Zinc in PDB 7knd: C1B Domain of Protein Kinase C in Apo Form

The structure of C1B Domain of Protein Kinase C in Apo Form, PDB code: 7knd was solved by S.S.Katti, I.Krieger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.26 / 1.39
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	37.264, 37.264, 31.888, 90, 90, 90
R / Rfree (%)	21.7 / 24.6

The binding sites of Zinc atom in the C1B Domain of Protein Kinase C in Apo Form (pdb code 7knd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the C1B Domain of Protein Kinase C in Apo Form, PDB code: 7knd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the C1B Domain of Protein Kinase C in Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of C1B Domain of Protein Kinase C in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.0 occ:1.00 ND1 A:HIS269 2.1 17.6 1.0 SG A:CYS272 2.3 22.0 1.0 SG A:CYS247 2.3 25.3 1.0 SG A:CYS244 2.3 20.8 1.0 CE1 A:HIS269 3.0 24.1 1.0 CB A:CYS244 3.1 23.2 1.0 CG A:HIS269 3.2 22.9 1.0 CB A:CYS247 3.2 25.6 1.0 CB A:CYS272 3.3 22.2 1.0 CB A:HIS269 3.6 19.8 1.0 N A:CYS247 3.8 26.7 1.0 CA A:CYS247 4.1 26.8 1.0 N A:HIS269 4.1 19.6 1.0 NE2 A:HIS269 4.1 20.5 1.0 CD2 A:HIS269 4.3 19.9 1.0 CA A:HIS269 4.5 23.8 1.0 CA A:CYS244 4.5 17.8 1.0 CA A:CYS272 4.7 23.8 1.0 C A:CYS247 4.8 28.2 1.0 CB A:HIS246 4.8 24.5 1.0 C A:HIS246 4.8 25.4 1.0 CD2 A:HIS246 4.9 26.4 1.0 N A:GLY248 4.9 23.4 1.0 CE A:LYS271 4.9 21.1 1.0

Zinc binding site 2 out of 2 in the C1B Domain of Protein Kinase C in Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of C1B Domain of Protein Kinase C in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.9 occ:1.00 ND1 A:HIS231 2.1 30.1 1.0 SG A:CYS264 2.3 28.2 1.0 SG A:CYS280 2.3 35.1 1.0 SG A:CYS261 2.3 32.2 1.0 CE1 A:HIS231 2.8 30.1 1.0 CB A:CYS264 3.2 27.7 1.0 CB A:CYS261 3.3 28.6 1.0 CB A:CYS280 3.3 35.8 1.0 CG A:HIS231 3.3 32.5 1.0 N A:CYS264 3.7 29.9 1.0 CA A:HIS231 3.8 37.6 1.0 CA A:CYS280 3.9 37.6 1.0 CB A:HIS231 3.9 34.2 1.0 CA A:CYS264 4.0 31.8 1.0 NE2 A:HIS231 4.0 29.4 1.0 CD2 A:HIS231 4.3 34.6 1.0 N A:HIS231 4.6 41.4 1.0 C A:ASP263 4.7 35.7 1.0 CA A:CYS261 4.7 31.4 1.0 C A:CYS280 4.7 43.8 1.0 C A:CYS264 4.8 26.6 1.0 N A:ARG232 4.8 37.7 1.0 CB A:ASP263 4.9 39.1 1.0 C A:HIS231 4.9 37.1 1.0 N A:GLY265 4.9 28.8 1.0 N A:ASP263 4.9 36.0 1.0 CB A:MET266 4.9 23.7 1.0 N A:CYS280 5.0 41.7 1.0

S.S.Katti, I.V.Krieger, J.Ann, J.Lee, J.C.Sacchettini, T.I.Igumenova. Structural Anatomy of Protein Kinase C C1 Domain Interactions with Diacylglycerol and Other Agonists. Nat Commun V. 13 2695 2022.
ISSN: ESSN 2041-1723
PubMed: 35577811
DOI: 10.1038/S41467-022-30389-2