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Cadmium in PDB 3t54: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium:
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 Atp and Cadmium, PDB code: 3t54 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) 27.50 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.957, 110.597, 41.307, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.6

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 Atp and Cadmium (pdb code 3t54). 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 Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium, PDB code: 3t54:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


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 Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:17.1
occ:0.53
 O A:HOH425 1.9 25.1 1.0
O3G A:ATP401 1.9 20.8 1.0
OD1 A:ASN323 2.1 18.9 1.0
O2B A:ATP401 2.1 17.5 1.0
OD1 A:ASP321 2.3 18.1 1.0
OD2 A:ASP321 2.5 16.7 1.0
CG A:ASP321 2.7 17.8 1.0
PG A:ATP401 3.2 25.6 1.0
CG A:ASN323 3.2 18.2 1.0
PB A:ATP401 3.3 20.5 1.0
O3B A:ATP401 3.6 22.0 1.0
O A:HOH550 3.7 32.3 1.0
ND2 A:ASN323 3.7 19.5 1.0
O1G A:ATP401 3.7 24.3 1.0
CD A:CD602 4.2 18.9 0.4
CB A:ASP321 4.2 17.0 1.0
O A:HOH472 4.3 39.9 1.0
O1B A:ATP401 4.3 21.9 1.0
O2G A:ATP401 4.4 23.9 1.0
NH1 A:ARG134 4.4 19.7 1.0
O A:ALA191 4.4 19.6 1.0
CB A:ASN323 4.5 16.9 1.0
O3A A:ATP401 4.5 18.6 1.0
CE1 A:HIS194 4.5 19.8 1.0
O A:HOH393 4.6 20.2 1.0
O2A A:ATP401 4.8 17.9 1.0
ND1 A:HIS194 4.8 20.0 1.0
CA A:ASN323 4.9 17.0 1.0
O A:HOH15 5.0 20.0 1.0

Cadmium binding site 2 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


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 Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:18.9
occ:0.40
 OD2 A:ASP309 1.7 15.4 0.7
O1G A:ATP401 2.1 24.3 1.0
O2A A:ATP401 2.1 17.9 1.0
O A:HOH424 2.1 27.6 1.0
OD2 A:ASP321 2.2 16.7 1.0
OD2 A:ASP309 2.6 14.3 0.3
CG A:ASP309 2.9 14.6 0.7
O3B A:ATP401 3.1 22.0 1.0
PG A:ATP401 3.2 25.6 1.0
CG A:ASP321 3.3 17.8 1.0
CG A:ASP309 3.5 13.7 0.3
PA A:ATP401 3.5 16.9 1.0
OD1 A:ASP309 3.6 15.8 0.7
CB A:ASP321 3.7 17.0 1.0
NZ A:LYS248 4.0 32.0 1.0
PB A:ATP401 4.0 20.5 1.0
O3G A:ATP401 4.0 20.8 1.0
CB A:ASP309 4.0 13.7 0.7
O2B A:ATP401 4.1 17.5 1.0
O3' A:ATP401 4.1 21.1 1.0
O3A A:ATP401 4.1 18.6 1.0
CB A:ASP309 4.2 14.0 0.3
CD A:CD601 4.2 17.1 0.5
OD1 A:ASP309 4.2 14.0 0.3
ND2 A:ASN323 4.2 19.5 1.0
O1A A:ATP401 4.3 17.6 1.0
O2G A:ATP401 4.3 23.9 1.0
OD1 A:ASP321 4.4 18.1 1.0
O5' A:ATP401 4.5 18.5 1.0
CE A:LYS248 4.5 29.9 1.0
C3' A:ATP401 4.6 20.7 1.0
C5' A:ATP401 4.6 17.8 1.0
O A:HOH527 4.8 27.5 1.0
OD1 A:ASN323 4.9 18.9 1.0

Cadmium binding site 3 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:14.1
occ:0.90
 O A:GLN303 2.3 20.7 1.0
OG1 A:THR251 2.3 19.1 1.0
SG A:CYS306 2.4 21.8 1.0
O A:THR304 2.4 18.7 1.0
SG A:CYS298 2.5 19.6 1.0
C A:THR304 3.1 19.2 1.0
CB A:CYS298 3.3 16.7 1.0
C A:GLN303 3.4 20.6 1.0
CB A:CYS306 3.4 18.1 1.0
N A:CYS306 3.5 17.3 1.0
CA A:THR304 3.7 20.1 1.0
CB A:THR251 3.7 15.5 1.0
CA A:CYS298 3.7 16.7 1.0
O A:HOH569 4.0 31.0 1.0
C A:VAL305 4.0 17.7 1.0
N A:THR304 4.0 21.0 1.0
N A:VAL305 4.0 17.7 1.0
CA A:CYS306 4.0 17.9 1.0
O A:THR251 4.2 15.0 1.0
N A:GLY253 4.3 15.7 1.0
CA A:VAL305 4.3 17.8 1.0
C A:THR251 4.4 15.5 1.0
CG2 A:THR251 4.5 16.1 1.0
O A:CYS298 4.6 16.1 1.0
CA A:GLN303 4.6 20.1 1.0
C A:CYS298 4.6 16.4 1.0
CA A:THR251 4.6 15.8 1.0
O A:VAL305 4.6 17.1 1.0
O A:CYS306 4.7 18.1 1.0
CA A:GLY253 4.7 15.8 1.0
O A:GLY253 4.7 15.5 1.0
C A:CYS306 4.7 17.2 1.0
C A:GLY253 4.7 16.2 1.0
CB A:GLN303 4.8 20.4 1.0
N A:CYS298 4.8 15.2 1.0
O A:HOH534 5.0 38.9 1.0
N A:VAL252 5.0 15.3 1.0

Cadmium binding site 4 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:25.4
occ:0.89
 O A:HOH423 1.9 23.8 1.0
O A:HOH426 2.2 30.1 1.0
SG A:CYS164 2.5 34.8 1.0
O A:HOH619 2.7 21.4 1.0
CB A:CYS164 3.4 38.9 1.0
O A:HOH422 3.8 54.1 1.0
O A:LEU166 4.1 32.0 1.0
CD A:CD605 4.2 26.4 0.5
O A:HOH623 4.6 37.4 1.0
CA A:CYS164 4.9 38.9 1.0

Cadmium binding site 5 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:26.4
occ:0.47
 O A:HOH623 2.2 37.4 1.0
O A:HOH629 2.3 46.3 1.0
SG A:CYS164 2.6 34.8 1.0
O A:HOH618 2.7 17.7 1.0
O A:HOH422 3.0 54.1 1.0
CB A:CYS164 3.4 38.9 1.0
CA A:CYS164 3.7 38.9 1.0
CD A:CD604 4.2 25.4 0.9
O A:LEU166 4.3 32.0 1.0
O A:GLU163 4.3 44.3 1.0
N A:ASN165 4.4 35.9 1.0
O A:HOH426 4.4 30.1 1.0
C A:CYS164 4.5 37.9 1.0
O A:HOH423 4.5 23.8 1.0
NH2 A:ARG156 4.6 25.7 1.0
NE A:ARG156 4.6 30.4 1.0
N A:LEU166 4.7 32.8 1.0
N A:CYS164 4.8 41.6 1.0
C A:GLU163 5.0 44.5 1.0

Cadmium binding site 6 out of 6 in 3t54

Go back to Cadmium Binding Sites List in 3t54
Cadmium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Atp and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd606

b:17.2
occ:0.76
 NZ A:LYS187 2.1 17.4 1.0
OE1 A:GLU237 2.1 22.6 1.0
SG A:CYS320 2.3 27.4 1.0
N7 A:ATP401 2.4 16.1 1.0
CE A:LYS187 2.9 17.7 1.0
CB A:CYS320 3.1 21.7 1.0
CD A:GLU237 3.2 22.4 1.0
C8 A:ATP401 3.2 17.9 1.0
C5 A:ATP401 3.4 16.6 1.0
O A:HOH527 3.4 27.5 1.0
OE2 A:GLU237 3.6 24.9 1.0
O A:CYS320 3.6 20.5 1.0
N6 A:ATP401 3.7 15.8 1.0
OH A:TYR138 3.8 27.9 1.0
C6 A:ATP401 3.9 17.0 1.0
C A:CYS320 4.2 20.0 1.0
CA A:CYS320 4.2 21.1 1.0
O1A A:ATP401 4.3 17.6 1.0
CD A:LYS187 4.3 17.1 1.0
N9 A:ATP401 4.4 18.1 1.0
C4 A:ATP401 4.4 18.7 1.0
CG A:GLU237 4.5 21.4 1.0
CG A:PRO149 4.5 22.2 1.0
CD1 A:LEU311 4.6 23.5 1.0
O A:HOH470 4.7 50.7 1.0
N A:CYS320 4.9 20.2 1.0
CZ A:TYR138 4.9 24.6 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: Sat Dec 12 08:23:12 2020

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