Calcium in PDB 6kz8: Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid

All present enzymatic activity of Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid:
3.1.4.4;

The structure of Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid, PDB code: 6kz8 was solved by J.X.Li, F.Yu, P.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.89 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.042, 123.030, 138.904, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.5

The binding sites of Calcium atom in the Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid (pdb code 6kz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid, PDB code: 6kz8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:4.6 occ:1.00 OE2 A:GLU722 2.1 7.5 1.0 NE2 A:HIS372 2.1 9.5 1.0 OD2 A:ASP187 2.2 6.7 1.0 ND1 A:HIS406 2.2 5.2 1.0 OD1 A:ASP187 2.4 8.9 1.0 CG A:ASP187 2.6 5.6 1.0 CD A:GLU722 2.9 6.8 1.0 OE1 A:GLU722 3.0 6.2 1.0 CE1 A:HIS372 3.1 8.3 1.0 CD2 A:HIS372 3.1 7.8 1.0 CE1 A:HIS406 3.1 5.4 1.0 CG A:HIS406 3.3 5.5 1.0 CB A:HIS406 3.6 4.0 1.0 CA A:HIS406 3.9 6.0 1.0 CA A:PRO370 4.0 5.6 1.0 CB A:ASP187 4.1 6.8 1.0 ND1 A:HIS372 4.2 4.4 1.0 CG A:HIS372 4.2 8.6 1.0 NE2 A:HIS406 4.3 8.2 1.0 CG A:GLU722 4.3 7.6 1.0 CD2 A:HIS406 4.4 4.6 1.0 O A:HOH1264 4.4 8.2 1.0 O A:THR369 4.5 7.6 1.0 N A:PRO370 4.5 6.8 1.0 CB A:PRO370 4.6 9.1 1.0 N A:ASP407 4.7 6.5 1.0 C A:THR369 4.7 8.5 1.0 C A:HIS406 4.8 7.5 1.0 CG A:PRO370 4.8 8.6 1.0 CE1 A:HIS723 4.9 6.8 1.0 O A:TRP405 4.9 8.5 1.0 N A:HIS406 4.9 7.4 1.0 C A:PRO370 4.9 8.2 1.0 CA A:ASP187 4.9 3.1 1.0 N A:ASP187 5.0 7.1 1.0 O A:PRO370 5.0 11.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Plant Phospholipase D Alpha Comlex with Phosphatidic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:5.1 occ:1.00 OE2 B:GLU722 2.1 9.8 1.0 NE2 B:HIS372 2.2 6.0 1.0 OD2 B:ASP187 2.2 11.8 1.0 ND1 B:HIS406 2.2 6.9 1.0 OD1 B:ASP187 2.4 10.8 1.0 CG B:ASP187 2.6 6.5 1.0 CD B:GLU722 2.9 8.1 1.0 OE1 B:GLU722 3.0 8.0 1.0 CE1 B:HIS372 3.1 9.4 1.0 CE1 B:HIS406 3.1 5.6 1.0 CD2 B:HIS372 3.1 7.6 1.0 CG B:HIS406 3.3 8.3 1.0 CB B:HIS406 3.6 3.0 1.0 CA B:HIS406 3.9 5.3 1.0 CA B:PRO370 4.1 5.2 1.0 CB B:ASP187 4.1 5.5 1.0 O B:HOH1129 4.2 6.2 1.0 ND1 B:HIS372 4.2 5.1 1.0 CG B:HIS372 4.3 7.4 1.0 NE2 B:HIS406 4.3 8.9 1.0 CG B:GLU722 4.3 8.3 1.0 CD2 B:HIS406 4.4 6.1 1.0 O B:THR369 4.4 9.5 1.0 N B:PRO370 4.6 7.3 1.0 CB B:PRO370 4.7 7.8 1.0 N B:ASP407 4.7 7.5 1.0 C B:THR369 4.7 8.3 1.0 C B:HIS406 4.8 6.5 1.0 CG B:PRO370 4.8 6.1 1.0 CE1 B:HIS723 4.9 7.2 1.0 O B:TRP405 4.9 9.8 1.0 N B:HIS406 4.9 6.3 1.0 CA B:ASP187 4.9 4.3 1.0 N B:ASP187 5.0 3.9 1.0

J.Li, F.Yu, H.Guo, R.Xiong, W.Zhang, F.He, M.Zhang, P.Zhang. Crystal Structure of Plant Pld Alpha 1 Reveals Catalytic and Regulatory Mechanisms of Eukaryotic Phospholipase D. Cell Res. 2019.
ISSN: ISSN 1001-0602
PubMed: 31619765
DOI: 10.1038/S41422-019-0244-6