Atomistry » Magnesium » PDB 4iir-4iwh » 4ijq
Atomistry »
  Magnesium »
    PDB 4iir-4iwh »
      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: Fri Aug 16 16:45:37 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy