Calcium in PDB 4n2d: Crystal Structure of Protein Arginine Deiminase 2 (D123N, 0 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (D123N, 0 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (D123N, 0 Mm CA2+), PDB code: 4n2d 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)	36.25 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.190, 51.820, 75.895, 90.00, 105.66, 90.00
R / Rfree (%)	17.8 / 22.4

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 0 Mm CA2+) (pdb code 4n2d). 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 (D123N, 0 Mm CA2+), PDB code: 4n2d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:34.7 occ:1.00 OD1 A:ASP125 2.1 42.0 1.0 OE1 A:GLU131 2.2 27.8 1.0 OD1 A:ASN123 2.2 31.3 1.0 O A:VAL129 2.2 29.7 1.0 OD1 A:ASP127 2.3 33.1 1.0 O A:HOH1029 2.4 32.0 1.0 CG A:ASP125 3.1 36.6 1.0 CG A:ASP127 3.2 37.3 1.0 CG A:ASN123 3.2 29.4 1.0 CD A:GLU131 3.3 29.9 1.0 C A:VAL129 3.4 30.0 1.0 OD2 A:ASP125 3.4 31.4 1.0 OD2 A:ASP127 3.6 43.4 1.0 OE2 A:GLU131 3.9 28.9 1.0 N A:VAL129 3.9 34.1 1.0 CB A:ASN123 3.9 23.0 1.0 CA A:ASN123 3.9 20.1 1.0 N A:ASP127 4.0 36.8 1.0 N A:GLU131 4.1 28.1 1.0 CA A:VAL129 4.1 31.5 1.0 ND2 A:ASN123 4.3 21.2 1.0 CB A:GLU131 4.3 29.1 1.0 N A:ASP125 4.3 21.9 1.0 CG A:GLU131 4.4 21.9 1.0 N A:ARG126 4.4 23.2 1.0 CB A:VAL129 4.4 40.0 1.0 CB A:ASP125 4.4 27.9 1.0 CB A:ASP127 4.4 37.0 1.0 N A:VAL130 4.4 28.1 1.0 C A:ASN123 4.5 29.4 1.0 N A:GLY128 4.5 37.9 1.0 CA A:ASP127 4.5 39.0 1.0 C A:ASP125 4.6 27.2 1.0 CA A:VAL130 4.6 30.1 1.0 CA A:ASP125 4.6 25.3 1.0 N A:ALA124 4.6 30.0 1.0 C A:VAL130 4.7 31.3 1.0 CA A:GLU131 4.8 31.3 1.0 C A:ASP127 4.8 40.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 0 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:44.0 occ:1.00 O A:PHE408 2.5 23.8 1.0 O A:LEU411 2.5 27.6 1.0 OE2 A:GLU354 2.5 25.7 1.0 O A:HOH984 2.5 39.4 1.0 CD A:GLU354 3.6 32.5 1.0 C A:PHE408 3.6 21.7 1.0 C A:LEU411 3.7 25.2 1.0 OE1 A:GLU354 3.9 44.8 1.0 CB A:LEU411 4.3 24.1 1.0 CB A:PHE408 4.4 24.6 1.0 N A:GLY409 4.4 18.6 1.0 CA A:LEU411 4.4 21.6 1.0 N A:LEU411 4.4 22.9 1.0 CA A:GLY409 4.5 20.7 1.0 CA A:PHE408 4.5 20.7 1.0 O A:GLN350 4.7 31.8 1.0 N A:GLU412 4.7 20.8 1.0 C A:GLY409 4.8 23.9 1.0 CG A:GLU412 4.9 38.9 1.0 CA A:GLU412 4.9 18.2 1.0 CE A:MET299 4.9 15.5 1.0 CG A:GLU354 4.9 21.8 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