Atomistry » Magnesium » PDB 4ijm-4ix3 » 4ijq
Atomistry »
  Magnesium »
    PDB 4ijm-4ix3 »
      4ijq »

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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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

Go back to Magnesium Binding Sites List in 4ijq
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: Mon Aug 11 14:13:22 2025

Last articles

Mg in 4JJS
Mg in 4JJ2
Mg in 4JIW
Mg in 4JIV
Mg in 4JIB
Mg in 4JI4
Mg in 4JI5
Mg in 4JI1
Mg in 4JI0
Mg in 4JI2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy