Calcium in PDB 5xmz: Verticillium Effector PEVD1

The structure of Verticillium Effector PEVD1, PDB code: 5xmz was solved by X.Liu, R.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.81 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	58.000, 79.489, 55.512, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26

The structure of Verticillium Effector PEVD1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Verticillium Effector PEVD1 (pdb code 5xmz). 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 Verticillium Effector PEVD1, PDB code: 5xmz:

Calcium binding site 1 out of 1 in the Verticillium Effector PEVD1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Verticillium Effector PEVD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:53.6 occ:1.00 O A:LEU148 2.2 26.5 1.0 OD1 A:ASP146 2.3 18.9 1.0 O A:TYR116 2.4 18.0 1.0 CL A:CL202 2.5 78.2 1.0 O A:ASP146 3.2 15.6 1.0 O A:HOH344 3.3 35.1 1.0 C A:LEU148 3.3 28.4 1.0 CG A:ASP146 3.4 23.1 1.0 C A:TYR116 3.4 18.2 1.0 O A:HOH368 3.5 32.4 1.0 N A:LEU148 3.7 21.2 1.0 CD2 A:TYR116 3.8 24.2 1.0 C A:ASP146 3.8 17.9 1.0 N A:ASP146 3.8 14.1 1.0 CA A:LEU148 4.0 26.4 1.0 OD2 A:ASP146 4.1 23.6 1.0 CA A:ASP146 4.2 16.0 1.0 O A:PRO149 4.2 31.4 1.0 N A:GLY117 4.3 13.7 1.0 CA A:TYR116 4.3 18.2 1.0 CA A:GLY117 4.3 17.1 1.0 CB A:LEU148 4.3 26.2 1.0 CB A:TYR116 4.3 18.6 1.0 CB A:ASP146 4.4 17.8 1.0 N A:TYR116 4.4 15.6 1.0 N A:PRO149 4.4 29.0 1.0 CG A:TYR116 4.5 21.0 1.0 CE2 A:TYR116 4.6 25.3 1.0 N A:SER147 4.6 19.1 1.0 C A:PRO149 4.6 34.8 1.0 C A:SER147 4.6 21.2 1.0 CA A:PRO149 4.7 32.0 1.0 C A:ILE145 4.8 16.7 1.0 CA A:SER147 5.0 17.9 1.0

R.Zhou, T.Zhu, L.Han, M.Liu, M.Xu, Y.Liu, D.Han, D.Qiu, Q.Gong, X.Liu. The Asparagine-Rich Protein Nrp Interacts with the Verticillium Effector PEVD1 and Regulates the Subcellular Localization of Cryptochrome 2 J. Exp. Bot. V. 68 3427 2017.
ISSN: ESSN 1460-2431
PubMed: 28633330
DOI: 10.1093/JXB/ERX192