Calcium in PDB 4n20: Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+), PDB code: 4n20 was solved by D.J.Slade, X.Zhang, P.Fang, C.J.Dreyton, Y.Zhang, M.L.Gross, M.Guo, S.A.Coonrod, P.R.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.45 / 1.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	201.206, 51.863, 75.649, 90.00, 105.44, 90.00
R / Rfree (%)	17.2 / 20.4

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+) (pdb code 4n20). 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 Protein Arginine Deiminase 2 (0 Mm CA2+), PDB code: 4n20:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+)


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 Protein Arginine Deiminase 2 (0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:26.0 occ:1.00 O A:VAL129 2.2 18.7 1.0 OE1 A:GLU131 2.2 14.8 1.0 OD1 A:ASP127 2.3 19.0 1.0 OD1 A:ASP125 2.3 19.3 1.0 OD1 A:ASP123 2.3 15.1 1.0 O A:HOH856 2.5 20.0 1.0 CG A:ASP125 3.2 22.1 1.0 CG A:ASP127 3.2 23.1 1.0 CG A:ASP123 3.3 16.2 1.0 CD A:GLU131 3.3 18.1 1.0 C A:VAL129 3.3 18.4 1.0 OD2 A:ASP125 3.5 21.1 1.0 OD2 A:ASP127 3.7 25.2 1.0 N A:VAL129 3.8 19.5 1.0 CA A:ASP123 3.8 11.9 1.0 CB A:ASP123 3.9 13.6 1.0 OE2 A:GLU131 4.0 15.3 1.0 N A:GLU131 4.0 15.4 1.0 CA A:VAL129 4.0 17.8 1.0 N A:ASP127 4.0 18.5 1.0 CB A:GLU131 4.2 16.2 1.0 CB A:VAL129 4.3 24.8 1.0 OD2 A:ASP123 4.3 18.5 1.0 CG A:GLU131 4.4 14.8 1.0 N A:VAL130 4.4 15.8 1.0 N A:ASP125 4.4 13.6 1.0 N A:ARG126 4.4 15.2 1.0 CB A:ASP127 4.4 20.2 1.0 C A:ASP123 4.4 12.4 1.0 CA A:ASP127 4.5 19.3 1.0 CB A:ASP125 4.5 20.3 1.0 CA A:VAL130 4.5 18.5 1.0 N A:GLY128 4.5 19.7 1.0 N A:ALA124 4.6 15.2 1.0 C A:ASP125 4.7 18.0 1.0 C A:VAL130 4.7 18.4 1.0 CA A:ASP125 4.7 16.5 1.0 CA A:GLU131 4.7 20.1 1.0 C A:ASP127 4.7 23.6 1.0 CG1 A:VAL129 4.9 32.5 1.0 C A:GLY128 4.9 22.9 1.0 O A:HOH1175 5.0 27.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (0 Mm CA2+)


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 Protein Arginine Deiminase 2 (0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:38.4 occ:1.00 O A:PHE408 2.4 11.5 1.0 O A:HOH1440 2.4 39.6 1.0 OE2 A:GLU354 2.5 23.9 1.0 O A:HOH1019 2.5 23.7 1.0 O A:HOH1252 2.5 35.6 1.0 O A:LEU411 2.6 14.0 1.0 OE1 A:GLU354 3.2 39.1 1.0 CD A:GLU354 3.2 27.3 1.0 C A:PHE408 3.4 10.5 1.0 C A:LEU411 3.7 10.4 1.0 CE A:MET299 4.0 32.1 1.0 O A:HOH1263 4.1 36.7 1.0 CB A:LEU411 4.2 14.3 1.0 N A:GLY409 4.3 11.7 1.0 CB A:PHE408 4.3 9.7 1.0 CA A:GLY409 4.4 11.5 1.0 CA A:LEU411 4.4 8.1 1.0 CA A:PHE408 4.4 7.7 1.0 N A:LEU411 4.4 6.7 1.0 O A:HOH1301 4.5 29.1 1.0 O A:GLN350 4.6 14.2 1.0 CG A:GLU354 4.7 17.6 1.0 C A:GLY409 4.7 12.6 1.0 N A:GLU412 4.8 7.1 1.0 O A:HOH1358 4.8 22.0 1.0 CA A:GLU412 5.0 8.1 1.0

D.J.Slade, P.Fang, C.J.Dreyton, Y.Zhang, J.Furhmann, D.Rempel, B.D.Bax, S.A.Coonrod, H.D.Lewis, M.Guo, M.L.Gross, P.R.Thompson. Protein Arginine Deiminase 2 Binds Calcium in An Ordered Fashion: Implications For Inhibitor Design. Acs Chem.Biol. 2015.
ISSN: ESSN 1554-8937
PubMed: 25621824
DOI: 10.1021/CB500933J