134 4.4 26.0 1.0
CG1 C:VAL66 4.5 31.1 1.0
O3 C:SO4304 4.7 60.7 1.0
CA C:ASP134 4.7 21.8 1.0
CG2 C:ILE135 4.7 33.2 1.0
O C:VAL66 4.8 20.0 1.0
CB C:GLU133 4.8 32.1 1.0
CA C:GLU133 4.9 25.0 1.0
CAK C:SV2301 5.0 43.4 1.0

Magnesium binding site 6 out of 8 in 4ijq

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Magnesium binding site 6 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 6 of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:70.6
occ:1.00
 OD2 C:ASP193 2.3 27.0 1.0
OAC C:SV2301 2.6 58.7 1.0
CG C:ASP193 3.0 28.0 1.0
OD1 C:ASP193 3.1 29.3 1.0
O1 C:SO4304 3.5 54.0 1.0
NH2 C:ARG199 3.6 22.1 1.0
OE2 C:GLU196 3.6 52.5 1.0
PAZ C:SV2301 4.0 0.6 1.0
O C:HOH429 4.1 45.8 1.0
CD C:GLU196 4.2 45.0 1.0
N C:GLU196 4.2 25.2 1.0
OAE C:SV2301 4.4 1.0 1.0
CB C:ASP193 4.5 22.1 1.0
CZ C:ARG199 4.6 22.9 1.0
OAF C:SV2301 4.7 80.3 1.0
S C:SO4304 4.7 58.1 1.0
OE1 C:GLU196 4.8 36.5 1.0
O C:HOH425 4.8 39.2 1.0
N C:ASN195 4.8 26.9 1.0
CG C:GLU196 4.8 36.0 1.0
CA C:ASN195 4.8 30.2 1.0
CA C:GLU196 4.8 27.6 1.0
C C:ASN195 4.9 30.4 1.0
O2 C:SO4304 5.0 54.0 1.0

Magnesium binding site 7 out of 8 in 4ijq

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Magnesium binding site 7 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 7 of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:50.6
occ:1.00
 OAE D:SV2302 2.1 96.2 1.0
OD1 D:ASP193 2.1 27.3 1.0
O D:HOH465 2.1 49.8 1.0
O D:HOH433 2.1 43.5 1.0
O D:HOH460 2.2 40.9 1.0
O4 D:SO4304 2.5 53.7 1.0
CG D:ASP193 2.9 32.4 1.0
OD2 D:ASP193 3.0 31.5 1.0
PAZ D:SV2302 3.4 96.9 1.0
S D:SO4304 3.6 57.4 1.0
O3 D:SO4304 3.7 57.1 1.0
O D:HOH455 3.8 30.4 1.0
CAL D:SV2302 3.9 50.1 1.0
NH2 D:ARG199 4.1 28.1 1.0
OAF D:SV2302 4.1 57.7 1.0
O D:ASP193 4.2 26.0 1.0
CB D:ASP193 4.3 21.5 1.0
OAR D:SV2302 4.4 51.1 1.0
O2 D:SO4304 4.5 54.8 1.0
OAC D:SV2302 4.6 78.8 1.0
NH1 D:ARG199 4.6 20.1 1.0
O1 D:SO4304 4.6 53.7 1.0
N2 D:SV2302 4.7 24.2 1.0
N D:ASP193 4.7 22.5 1.0
C D:ASP193 4.7 25.2 1.0
CZ D:ARG199 4.8 22.8 1.0
CA D:ASP193 4.8 20.4 1.0

Magnesium binding site 8 out of 8 in 4ijq

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Magnesium binding site 8 out of 8 in the Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-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 8 of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with [(2-((Guanine-9H-Yl)Methyl)Propane-1,3-Diyl)Bis(Oxy)]Bis(Methylene)) Diphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:34.3
occ:1.00
 O D:HOH404 2.1 30.8 1.0
O D:HOH402 2.1 29.4 1.0
OE1 D:GLU133 2.1 38.2 1.0
O D:HOH403 2.1 32.0 1.0
O D:HOH401 2.1 29.4 1.0
OD1 D:ASP134 2.2 25.3 1.0
CD D:GLU133 2.9 37.7 1.0
CG D:ASP134 3.2 25.6 1.0
OE2 D:GLU133 3.4 35.2 1.0
OD2 D:ASP134 3.5 31.2 1.0
CG D:GLU133 3.9 38.1 1.0
O1 D:SO4304 3.9 53.7 1.0
N D:ASP134 4.2 20.0 1.0
CAJ D:SV2302 4.4 49.1 1.0
CG1 D:VAL66 4.4 25.3 1.0
CB D:ASP134 4.5 23.1 1.0
O D:ILE135 4.5 24.3 1.0
N D:ILE135 4.6 21.8 1.0
O3 D:SO4304 4.6 57.1 1.0
O D:VAL66 4.7 22.0 1.0
CA D:ASP134 4.8 14.5 1.0
S D:SO4304 4.9 57.4 1.0
CB D:VAL66 5.0 23.5 1.0

Reference:

D.T.Keough, P.Spacek, D.Hockova, T.Tichy, S.Vrbkova, L.Slavetinska, Z.Janeba, L.Naesens, M.D.Edstein, M.Chavchich, T.H.Wang, J.Jersey, L.W.Guddat. Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group Are Potent Inhibitors of 6-Oxopurine Phosphoribosyltransferases and Have Antimalarial Activity J.Med.Chem. V. 56 2513 2013.
ISSN: ISSN 0022-2623
PubMed: 23448281
DOI: 10.1021/JM301893B
Page generated: Fri Aug 16 16:45:37 2024

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