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Cadmium in PDB 3t9a: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0:
2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0, PDB code: 3t9a was solved by H.Wang, J.Falck, T.M.T.Hall, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.80 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.134, 110.504, 41.437, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.6

Other elements in 3t9a:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0 (pdb code 3t9a). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0, PDB code: 3t9a:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3t9a

Go back to Cadmium Binding Sites List in 3t9a
Cadmium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:28.0
occ:0.53
 O A:HOH597 2.3 44.0 1.0
O A:HOH527 2.4 38.2 1.0
O A:HOH622 2.5 37.1 1.0
SG A:CYS164 2.6 33.4 1.0
O A:HOH8 2.7 19.6 1.0
O A:HOH704 2.9 42.9 1.0
CB A:CYS164 3.3 37.4 1.0
CA A:CYS164 3.6 37.6 1.0
CD A:CD605 4.1 27.2 0.8
O A:LEU166 4.2 31.1 1.0
O A:GLU163 4.3 42.8 1.0
N A:ASN165 4.3 35.1 1.0
C A:CYS164 4.4 36.6 1.0
O A:HOH593 4.5 32.5 1.0
O A:HOH705 4.5 19.4 1.0
N A:LEU166 4.6 32.1 1.0
NH2 A:ARG156 4.6 30.3 1.0
N A:CYS164 4.7 40.4 1.0
NE A:ARG156 4.8 33.1 1.0
C A:GLU163 5.0 42.7 1.0

Cadmium binding site 2 out of 2 in 3t9a

Go back to Cadmium Binding Sites List in 3t9a
Cadmium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:27.2
occ:0.83
 O A:HOH593 2.4 32.5 1.0
SG A:CYS164 2.5 33.4 1.0
O A:HOH670 2.5 16.5 1.0
O A:HOH705 2.6 19.4 1.0
CB A:CYS164 3.4 37.4 1.0
O A:HOH704 3.7 42.9 1.0
CD A:CD604 4.1 28.0 0.5
O A:LEU166 4.2 31.1 1.0
O A:HOH527 4.7 38.2 1.0
CA A:CYS164 4.8 37.6 1.0
CG1 A:ILE167 4.9 31.4 1.0

Reference:

H.Wang, J.R.Falck, T.M.Hall, S.B.Shears. Structural Basis For An Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nat.Chem.Biol. V. 8 111 2011.
ISSN: ISSN 1552-4450
PubMed: 22119861
DOI: 10.1038/NCHEMBIO.733
Page generated: Thu Jul 10 13:01:07 2025

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