Calcium in PDB 4n24: Crystal Structure of Protein Arginine Deiminase 2 (100 Um CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (100 Um CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (100 Um CA2+), PDB code: 4n24 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)	33.82 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	201.760, 51.585, 75.707, 90.00, 105.43, 90.00
R / Rfree (%)	17.4 / 21.7

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (100 Um CA2+) (pdb code 4n24). 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 (100 Um CA2+), PDB code: 4n24:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (100 Um 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 (100 Um CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:25.5 occ:1.00 OD1 A:ASP125 2.2 27.1 1.0 O A:VAL129 2.2 19.6 1.0 OD1 A:ASP123 2.2 16.4 1.0 OE1 A:GLU131 2.3 18.1 1.0 O A:HOH1251 2.3 26.8 1.0 OD1 A:ASP127 2.4 23.9 1.0 CG A:ASP125 3.2 26.9 1.0 CG A:ASP127 3.2 26.6 1.0 CG A:ASP123 3.2 17.8 1.0 CD A:GLU131 3.3 22.2 1.0 C A:VAL129 3.4 19.6 1.0 OD2 A:ASP125 3.6 24.6 1.0 OD2 A:ASP127 3.6 29.5 1.0 CB A:ASP123 3.8 14.0 1.0 CA A:ASP123 3.8 14.8 1.0 N A:VAL129 3.9 18.5 1.0 CG2 A:VAL129 3.9 38.8 1.0 OE2 A:GLU131 3.9 17.9 1.0 N A:GLU131 4.0 18.4 1.0 N A:ASP127 4.0 25.3 1.0 CA A:VAL129 4.2 20.3 1.0 OD2 A:ASP123 4.2 18.0 1.0 CB A:GLU131 4.3 23.1 1.0 N A:ARG126 4.3 19.3 1.0 N A:ASP125 4.3 17.1 1.0 N A:VAL130 4.4 15.8 1.0 C A:ASP123 4.4 21.3 1.0 CB A:ASP127 4.4 26.9 1.0 CG A:GLU131 4.4 15.0 1.0 CB A:ASP125 4.5 23.8 1.0 CA A:VAL130 4.5 20.9 1.0 N A:GLY128 4.5 20.8 1.0 CA A:ASP127 4.5 19.8 1.0 C A:ASP125 4.6 24.2 1.0 N A:ALA124 4.6 18.6 1.0 CA A:ASP125 4.6 21.3 1.0 CB A:VAL129 4.7 31.1 1.0 C A:VAL130 4.7 25.3 1.0 CA A:GLU131 4.7 21.7 1.0 C A:ASP127 4.8 27.3 1.0 O A:ASP123 5.0 18.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (100 Um 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 (100 Um CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:38.0 occ:1.00 O A:PHE408 2.3 11.1 1.0 O A:HOH1090 2.4 32.7 1.0 O A:LEU411 2.5 26.4 1.0 O A:HOH1274 2.5 39.8 1.0 O A:HOH982 2.5 24.2 1.0 OE1 A:GLU354 2.5 21.8 1.0 C A:PHE408 3.4 11.9 1.0 CD A:GLU354 3.6 24.3 1.0 C A:LEU411 3.7 23.4 1.0 OE2 A:GLU354 4.0 23.8 1.0 O A:HOH1092 4.2 38.1 1.0 CB A:PHE408 4.2 13.2 1.0 N A:GLY409 4.3 11.1 1.0 CA A:PHE408 4.3 14.9 1.0 CB A:LEU411 4.3 13.3 1.0 N A:LEU411 4.3 8.7 1.0 CA A:LEU411 4.4 12.9 1.0 CA A:GLY409 4.4 15.4 1.0 O A:GLN350 4.5 18.6 1.0 C A:GLY409 4.7 20.5 1.0 N A:GLU412 4.7 14.0 1.0 CE A:MET299 4.9 12.7 1.0 CG A:GLU354 4.9 18.0 1.0 CA A:GLU412 4.9 13.4 1.0 O A:GLY409 5.0 12.2 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