Calcium in PDB 4n28: Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+), PDB code: 4n28 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)	37.90 / 1.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.689, 51.632, 76.270, 90.00, 105.57, 90.00
R / Rfree (%)	17.2 / 21.6

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+) (pdb code 4n28). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+), PDB code: 4n28:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (1 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 (1 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:30.5 occ:1.00 OD1 A:ASP125 2.1 31.0 1.0 O A:VAL129 2.2 23.6 1.0 OD1 A:ASP123 2.2 23.6 1.0 OE1 A:GLU131 2.3 19.8 1.0 O A:HOH1210 2.3 25.7 1.0 OD1 A:ASP127 2.3 37.0 1.0 CG A:ASP125 3.1 27.6 1.0 CG A:ASP127 3.2 35.2 1.0 CG A:ASP123 3.2 24.4 1.0 CD A:GLU131 3.3 23.7 1.0 C A:VAL129 3.3 28.0 1.0 OD2 A:ASP125 3.4 35.7 1.0 OD2 A:ASP127 3.6 37.7 1.0 CG1 A:VAL129 3.8 48.5 1.0 CB A:ASP123 3.8 19.7 1.0 N A:VAL129 3.8 30.7 1.0 OE2 A:GLU131 3.8 21.4 1.0 CA A:ASP123 3.9 15.8 1.0 N A:GLU131 4.0 18.5 1.0 N A:ASP127 4.1 30.0 1.0 CA A:VAL129 4.1 30.4 1.0 OD2 A:ASP123 4.2 20.3 1.0 CB A:ASP127 4.3 36.0 1.0 CB A:GLU131 4.3 26.7 1.0 N A:VAL130 4.3 27.2 1.0 N A:ASP125 4.4 19.0 1.0 CG A:GLU131 4.4 17.1 1.0 CB A:ASP125 4.4 22.9 1.0 N A:ARG126 4.4 15.8 1.0 C A:ASP123 4.4 23.9 1.0 CA A:VAL130 4.5 23.4 1.0 N A:GLY128 4.5 36.6 1.0 CA A:ASP127 4.5 32.7 1.0 CB A:VAL129 4.6 38.9 1.0 N A:ALA124 4.6 22.1 1.0 C A:ASP125 4.6 21.4 1.0 C A:VAL130 4.7 26.4 1.0 CA A:ASP125 4.7 22.9 1.0 C A:ASP127 4.7 35.5 1.0 CA A:GLU131 4.8 26.6 1.0 C A:GLY128 4.9 34.2 1.0 O A:ASP123 5.0 18.6 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (1 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 (1 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:17.7 occ:1.00 OD2 A:ASP180 2.1 13.7 1.0 OD1 A:ASP166 2.2 23.2 1.0 OD1 A:ASN154 2.3 13.5 1.0 OD1 A:ASP156 2.3 20.8 1.0 OE2 A:GLU158 2.4 22.8 1.0 OD1 A:ASP177 2.4 20.0 1.0 CG A:ASP156 3.2 24.2 1.0 CG A:ASN154 3.3 18.2 1.0 CG A:ASP180 3.3 20.5 1.0 CD A:GLU158 3.3 28.5 1.0 CG A:ASP166 3.3 28.1 1.0 OD2 A:ASP156 3.4 18.5 1.0 CG A:GLU158 3.5 26.6 1.0 CG A:ASP177 3.6 23.9 1.0 ND2 A:ASN154 3.6 19.0 1.0 CA A:CA709 3.7 18.7 1.0 CB A:ASP166 3.8 20.6 1.0 CB A:ASP180 4.0 17.4 1.0 CA A:ASP177 4.3 20.8 1.0 OD1 A:ASP180 4.3 18.6 1.0 OD2 A:ASP166 4.4 22.7 1.0 O A:ASP177 4.4 19.9 1.0 CB A:ASP177 4.5 21.1 1.0 OD2 A:ASP177 4.5 21.8 1.0 OE1 A:GLU158 4.5 26.9 1.0 C A:ASP156 4.6 22.9 1.0 CB A:ASP156 4.6 18.3 1.0 O A:ASP156 4.6 21.6 1.0 CB A:ASN154 4.7 13.7 1.0 N A:ASP156 4.8 16.5 1.0 C A:ASP177 4.9 23.1 1.0 N A:GLU158 4.9 25.0 1.0 CA A:ASP156 4.9 17.2 1.0 CB A:GLU158 4.9 24.0 1.0 N A:ARG157 5.0 22.9 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:19.0 occ:1.00 O A:LYS171 2.3 25.7 1.0 O A:HOH1341 2.3 22.8 1.0 O A:HOH835 2.3 18.5 1.0 OD1 A:ASP169 2.3 22.4 1.0 O A:ASP166 2.4 18.7 1.0 O A:HOH828 2.4 18.3 1.0 O A:HOH1057 2.4 23.1 1.0 CG A:ASP169 3.4 26.5 1.0 C A:ASP166 3.4 20.1 1.0 C A:LYS171 3.5 30.2 1.0 OD2 A:ASP169 3.7 29.6 1.0 CA A:ASP166 4.0 19.9 1.0 N A:LYS171 4.2 25.1 1.0 OD2 A:ASP177 4.2 21.8 1.0 CB A:ASP166 4.3 20.6 1.0 O A:HOH1054 4.3 34.8 1.0 O A:ASP169 4.4 21.0 1.0 CA A:LYS171 4.4 27.0 1.0 N A:VAL172 4.4 23.8 1.0 CA A:VAL172 4.5 25.0 1.0 N A:CYS167 4.5 19.9 1.0 C A:ASP169 4.6 25.4 1.0 OE1 A:GLU253 4.6 21.9 1.0 CG2 A:VAL172 4.6 23.2 1.0 CB A:ASP169 4.7 23.6 1.0 N A:ASP169 4.7 25.4 1.0 CA A:CYS167 4.8 19.4 1.0 OE2 A:GLU253 4.8 19.0 1.0 O A:HOH1118 4.9 44.2 1.0 CA A:ASP169 4.9 27.4 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:18.7 occ:1.00 OD2 A:ASP156 2.3 18.5 1.0 OD1 A:ASP389 2.4 20.9 1.0 OD2 A:ASP180 2.4 13.7 1.0 O A:HOH883 2.4 17.6 1.0 O A:HOH843 2.4 17.7 1.0 OE2 A:GLU158 2.4 22.8 1.0 OD1 A:ASP180 2.5 18.6 1.0 CG A:ASP180 2.8 20.5 1.0 CD A:GLU158 3.4 28.5 1.0 CG A:ASP156 3.4 24.2 1.0 CG A:ASP389 3.5 27.4 1.0 OE1 A:GLU158 3.6 26.9 1.0 CA A:CA707 3.7 17.7 1.0 OD1 A:ASP156 3.8 20.8 1.0 N A:ASP389 3.8 18.0 1.0 NZ A:LYS363 3.9 36.5 1.0 OD2 A:ASP389 4.2 32.8 1.0 CA A:ASP389 4.2 18.2 1.0 CB A:ASP180 4.3 17.4 1.0 CB A:ASP389 4.5 22.2 1.0 CE A:LYS363 4.6 39.8 1.0 O A:GLU176 4.6 20.7 1.0 CE2 A:PHE365 4.6 24.6 1.0 CB A:ASP156 4.7 18.3 1.0 O A:HOH1070 4.7 35.5 1.0 CG A:GLU158 4.8 26.6 1.0 CD2 A:PHE365 4.8 22.8 1.0 C A:PRO388 4.9 25.0 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Protein Arginine Deiminase 2 (1 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:20.4 occ:1.00 O A:HOH1350 2.3 28.6 1.0 O A:PHE408 2.3 13.5 1.0 OE1 A:GLU354 2.3 14.8 1.0 O A:LEU411 2.4 17.9 1.0 O A:HOH809 2.5 21.6 1.0 OE2 A:GLU412 2.5 21.8 1.0 OE1 A:GLN350 2.7 15.7 0.4 CD A:GLU354 3.4 22.9 1.0 CD A:GLU412 3.4 28.1 1.0 C A:PHE408 3.5 13.3 1.0 C A:LEU411 3.6 15.4 1.0 OE2 A:GLU354 3.7 19.4 1.0 CD A:GLN350 3.8 23.2 0.4 OE1 A:GLU412 3.9 37.2 1.0 CB A:PHE408 4.3 11.9 1.0 N A:GLY409 4.3 12.3 1.0 NE2 A:GLN350 4.3 11.0 0.4 CA A:LEU411 4.3 12.9 1.0 N A:LEU411 4.4 14.0 1.0 CA A:GLY409 4.4 10.6 1.0 CA A:PHE408 4.4 13.6 1.0 CG A:GLU412 4.5 24.4 1.0 CB A:LEU411 4.5 12.9 1.0 O A:GLN350 4.5 28.0 1.0 N A:GLU412 4.6 15.6 1.0 CG A:GLU354 4.7 9.9 1.0 CA A:GLU412 4.7 11.3 1.0 O A:HOH1060 4.7 39.9 1.0 C A:GLY409 4.8 13.4 1.0 O A:HOH1180 4.8 43.8 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