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Cobalt in PDB 4pgz: Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation

Enzymatic activity of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation

All present enzymatic activity of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation:
2.7.10.1;

Protein crystallography data

The structure of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation, PDB code: 4pgz was solved by A.V.Reshetnyak, T.J.Boggon, I.Lax, J.Schlessinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.39 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.592, 63.548, 81.547, 90.00, 117.46, 90.00
R / Rfree (%) 23.2 / 26.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation (pdb code 4pgz). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation, PDB code: 4pgz:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 4pgz

Go back to Cobalt Binding Sites List in 4pgz
Cobalt binding site 1 out of 5 in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co602

b:86.5
occ:1.00
 OE2 C:GLU360 2.1 0.3 1.0
O C:HOH717 2.3 58.8 1.0
CD C:GLU360 3.1 89.7 1.0
OE1 C:GLU360 3.4 93.3 1.0
O C:ASP357 4.1 99.2 1.0
O C:TRP359 4.3 50.8 1.0
CG C:GLU360 4.5 77.3 1.0
C C:ASP357 4.8 97.6 1.0
CB C:ASP357 4.9 0.5 1.0
CA C:ASP357 5.0 0.1 1.0

Cobalt binding site 2 out of 5 in 4pgz

Go back to Cobalt Binding Sites List in 4pgz
Cobalt binding site 2 out of 5 in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co603

b:91.8
occ:1.00
 OE2 C:GLU435 2.3 0.7 1.0
O C:HOH703 2.3 73.4 1.0
OE1 C:GLU435 2.8 0.7 1.0
CD C:GLU435 2.9 0.6 1.0
CG C:GLU435 4.4 84.4 1.0
OG1 C:THR461 4.9 0.4 1.0

Cobalt binding site 3 out of 5 in 4pgz

Go back to Cobalt Binding Sites List in 4pgz
Cobalt binding site 3 out of 5 in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co602

b:93.4
occ:1.00
 OE1 A:GLU435 2.2 79.2 1.0
CD A:GLU435 2.9 72.0 1.0
OE2 A:GLU435 2.9 82.3 1.0
OG1 A:THR461 4.3 95.4 1.0
CG A:GLU435 4.4 57.7 1.0

Cobalt binding site 4 out of 5 in 4pgz

Go back to Cobalt Binding Sites List in 4pgz
Cobalt binding site 4 out of 5 in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co603

b:59.0
occ:0.45
 OE2 A:GLU360 2.1 85.2 1.0
O A:HOH712 2.4 59.3 1.0
CD A:GLU360 3.0 92.0 1.0
OE1 A:GLU360 3.2 99.0 1.0
O A:TRP359 4.4 49.5 1.0
CG A:GLU360 4.4 83.2 1.0

Cobalt binding site 5 out of 5 in 4pgz

Go back to Cobalt Binding Sites List in 4pgz
Cobalt binding site 5 out of 5 in the Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structural Basis of Kit Activation By Oncogenic Mutations in the Extracellular Region Reveals A Zipper-Like Mechanism For Ligand- Dependent or Oncogenic Receptor Tyrosine Kinase Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co604

b:0.4
occ:1.00
 OE1 A:GLU376 2.8 87.7 1.0
CE1 A:HIS378 3.5 97.8 1.0
O A:HOH704 3.7 59.5 1.0
CD A:GLU376 3.8 84.0 1.0
OD2 A:ASP332 4.1 74.8 1.0
OE2 A:GLU376 4.2 91.1 1.0
NE2 A:HIS378 4.2 93.7 1.0
ND1 A:HIS378 4.4 90.7 1.0
CG A:ASP332 4.7 69.8 1.0

Reference:

A.V.Reshetnyak, Y.Opatowsky, T.J.Boggon, E.Folta-Stogniew, F.Tome, I.Lax, J.Schlessinger. The Strength and Cooperativity of Kit Ectodomain Contacts Determine Normal Ligand-Dependent Stimulation or Oncogenic Activation in Cancer. Mol.Cell V. 57 191 2015.
ISSN: ISSN 1097-2765
PubMed: 25544564
DOI: 10.1016/J.MOLCEL.2014.11.021
Page generated: Sun Dec 13 10:45:31 2020

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