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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

Go back to 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

Go back to 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

Go back to 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

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