Magnesium in PDB 5w8v: Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid
Enzymatic activity of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid
All present enzymatic activity of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid:
2.4.2.8;
Protein crystallography data
The structure of Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid, PDB code: 5w8v
was solved by
L.W.Guddat,
D.T.Keough,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.03 /
2.35
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.667,
128.399,
65.326,
90.00,
102.98,
90.00
|
R / Rfree (%)
|
19.6 /
24.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid
(pdb code 5w8v). 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 [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid, PDB code: 5w8v:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5w8v
Go back to
Magnesium Binding Sites List in 5w8v
Magnesium binding site 1 out
of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:41.6
occ:1.00
|
O
|
A:HOH433
|
1.9
|
29.7
|
1.0
|
O
|
A:HOH436
|
2.1
|
36.1
|
1.0
|
OE1
|
A:GLU133
|
2.1
|
43.2
|
1.0
|
O
|
A:HOH455
|
2.1
|
43.7
|
1.0
|
OD1
|
A:ASP134
|
2.1
|
35.9
|
1.0
|
O
|
A:HOH476
|
2.6
|
42.4
|
1.0
|
CD
|
A:GLU133
|
2.9
|
41.6
|
1.0
|
CG
|
A:ASP134
|
3.1
|
37.0
|
1.0
|
OE2
|
A:GLU133
|
3.2
|
41.1
|
1.0
|
OD2
|
A:ASP134
|
3.4
|
38.0
|
1.0
|
O
|
A:HOH493
|
3.7
|
54.8
|
1.0
|
OAF
|
A:9YP301
|
4.1
|
69.2
|
1.0
|
N
|
A:ASP134
|
4.2
|
33.8
|
1.0
|
O
|
A:ILE135
|
4.3
|
41.6
|
1.0
|
CG
|
A:GLU133
|
4.3
|
40.7
|
1.0
|
N
|
A:ILE135
|
4.4
|
35.3
|
1.0
|
CB
|
A:ASP134
|
4.4
|
31.4
|
1.0
|
CG1
|
A:VAL66
|
4.5
|
31.1
|
1.0
|
O
|
A:HOH487
|
4.7
|
37.7
|
1.0
|
CG2
|
A:ILE135
|
4.7
|
30.9
|
1.0
|
CB
|
A:GLU133
|
4.7
|
34.0
|
1.0
|
CA
|
A:ASP134
|
4.8
|
32.2
|
1.0
|
O
|
A:VAL66
|
4.8
|
32.1
|
1.0
|
CAM
|
A:9YP301
|
4.9
|
57.2
|
1.0
|
O
|
A:HOH439
|
4.9
|
36.6
|
1.0
|
CB
|
A:VAL66
|
5.0
|
34.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5w8v
Go back to
Magnesium Binding Sites List in 5w8v
Magnesium binding site 2 out
of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Hgprt in Complex with [(2-[(Guanin-9-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:37.2
occ:1.00
|
O
|
B:HOH455
|
2.0
|
45.4
|
1.0
|
OD1
|
B:ASP134
|
2.1
|
39.5
|
1.0
|
OE2
|
B:GLU133
|
2.1
|
44.5
|
1.0
|
O
|
B:HOH490
|
2.2
|
44.7
|
1.0
|
O
|
B:HOH452
|
2.3
|
26.1
|
1.0
|
O
|
B:HOH423
|
2.4
|
33.0
|
1.0
|
CD
|
B:GLU133
|
2.9
|
44.3
|
1.0
|
CG
|
B:ASP134
|
3.0
|
37.1
|
1.0
|
OD2
|
B:ASP134
|
3.3
|
32.8
|
1.0
|
OE1
|
B:GLU133
|
3.6
|
44.0
|
1.0
|
CG
|
B:GLU133
|
3.7
|
47.9
|
1.0
|
O
|
B:HOH501
|
3.8
|
41.5
|
1.0
|
O
|
B:HOH444
|
3.9
|
48.8
|
1.0
|
N
|
B:ASP134
|
4.0
|
28.8
|
1.0
|
CAM
|
B:9YP301
|
4.2
|
65.9
|
1.0
|
CB
|
B:ASP134
|
4.3
|
32.0
|
1.0
|
N
|
B:ILE135
|
4.3
|
29.6
|
1.0
|
OAE
|
B:9YP301
|
4.3
|
66.3
|
1.0
|
O
|
B:ILE135
|
4.4
|
44.4
|
1.0
|
O
|
B:HOH466
|
4.6
|
33.1
|
1.0
|
CG1
|
B:VAL66
|
4.6
|
30.1
|
1.0
|
CG2
|
B:ILE135
|
4.6
|
40.4
|
1.0
|
CA
|
B:ASP134
|
4.6
|
28.5
|
1.0
|
O
|
B:VAL66
|
4.8
|
37.1
|
1.0
|
CB
|
B:GLU133
|
4.9
|
39.8
|
1.0
|
O
|
B:HOH426
|
5.0
|
33.8
|
1.0
|
CB
|
B:VAL66
|
5.0
|
39.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5w8v
Go back to
Magnesium Binding Sites List in 5w8v
Magnesium binding site 3 out
of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Hgprt in Complex with [(2-[(Guanin-9-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:42.5
occ:1.00
|
O
|
C:HOH427
|
2.0
|
49.5
|
1.0
|
O
|
C:HOH418
|
2.0
|
34.4
|
1.0
|
O
|
C:HOH410
|
2.0
|
27.9
|
1.0
|
OD1
|
C:ASP134
|
2.1
|
47.8
|
1.0
|
OE1
|
C:GLU133
|
2.2
|
33.9
|
1.0
|
O
|
C:HOH453
|
2.2
|
38.6
|
1.0
|
CD
|
C:GLU133
|
3.0
|
39.1
|
1.0
|
CG
|
C:ASP134
|
3.1
|
42.0
|
1.0
|
OE2
|
C:GLU133
|
3.2
|
43.9
|
1.0
|
OD2
|
C:ASP134
|
3.3
|
40.0
|
1.0
|
OAC
|
C:9YP301
|
3.9
|
67.0
|
1.0
|
O
|
C:HOH481
|
4.3
|
45.4
|
1.0
|
N
|
C:ASP134
|
4.3
|
34.6
|
1.0
|
O
|
C:ILE135
|
4.3
|
47.4
|
1.0
|
CG
|
C:GLU133
|
4.4
|
36.0
|
1.0
|
N
|
C:ILE135
|
4.4
|
34.7
|
1.0
|
CB
|
C:ASP134
|
4.5
|
33.8
|
1.0
|
CG1
|
C:VAL66
|
4.5
|
35.7
|
1.0
|
O
|
C:HOH502
|
4.5
|
43.9
|
1.0
|
CAM
|
C:9YP301
|
4.5
|
62.9
|
1.0
|
CG2
|
C:ILE135
|
4.7
|
35.5
|
1.0
|
CB
|
C:GLU133
|
4.8
|
34.6
|
1.0
|
CA
|
C:ASP134
|
4.9
|
30.6
|
1.0
|
O
|
C:HOH403
|
5.0
|
52.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5w8v
Go back to
Magnesium Binding Sites List in 5w8v
Magnesium binding site 4 out
of 4 in the Human Hgprt in Complex with [(2-[(Guanin-9-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 Hgprt in Complex with [(2-[(Guanin-9-Yl)Methyl]Propane-1,3- Diyl)Bis(Oxy)]Bis(Methylene)Diphosphonic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:33.0
occ:1.00
|
O
|
D:HOH462
|
2.0
|
30.5
|
1.0
|
O
|
D:HOH484
|
2.1
|
30.9
|
1.0
|
OD1
|
D:ASP134
|
2.1
|
37.8
|
1.0
|
OE1
|
D:GLU133
|
2.1
|
34.7
|
1.0
|
O
|
D:HOH458
|
2.2
|
33.3
|
1.0
|
O
|
D:HOH446
|
2.3
|
29.5
|
1.0
|
CD
|
D:GLU133
|
3.0
|
37.2
|
1.0
|
CG
|
D:ASP134
|
3.1
|
40.0
|
1.0
|
OE2
|
D:GLU133
|
3.3
|
39.1
|
1.0
|
OD2
|
D:ASP134
|
3.4
|
43.1
|
1.0
|
O
|
D:HOH416
|
4.0
|
38.1
|
1.0
|
OAC
|
D:9YP301
|
4.1
|
56.8
|
1.0
|
N
|
D:ASP134
|
4.2
|
36.6
|
1.0
|
O
|
D:HOH500
|
4.3
|
49.8
|
1.0
|
CB
|
D:ASP134
|
4.4
|
36.1
|
1.0
|
N
|
D:ILE135
|
4.4
|
37.9
|
1.0
|
CG
|
D:GLU133
|
4.4
|
38.1
|
1.0
|
CG2
|
D:ILE135
|
4.4
|
43.0
|
1.0
|
O
|
D:ILE135
|
4.5
|
40.5
|
1.0
|
CAM
|
D:9YP301
|
4.6
|
57.6
|
1.0
|
CG1
|
D:VAL66
|
4.6
|
34.8
|
1.0
|
O
|
D:HOH443
|
4.7
|
39.9
|
1.0
|
O
|
D:VAL66
|
4.8
|
33.6
|
1.0
|
CA
|
D:ASP134
|
4.8
|
37.2
|
1.0
|
CB
|
D:GLU133
|
4.8
|
35.8
|
1.0
|
|
Reference:
P.Spacek,
D.T.Keough,
M.Chavchich,
M.Dracinsky,
Z.Janeba,
L.Naesens,
M.D.Edstein,
L.W.Guddat,
D.Hockova.
Synthesis and Evaluation of Asymmetric Acyclic Nucleoside Bisphosphonates As Inhibitors of Plasmodium Falciparum and Human Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase. J. Med. Chem. V. 60 7539 2017.
ISSN: ISSN 1520-4804
PubMed: 28813147
DOI: 10.1021/ACS.JMEDCHEM.7B00926
Page generated: Mon Sep 30 06:30:58 2024
|