Zinc in PDB 7leo: C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine

The structure of C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine, PDB code: 7leo 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)	29.96 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.388, 50.888, 37.485, 90, 107.72, 90
R / Rfree (%)	22.4 / 24.4

The binding sites of Zinc atom in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine (pdb code 7leo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine, PDB code: 7leo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine


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 Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:29.6 occ:1.00 ND1 A:HIS231 2.0 27.7 1.0 SG A:CYS280 2.3 30.0 1.0 SG A:CYS261 2.3 27.1 1.0 SG A:CYS264 2.3 32.1 1.0 CE1 A:HIS231 2.9 31.4 1.0 CG A:HIS231 3.1 28.3 1.0 CB A:CYS264 3.2 31.3 1.0 CB A:CYS261 3.2 26.1 1.0 CB A:CYS280 3.2 28.5 1.0 CB A:HIS231 3.5 29.3 1.0 N A:CYS264 3.7 36.0 1.0 CA A:HIS231 3.8 30.2 1.0 CA A:CYS280 3.9 30.8 1.0 CA A:CYS264 4.0 32.1 1.0 NE2 A:HIS231 4.1 31.9 1.0 CD2 A:HIS231 4.2 29.7 1.0 C A:ASP263 4.6 36.0 1.0 N A:ARG232 4.6 27.2 1.0 CA A:CYS261 4.7 27.8 1.0 CB A:ASP263 4.7 30.4 1.0 C A:CYS264 4.7 33.7 1.0 C A:CYS280 4.8 40.3 1.0 C A:HIS231 4.8 27.1 1.0 N A:HIS231 4.8 30.8 1.0 N A:ASP263 4.9 31.6 1.0 CA A:ASP263 4.9 31.6 1.0 N A:GLY265 4.9 34.1 1.0 CB A:MET266 5.0 28.5 1.0 N A:CYS280 5.0 33.9 1.0

Zinc binding site 2 out of 4 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine


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 Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.8 occ:1.00 ND1 A:HIS269 2.1 25.6 1.0 SG A:CYS272 2.3 27.7 1.0 SG A:CYS244 2.3 23.9 1.0 SG A:CYS247 2.3 25.4 1.0 CE1 A:HIS269 3.0 26.8 1.0 CB A:CYS244 3.1 23.2 1.0 CG A:HIS269 3.2 26.6 1.0 CB A:CYS247 3.3 29.5 1.0 CB A:CYS272 3.4 27.2 1.0 CB A:HIS269 3.6 23.1 1.0 N A:CYS247 3.8 24.8 1.0 N A:HIS269 3.9 21.4 1.0 C2 A:XP5303 4.1 42.6 1.0 CA A:CYS247 4.1 25.6 1.0 NE2 A:HIS269 4.1 25.1 1.0 CD2 A:HIS269 4.2 28.6 1.0 CA A:HIS269 4.4 24.0 1.0 CA A:CYS244 4.5 25.7 1.0 CA A:CYS272 4.7 27.4 1.0 C1 A:XP5303 4.8 43.7 1.0 CB A:HIS246 4.8 29.7 1.0 C A:CYS247 4.8 26.4 1.0 C A:HIS246 4.9 28.3 1.0 N A:GLY248 4.9 26.2 1.0

Zinc binding site 3 out of 4 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:42.5 occ:1.00 ND1 D:HIS231 2.0 42.0 1.0 SG D:CYS261 2.3 37.3 1.0 SG D:CYS264 2.3 49.9 1.0 SG D:CYS280 2.3 46.5 1.0 CE1 D:HIS231 2.5 47.8 1.0 CB D:CYS264 3.1 49.1 1.0 CG D:HIS231 3.2 44.3 1.0 CB D:CYS261 3.3 42.8 1.0 CB D:CYS280 3.3 52.0 1.0 N D:CYS264 3.5 46.9 1.0 NE2 D:HIS231 3.7 49.2 1.0 O D:HOH419 3.7 56.0 1.0 CA D:CYS264 3.9 50.8 1.0 CB D:HIS231 3.9 47.3 1.0 CA D:CYS280 3.9 52.4 1.0 CA D:HIS231 4.0 46.1 1.0 CD2 D:HIS231 4.0 50.1 1.0 CB D:ASP263 4.3 52.7 1.0 C D:ASP263 4.6 52.5 1.0 C D:CYS264 4.6 50.0 1.0 C D:CYS280 4.7 56.5 1.0 CA D:CYS261 4.7 39.1 1.0 N D:ARG232 4.8 44.8 1.0 N D:GLY265 4.8 47.7 1.0 OD2 D:ASP263 4.8 54.6 1.0 N D:HIS231 4.8 50.8 1.0 CA D:ASP263 4.9 51.1 1.0 N D:ASP263 4.9 48.6 1.0 C D:HIS231 5.0 48.4 1.0

Zinc binding site 4 out of 4 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol-Lactone (Ajh-836) and 1,2-Diheptanoyl-Sn-Glycero-3-Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:35.3 occ:1.00 ND1 D:HIS269 2.1 44.7 1.0 SG D:CYS247 2.3 31.8 1.0 SG D:CYS272 2.3 40.3 1.0 SG D:CYS244 2.3 31.7 1.0 CB D:CYS244 3.0 32.6 1.0 CE1 D:HIS269 3.0 37.5 1.0 CG D:HIS269 3.1 39.1 1.0 CB D:CYS247 3.3 38.6 1.0 CB D:CYS272 3.4 39.1 1.0 CB D:HIS269 3.5 38.4 1.0 N D:CYS247 3.9 32.5 1.0 N D:HIS269 3.9 33.4 1.0 NE2 D:HIS269 4.1 36.8 1.0 CA D:CYS247 4.2 35.4 1.0 CD2 D:HIS269 4.2 36.7 1.0 CA D:HIS269 4.3 35.7 1.0 CA D:CYS244 4.5 30.6 1.0 CA D:CYS272 4.8 41.9 1.0 CB D:HIS246 4.8 36.8 1.0 C D:CYS247 4.9 35.2 1.0 N D:GLY248 4.9 31.5 1.0 CD2 D:HIS246 4.9 37.6 1.0 C D:HIS246 5.0 36.2 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