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Cadmium in PDB 3t9f: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8):
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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8), PDB code: 3t9f 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) 38.82 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.036, 110.009, 41.484, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 3t9f:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8) also contains other interesting chemical elements:

Magnesium (Mg) 5 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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) (pdb code 3t9f). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8), PDB code: 3t9f:

Cadmium binding site 1 out of 1 in 3t9f

Go back to Cadmium Binding Sites List in 3t9f
Cadmium binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pp)2-IP4 (1,5-IP8)


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 Adp and 1,5- (Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:13.4
occ:1.00
 O51 A:I8P501 2.1 18.1 1.0
O A:HOH399 2.1 18.5 1.0
O2B A:ADP401 2.2 7.2 1.0
OD1 A:ASN323 2.2 10.5 1.0
OD2 A:ASP321 2.4 7.1 1.0
OD1 A:ASP321 2.6 6.1 1.0
CG A:ASP321 2.8 6.2 1.0
CG A:ASN323 3.2 10.0 1.0
PB A:ADP401 3.3 9.1 1.0
O3B A:ADP401 3.3 6.4 1.0
PB1 A:I8P501 3.4 27.6 1.0
ND2 A:ASN323 3.6 8.5 1.0
O61 A:I8P501 3.6 21.1 1.0
MG A:MG602 3.8 7.0 1.0
O A:HOH594 3.9 26.0 1.0
NH1 A:ARG134 4.1 9.0 0.6
CE1 A:HIS194 4.1 14.7 1.0
O41 A:I8P501 4.3 25.9 1.0
O3A A:ADP401 4.3 8.6 1.0
CB A:ASP321 4.4 6.4 1.0
O1B A:ADP401 4.4 11.4 1.0
O A:ALA191 4.4 12.3 1.0
O71 A:I8P501 4.5 24.6 1.0
ND1 A:HIS194 4.5 13.3 1.0
O A:HOH608 4.5 20.8 1.0
CB A:ASN323 4.6 9.7 1.0
O A:HOH477 4.7 16.2 1.0
O2A A:ADP401 4.8 10.9 1.0
NH2 A:ARG134 4.8 7.3 0.4
NH2 A:ARG134 4.9 3.0 0.6
O A:HOH517 4.9 25.0 1.0
O A:HOH5 4.9 12.8 1.0
CZ A:ARG134 5.0 7.4 0.6

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: Sun Jan 24 09:56:01 2021

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