Calcium in PDB 4n2h: Crystal Structure of Protein Arginine Deiminase 2 (D177A, 0 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (D177A, 0 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (D177A, 0 Mm CA2+), PDB code: 4n2h 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)	40.63 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.312, 52.035, 76.072, 90.00, 105.31, 90.00
R / Rfree (%)	17.2 / 21.1

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 0 Mm CA2+) (pdb code 4n2h). 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 (D177A, 0 Mm CA2+), PDB code: 4n2h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:38.8 occ:1.00 O A:VAL129 2.3 27.7 1.0 OE1 A:GLU131 2.3 20.8 1.0 OD1 A:ASP125 2.3 29.4 1.0 OD1 A:ASP127 2.3 28.6 1.0 OD1 A:ASP123 2.4 23.4 1.0 O A:HOH857 2.5 26.4 1.0 CG A:ASP125 3.2 30.1 1.0 CG A:ASP127 3.2 31.7 1.0 CG A:ASP123 3.3 24.8 1.0 CD A:GLU131 3.3 28.1 1.0 C A:VAL129 3.3 25.3 1.0 OD2 A:ASP125 3.5 26.4 1.0 OD2 A:ASP127 3.7 32.1 1.0 N A:VAL129 3.8 24.6 1.0 CB A:ASP123 3.9 20.5 1.0 CA A:ASP123 3.9 18.4 1.0 OE2 A:GLU131 4.0 24.4 1.0 CA A:VAL129 4.0 26.4 1.0 N A:ASP127 4.0 29.2 1.0 N A:GLU131 4.0 21.5 1.0 CB A:VAL129 4.2 29.4 1.0 OD2 A:ASP123 4.2 28.2 1.0 CB A:GLU131 4.2 25.6 1.0 N A:ASP125 4.3 22.0 1.0 N A:ARG126 4.3 21.6 1.0 CG A:GLU131 4.4 21.4 1.0 N A:VAL130 4.4 25.4 1.0 CB A:ASP127 4.4 32.2 1.0 N A:GLY128 4.5 28.0 1.0 CB A:ASP125 4.5 27.8 1.0 C A:ASP123 4.5 23.4 1.0 CA A:ASP127 4.5 29.7 1.0 CA A:VAL130 4.5 27.1 1.0 C A:ASP125 4.6 23.3 1.0 N A:ALA124 4.7 24.0 1.0 CA A:ASP125 4.7 23.2 1.0 C A:ASP127 4.7 34.2 1.0 C A:VAL130 4.7 26.8 1.0 CA A:GLU131 4.7 30.5 1.0 CG1 A:VAL129 4.9 37.0 1.0 C A:GLY128 4.9 33.0 1.0 O A:HOH1149 5.0 32.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (D177A, 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 (D177A, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:39.0 occ:1.00 O A:PHE408 2.3 19.5 1.0 O A:HOH1157 2.5 30.9 1.0 OE2 A:GLU354 2.5 29.7 1.0 O A:HOH1211 2.5 38.9 1.0 O A:LEU411 2.5 22.3 1.0 O A:HOH1233 2.6 35.3 1.0 C A:PHE408 3.5 16.3 1.0 CD A:GLU354 3.5 31.5 1.0 C A:LEU411 3.6 22.6 1.0 OE1 A:GLU354 3.8 40.1 1.0 CE A:MET299 4.0 40.6 1.0 CB A:LEU411 4.3 18.7 1.0 N A:GLY409 4.3 18.9 1.0 CA A:LEU411 4.3 12.7 1.0 CB A:PHE408 4.3 14.1 1.0 CA A:GLY409 4.3 15.7 1.0 N A:LEU411 4.4 13.8 1.0 CA A:PHE408 4.4 13.2 1.0 O A:HOH1312 4.6 30.8 1.0 O A:GLN350 4.6 18.7 1.0 C A:GLY409 4.7 20.4 1.0 N A:GLU412 4.7 17.6 1.0 CG A:GLU354 4.9 18.7 1.0 CA A:GLU412 4.9 15.5 1.0 O A:GLY409 4.9 16.2 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