Calcium in PDB 6kz9: Crystal Structure of Plant Phospholipase D Alpha

All present enzymatic activity of Crystal Structure of Plant Phospholipase D Alpha:
3.1.4.4;

The structure of Crystal Structure of Plant Phospholipase D Alpha, PDB code: 6kz9 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)	42.40 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.885, 127.444, 55.363, 90.00, 95.47, 90.00
R / Rfree (%)	16.7 / 18.7

The binding sites of Calcium atom in the Crystal Structure of Plant Phospholipase D Alpha (pdb code 6kz9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Plant Phospholipase D Alpha, PDB code: 6kz9:

Calcium binding site 1 out of 1 in the Crystal Structure of Plant Phospholipase D Alpha


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:5.6 occ:1.00 OE2 A:GLU722 2.1 4.8 1.0 NE2 A:HIS372 2.2 5.1 1.0 OD2 A:ASP187 2.2 6.7 1.0 ND1 A:HIS406 2.2 4.5 1.0 OD1 A:ASP187 2.5 3.1 1.0 CG A:ASP187 2.6 5.5 1.0 CD A:GLU722 2.9 5.1 1.0 OE1 A:GLU722 3.0 5.7 1.0 CE1 A:HIS372 3.1 4.2 1.0 CE1 A:HIS406 3.1 4.9 1.0 CD2 A:HIS372 3.1 3.9 1.0 CG A:HIS406 3.3 3.4 1.0 CB A:HIS406 3.6 3.0 1.0 CA A:HIS406 3.9 4.0 1.0 CA A:PRO370 4.0 6.0 1.0 CB A:ASP187 4.1 3.7 1.0 ND1 A:HIS372 4.2 6.2 1.0 NE2 A:HIS406 4.3 3.1 1.0 CG A:HIS372 4.3 5.4 1.0 CG A:GLU722 4.3 3.6 1.0 O A:HOH1245 4.4 11.4 1.0 CD2 A:HIS406 4.4 3.6 1.0 O A:THR369 4.5 4.9 1.0 N A:PRO370 4.5 5.5 1.0 CB A:PRO370 4.6 8.0 1.0 N A:ASP407 4.7 2.9 1.0 CG A:PRO370 4.7 7.1 1.0 C A:THR369 4.8 6.0 1.0 C A:HIS406 4.8 3.6 1.0 CE1 A:HIS723 4.9 3.7 1.0 N A:ASP187 4.9 2.0 1.0 O A:TRP405 4.9 3.1 1.0 N A:HIS406 4.9 4.0 1.0 CA A:ASP187 5.0 5.2 1.0 C A:PRO370 5.0 5.9 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