Calcium in PDB 4n2k: Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 0 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 0 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 0 Mm CA2+), PDB code: 4n2k 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)	40.58 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.242, 51.940, 75.969, 90.00, 105.31, 90.00
R / Rfree (%)	17.8 / 20.8

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 0 Mm CA2+) (pdb code 4n2k). 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 (Q350A, 0 Mm CA2+), PDB code: 4n2k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 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 (Q350A, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:38.9 occ:1.00 O A:HOH1110 2.1 68.1 1.0 O A:LEU411 2.7 22.1 1.0 O A:PHE408 2.7 17.9 1.0 OE2 A:GLU354 2.8 28.2 1.0 O A:HOH1226 3.0 53.6 1.0 O A:HOH1135 3.2 34.4 1.0 CD A:GLU354 3.7 27.8 1.0 C A:PHE408 3.8 16.4 1.0 C A:LEU411 3.8 19.2 1.0 CE A:MET299 3.9 34.9 1.0 OE1 A:GLU354 3.9 34.3 1.0 CB A:LEU411 4.4 19.6 1.0 CA A:LEU411 4.5 15.8 1.0 CB A:PHE408 4.5 18.6 1.0 N A:GLY409 4.5 16.0 1.0 O A:HOH1497 4.6 47.4 1.0 C3 A:GOL706 4.6 29.8 1.0 N A:LEU411 4.6 13.5 1.0 CA A:GLY409 4.6 17.1 1.0 CA A:PHE408 4.7 13.7 1.0 N A:GLU412 4.8 16.3 1.0 O A:ALA350 4.8 27.1 1.0 CA A:GLU412 4.9 15.4 1.0 C A:GLY409 4.9 17.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 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 (Q350A, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:35.9 occ:1.00 OE1 A:GLU131 2.5 20.5 1.0 OD1 A:ASP125 2.6 27.2 1.0 OD1 A:ASP123 2.6 21.9 1.0 O A:VAL129 2.6 35.7 1.0 O A:HOH865 2.9 39.6 1.0 OD1 A:ASP127 3.0 60.5 1.0 CG A:ASP127 3.2 43.0 1.0 OD2 A:ASP127 3.3 36.5 1.0 C A:VAL129 3.4 27.9 1.0 CG A:ASP125 3.5 26.1 1.0 CG A:ASP123 3.5 25.7 1.0 CD A:GLU131 3.6 29.4 1.0 N A:VAL129 3.6 28.3 1.0 OD2 A:ASP125 3.7 26.0 1.0 CA A:VAL129 3.8 24.9 1.0 CB A:VAL129 3.9 26.8 1.0 N A:ASP127 4.0 25.2 1.0 N A:GLU131 4.0 22.8 1.0 CB A:ASP123 4.1 16.0 1.0 CB A:ASP127 4.2 30.3 1.0 CA A:ASP123 4.2 17.9 1.0 OE2 A:GLU131 4.2 21.2 1.0 CB A:GLU131 4.3 20.8 1.0 OD2 A:ASP123 4.3 23.7 1.0 N A:VAL130 4.3 22.8 1.0 CA A:ASP127 4.4 29.0 1.0 N A:GLY128 4.4 24.8 1.0 O A:HOH1063 4.4 33.1 1.0 CG A:GLU131 4.5 19.6 1.0 C A:ASP127 4.5 32.4 1.0 CA A:VAL130 4.6 25.7 1.0 N A:ARG126 4.6 21.7 1.0 CG1 A:VAL129 4.7 33.3 1.0 C A:VAL130 4.7 22.9 1.0 CA A:GLU131 4.7 24.5 1.0 N A:ASP125 4.7 18.6 1.0 C A:GLY128 4.8 29.9 1.0 CB A:ASP125 4.8 25.6 1.0 C A:ASP123 4.8 20.3 1.0 C A:ASP125 4.9 23.1 1.0 CG2 A:VAL129 5.0 39.5 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