Cadmium in PDB 8ypy: Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
Enzymatic activity of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
All present enzymatic activity of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands:
2.7.6.1;
Protein crystallography data
The structure of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands, PDB code: 8ypy
was solved by
L.Zhang,
L.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.91 /
2.74
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.701,
73.598,
170.5,
90,
94.44,
90
|
R / Rfree (%)
|
27.2 /
28.6
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
(pdb code 8ypy). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the
Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands, PDB code: 8ypy:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
Cadmium binding site 1 out
of 6 in 8ypy
Go back to
Cadmium Binding Sites List in 8ypy
Cadmium binding site 1 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1003
b:90.4
occ:1.00
|
OD2
|
A:ASP223
|
2.7
|
47.3
|
1.0
|
OD1
|
A:ASP174
|
3.2
|
64.0
|
1.0
|
OD2
|
A:ASP174
|
3.2
|
73.6
|
1.0
|
OD1
|
A:ASP223
|
3.3
|
32.1
|
1.0
|
CG
|
A:ASP223
|
3.3
|
34.4
|
1.0
|
CG
|
A:ASP174
|
3.4
|
57.1
|
1.0
|
O3G
|
A:APC1001
|
3.6
|
75.5
|
1.0
|
O
|
A:HOH1112
|
3.8
|
50.7
|
1.0
|
O2G
|
A:APC1001
|
3.9
|
77.6
|
1.0
|
O1A
|
A:APC1001
|
4.1
|
96.7
|
1.0
|
OD1
|
A:ASP224
|
4.1
|
30.8
|
1.0
|
PG
|
A:APC1001
|
4.3
|
93.5
|
1.0
|
CE1
|
A:HIS133
|
4.5
|
48.0
|
1.0
|
CB
|
A:ASP174
|
4.7
|
45.6
|
1.0
|
CB
|
A:ASP223
|
4.8
|
25.1
|
1.0
|
O1
|
A:HSX1002
|
5.0
|
71.9
|
1.0
|
|
Cadmium binding site 2 out
of 6 in 8ypy
Go back to
Cadmium Binding Sites List in 8ypy
Cadmium binding site 2 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd2002
b:93.0
occ:1.00
|
OD2
|
B:ASP174
|
2.3
|
62.6
|
1.0
|
CG
|
B:ASP174
|
3.0
|
57.7
|
1.0
|
OD1
|
B:ASP174
|
3.3
|
68.3
|
1.0
|
OD2
|
B:ASP223
|
3.3
|
48.8
|
1.0
|
O2A
|
C:APC1001
|
3.6
|
96.8
|
1.0
|
OD1
|
B:ASP223
|
3.9
|
60.2
|
1.0
|
CG
|
B:ASP223
|
4.0
|
58.1
|
1.0
|
O3G
|
C:APC1001
|
4.1
|
73.4
|
1.0
|
CB
|
B:ASP174
|
4.3
|
43.5
|
1.0
|
CE1
|
B:HIS133
|
4.4
|
55.7
|
1.0
|
O3B
|
C:APC1001
|
4.6
|
100.2
|
1.0
|
OD1
|
B:ASP224
|
4.9
|
54.0
|
1.0
|
|
Cadmium binding site 3 out
of 6 in 8ypy
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Cadmium Binding Sites List in 8ypy
Cadmium binding site 3 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd1004
b:129.3
occ:1.00
|
OD2
|
C:ASP174
|
2.5
|
107.5
|
1.0
|
OD1
|
C:ASP174
|
2.6
|
101.4
|
1.0
|
OD2
|
C:ASP223
|
2.7
|
95.7
|
1.0
|
CG
|
C:ASP174
|
2.8
|
100.7
|
1.0
|
O2G
|
C:APC1002
|
2.9
|
125.2
|
1.0
|
CG
|
C:ASP223
|
3.6
|
88.5
|
1.0
|
OD1
|
C:ASP223
|
3.6
|
86.7
|
1.0
|
O2A
|
C:APC1002
|
3.7
|
121.3
|
1.0
|
O3B
|
C:APC1002
|
3.8
|
129.9
|
1.0
|
PG
|
C:APC1002
|
3.8
|
131.3
|
1.0
|
O3G
|
C:APC1002
|
4.1
|
118.0
|
1.0
|
CB
|
C:ASP174
|
4.2
|
90.5
|
1.0
|
O1A
|
C:APC1002
|
4.3
|
128.1
|
1.0
|
PA
|
C:APC1002
|
4.5
|
133.0
|
1.0
|
OD1
|
C:ASP224
|
4.5
|
78.9
|
1.0
|
CE1
|
C:HIS133
|
4.9
|
86.8
|
1.0
|
N
|
C:GLY177
|
5.0
|
93.0
|
1.0
|
|
Cadmium binding site 4 out
of 6 in 8ypy
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Cadmium Binding Sites List in 8ypy
Cadmium binding site 4 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd1003
b:114.2
occ:1.00
|
OD2
|
D:ASP223
|
2.6
|
75.4
|
1.0
|
O2G
|
D:APC1001
|
2.9
|
118.6
|
1.0
|
CG
|
D:ASP223
|
3.4
|
76.6
|
1.0
|
OD1
|
D:ASP223
|
3.4
|
77.3
|
1.0
|
O2A
|
D:APC1001
|
4.2
|
123.4
|
1.0
|
O1A
|
D:APC1001
|
4.3
|
132.3
|
1.0
|
OD2
|
D:ASP174
|
4.3
|
98.9
|
1.0
|
PG
|
D:APC1001
|
4.4
|
135.6
|
1.0
|
OD1
|
D:ASP224
|
4.4
|
71.7
|
1.0
|
OD1
|
D:ASP174
|
4.7
|
105.2
|
1.0
|
N
|
D:GLY177
|
4.7
|
88.5
|
1.0
|
CG
|
D:ASP174
|
4.8
|
95.9
|
1.0
|
CB
|
D:ASP223
|
4.8
|
70.6
|
1.0
|
O3B
|
D:APC1001
|
4.8
|
133.6
|
1.0
|
PA
|
D:APC1001
|
4.8
|
138.2
|
1.0
|
|
Cadmium binding site 5 out
of 6 in 8ypy
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Cadmium Binding Sites List in 8ypy
Cadmium binding site 5 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cd1003
b:87.3
occ:1.00
|
OD2
|
E:ASP174
|
3.0
|
73.7
|
1.0
|
O2A
|
E:APC1001
|
3.1
|
88.4
|
1.0
|
OD1
|
E:ASP174
|
3.2
|
60.7
|
1.0
|
OD2
|
E:ASP223
|
3.4
|
72.2
|
1.0
|
CG
|
E:ASP174
|
3.5
|
56.8
|
1.0
|
O2G
|
E:APC1001
|
3.5
|
81.6
|
1.0
|
OD1
|
E:ASP223
|
3.9
|
56.3
|
1.0
|
CG
|
E:ASP223
|
4.0
|
59.0
|
1.0
|
CE1
|
E:HIS133
|
4.4
|
56.7
|
1.0
|
PA
|
E:APC1001
|
4.4
|
94.9
|
1.0
|
PG
|
E:APC1001
|
4.7
|
91.4
|
1.0
|
O3B
|
E:APC1001
|
4.8
|
96.1
|
1.0
|
O1A
|
E:APC1001
|
4.9
|
97.7
|
1.0
|
CB
|
E:ASP174
|
4.9
|
54.4
|
1.0
|
NE2
|
E:HIS133
|
5.0
|
60.1
|
1.0
|
|
Cadmium binding site 6 out
of 6 in 8ypy
Go back to
Cadmium Binding Sites List in 8ypy
Cadmium binding site 6 out
of 6 in the Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cd2002
b:86.9
occ:1.00
|
OD2
|
F:ASP174
|
2.6
|
54.9
|
1.0
|
O
|
F:HOH2128
|
3.1
|
46.8
|
1.0
|
O2A
|
A:APC1004
|
3.1
|
97.3
|
1.0
|
OD2
|
F:ASP223
|
3.2
|
45.3
|
1.0
|
CG
|
F:ASP174
|
3.4
|
48.5
|
1.0
|
OD1
|
F:ASP223
|
3.6
|
32.3
|
1.0
|
CG
|
F:ASP223
|
3.8
|
33.3
|
1.0
|
OD1
|
F:ASP174
|
3.8
|
51.9
|
1.0
|
CE1
|
F:HIS133
|
4.1
|
39.2
|
1.0
|
PA
|
A:APC1004
|
4.3
|
113.8
|
1.0
|
OD1
|
F:ASP224
|
4.3
|
37.9
|
1.0
|
O3G
|
A:APC1004
|
4.4
|
85.0
|
1.0
|
CB
|
F:ASP174
|
4.5
|
36.8
|
1.0
|
C3A
|
A:APC1004
|
4.8
|
89.4
|
1.0
|
O1A
|
A:APC1004
|
4.8
|
94.4
|
1.0
|
NE2
|
F:HIS133
|
4.9
|
40.8
|
1.0
|
O1
|
F:HSX2001
|
5.0
|
71.9
|
1.0
|
|
Reference:
L.Zhang,
L.Zhang.
Crystal Strcuture of Human Phosphoribosyl Pyrophosphate SYNTHETASE2 (PRPS2) in Complex with Ligands To Be Published.
Page generated: Thu Jul 10 15:58:47 2025
|