Atomistry » Cadmium » PDB 3oeo-3umh » 3t9a
Atomistry »
  Cadmium »
    PDB 3oeo-3umh »
      3t9a »

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: Fri Jul 19 16:33:13 2024

Last articles

Zn in 7WTZ
Zn in 7WTX
Zn in 7WTW
Zn in 7WT5
Zn in 7WTU
Zn in 7WTV
Zn in 7WTT
Zn in 7WT4
Zn in 7WT3
Zn in 7WSS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy