Zinc in PDB 6ra0: A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation

All present enzymatic activity of A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation:
2.7.11.13;

The structure of A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation, PDB code: 6ra0 was solved by D.J.Elsner, T.A.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.51 / 2.26
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.413, 83.018, 37.080, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.6

The binding sites of Zinc atom in the A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation (pdb code 6ra0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation, PDB code: 6ra0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:84.5 occ:1.00 ND1 A:HIS99 2.2 66.0 1.0 SG A:CYS132 2.2 63.2 1.0 SG A:CYS129 2.4 76.8 1.0 SG A:CYS148 2.5 80.5 1.0 CB A:CYS132 3.0 73.4 1.0 CE1 A:HIS99 3.1 64.3 1.0 CB A:CYS129 3.1 76.0 1.0 CG A:HIS99 3.2 64.4 1.0 CB A:CYS148 3.3 79.0 1.0 CB A:HIS99 3.5 66.8 1.0 N A:CYS132 3.6 74.0 1.0 CA A:HIS99 3.7 70.3 1.0 CA A:CYS132 3.8 74.3 1.0 CA A:CYS148 4.1 75.7 1.0 NE2 A:HIS99 4.2 64.5 1.0 CD2 A:HIS99 4.3 62.6 1.0 C A:CYS132 4.4 76.7 1.0 CA A:CYS129 4.6 78.0 1.0 N A:HIS99 4.6 73.6 1.0 N A:ASN133 4.7 93.5 1.0 C A:ASN131 4.7 88.0 1.0 C A:HIS99 4.8 71.1 1.0 N A:VAL100 4.8 82.1 1.0 C A:CYS129 5.0 75.2 1.0

Zinc binding site 2 out of 2 in the A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Ubiquitin-Like Dimerization Domain Controls Protein Kinase D Activation By Trans-Autophosphorylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:62.3 occ:1.00 ND1 A:HIS137 2.1 59.4 1.0 SG A:CYS112 2.3 54.1 1.0 SG A:CYS140 2.3 54.6 1.0 SG A:CYS115 2.4 65.8 1.0 CE1 A:HIS137 2.7 62.6 1.0 CB A:CYS112 3.0 57.1 1.0 CB A:CYS115 3.1 65.5 1.0 CB A:CYS140 3.3 53.4 1.0 CG A:HIS137 3.4 61.1 1.0 N A:CYS115 3.9 62.1 1.0 NE2 A:HIS137 4.0 61.4 1.0 CB A:HIS137 4.0 57.9 1.0 CA A:CYS115 4.1 63.6 1.0 N A:HIS137 4.1 59.5 1.0 CD2 A:HIS137 4.3 60.0 1.0 CA A:CYS112 4.5 58.4 1.0 CA A:HIS137 4.7 58.7 1.0 CA A:CYS140 4.8 54.4 1.0 CD2 A:PHE114 4.8 65.8 1.0 C A:CYS115 4.8 68.5 1.0 N A:GLY116 4.9 92.7 1.0 C A:CYS112 4.9 59.0 1.0 O A:CYS112 4.9 59.0 1.0

D.J.Elsner, K.M.Siess, T.Gossenreiter, M.Hartl, T.A.Leonard. A Ubiquitin-Like Domain Controls Protein Kinase D Dimerization and Activation By Trans-Autophosphorylation. J.Biol.Chem. V. 294 14422 2019.
ISSN: ESSN 1083-351X
PubMed: 31406020
DOI: 10.1074/JBC.RA119.008713