Calcium in PDB 4n2l: Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 Mm CA2+), PDB code: 4n2l 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)	40.24 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.380, 51.100, 76.180, 90.00, 105.60, 90.00
R / Rfree (%)	16.5 / 21.5

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 Mm CA2+) (pdb code 4n2l). 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 (Q350A, 10 Mm CA2+), PDB code: 4n2l:
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 (Q350A, 10 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, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:23.5 occ:1.00 O A:HOH1186 2.3 37.2 1.0 O A:PHE408 2.3 19.3 1.0 OE1 A:GLU354 2.4 21.3 1.0 O A:LEU411 2.5 21.1 1.0 O A:HOH828 2.5 18.5 1.0 O A:HOH1123 2.5 29.6 1.0 OE2 A:GLU412 2.5 21.5 1.0 CD A:GLU354 3.4 22.4 1.0 CD A:GLU412 3.4 30.6 1.0 C A:PHE408 3.5 21.9 1.0 C A:LEU411 3.6 20.1 1.0 OE2 A:GLU354 3.7 24.0 1.0 OE1 A:GLU412 4.0 40.4 1.0 N A:GLY409 4.3 22.2 1.0 O A:HOH952 4.3 26.0 1.0 CB A:PHE408 4.3 15.5 1.0 CA A:GLY409 4.4 22.0 1.0 N A:LEU411 4.4 17.8 1.0 CA A:LEU411 4.4 20.3 1.0 CA A:PHE408 4.5 17.8 1.0 CG A:GLU412 4.5 26.4 1.0 CB A:LEU411 4.5 17.7 1.0 O A:HOH1172 4.6 33.8 1.0 N A:GLU412 4.7 20.5 1.0 O A:ALA350 4.7 37.3 1.0 CG A:GLU354 4.7 18.4 1.0 OD2 A:ASP473 4.7 44.6 1.0 C A:GLY409 4.8 25.9 1.0 CA A:GLU412 4.8 18.2 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 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, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:29.7 occ:1.00 O A:HOH859 2.2 24.2 1.0 OD1 A:ASP169 2.3 29.5 1.0 O A:HOH1047 2.3 24.0 1.0 O A:LYS171 2.3 41.1 1.0 O A:HOH864 2.4 24.3 1.0 O A:ASP166 2.4 36.6 1.0 O A:HOH988 2.5 33.7 1.0 C A:ASP166 3.4 33.7 1.0 CG A:ASP169 3.4 39.8 1.0 C A:LYS171 3.5 39.7 1.0 OD2 A:ASP169 3.9 44.8 1.0 CA A:ASP166 3.9 35.6 1.0 CB A:ASP166 4.1 37.3 1.0 N A:LYS171 4.2 36.7 1.0 O A:ASP169 4.2 29.0 1.0 OD2 A:ASP177 4.3 36.6 1.0 N A:CYS167 4.4 31.3 1.0 CA A:LYS171 4.4 36.0 1.0 OE1 A:GLU253 4.4 26.0 1.0 N A:VAL172 4.4 36.9 1.0 C A:ASP169 4.5 35.0 1.0 CA A:VAL172 4.6 36.6 1.0 O A:HOH1026 4.6 41.9 1.0 OE2 A:GLU253 4.7 28.8 1.0 CG2 A:VAL172 4.7 28.7 1.0 N A:ASP169 4.7 40.4 1.0 CB A:ASP169 4.7 33.0 1.0 CA A:CYS167 4.7 34.7 1.0 CA A:ASP169 4.8 36.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 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 (Q350A, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:25.1 occ:1.00 OD2 A:ASP180 2.2 29.6 1.0 OD1 A:ASP166 2.3 31.2 1.0 OD1 A:ASP156 2.3 28.6 1.0 OD1 A:ASN154 2.4 24.4 1.0 OD1 A:ASP177 2.4 35.3 1.0 OE2 A:GLU158 2.5 31.5 1.0 CG A:ASP156 3.2 31.2 1.0 CG A:ASN154 3.4 23.8 1.0 CG A:ASP180 3.4 37.6 1.0 CD A:GLU158 3.4 32.2 1.0 CG A:ASP166 3.4 36.3 1.0 OD2 A:ASP156 3.5 36.2 1.0 CG A:GLU158 3.6 32.9 1.0 CG A:ASP177 3.7 37.3 1.0 ND2 A:ASN154 3.7 24.4 1.0 CA A:CA707 3.7 26.4 1.0 CB A:ASP166 3.9 37.3 1.0 CB A:ASP180 4.0 31.9 1.0 CA A:ASP177 4.2 34.2 1.0 OD1 A:ASP180 4.4 30.1 1.0 O A:ASP177 4.4 30.3 1.0 CB A:ASP177 4.5 36.2 1.0 O A:ASP156 4.5 32.5 1.0 OD2 A:ASP166 4.5 32.0 1.0 C A:ASP156 4.5 33.0 1.0 OE1 A:GLU158 4.6 33.8 1.0 OD2 A:ASP177 4.6 36.6 1.0 CB A:ASP156 4.6 29.1 1.0 CB A:ASN154 4.7 21.9 1.0 N A:GLU158 4.8 34.0 1.0 N A:ASP156 4.8 25.1 1.0 C A:ASP177 4.8 32.1 1.0 CA A:ASP156 4.9 30.1 1.0 N A:ARG157 4.9 33.3 1.0 CB A:GLU158 4.9 35.3 1.0 O A:HOH887 5.0 20.8 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 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 (Q350A, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:26.4 occ:1.00 OD1 A:ASP389 2.4 35.4 1.0 O A:HOH887 2.4 20.8 1.0 OD2 A:ASP156 2.4 36.2 1.0 OD2 A:ASP180 2.4 29.6 1.0 OE2 A:GLU158 2.4 31.5 1.0 O A:HOH898 2.5 27.3 1.0 OD1 A:ASP180 2.6 30.1 1.0 CG A:ASP180 2.8 37.6 1.0 CG A:ASP389 3.4 35.8 1.0 CD A:GLU158 3.4 32.2 1.0 CG A:ASP156 3.4 31.2 1.0 NZ A:LYS363 3.5 44.8 1.0 OE1 A:GLU158 3.7 33.8 1.0 CA A:CA706 3.7 25.1 1.0 N A:ASP389 3.8 33.0 1.0 OD1 A:ASP156 3.8 28.6 1.0 OD2 A:ASP389 4.0 36.4 1.0 CA A:ASP389 4.2 33.2 1.0 CB A:ASP180 4.3 31.9 1.0 CB A:ASP389 4.4 31.7 1.0 O A:GLU176 4.6 33.5 1.0 CE A:LYS363 4.7 42.1 1.0 CE2 A:PHE365 4.7 26.9 1.0 CB A:ASP156 4.7 29.1 1.0 CD2 A:PHE365 4.8 19.9 1.0 CG A:GLU158 4.8 32.9 1.0 C A:PRO388 4.9 36.6 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (Q350A, 10 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 (Q350A, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:37.1 occ:1.00 OD1 A:ASP125 2.2 37.1 1.0 OD1 A:ASP123 2.2 33.8 1.0 O A:VAL129 2.2 37.2 1.0 OD2 A:ASP127 2.3 28.5 1.0 OE1 A:GLU131 2.3 35.4 1.0 O A:HOH1051 2.4 41.7 1.0 CG A:ASP127 3.2 35.9 1.0 CG A:ASP125 3.2 34.8 1.0 CG A:ASP123 3.3 28.4 1.0 CD A:GLU131 3.4 31.5 1.0 C A:VAL129 3.4 37.5 1.0 OD2 A:ASP125 3.6 35.0 1.0 OD1 A:ASP127 3.7 40.0 1.0 OE2 A:GLU131 3.9 31.4 1.0 N A:VAL129 3.9 42.2 1.0 CB A:ASP123 3.9 25.9 1.0 CG2 A:VAL129 4.0 52.9 1.0 N A:ASP127 4.0 34.3 1.0 CA A:ASP123 4.0 21.2 1.0 N A:GLU131 4.0 25.8 1.0 CA A:VAL129 4.2 41.5 1.0 OD2 A:ASP123 4.3 28.8 1.0 CB A:GLU131 4.3 29.2 1.0 CB A:ASP127 4.3 38.9 1.0 N A:ARG126 4.4 27.5 1.0 N A:VAL130 4.4 31.4 1.0 N A:ASP125 4.4 22.6 1.0 CG A:GLU131 4.4 23.4 1.0 CA A:ASP127 4.5 33.9 1.0 CB A:ASP125 4.5 29.5 1.0 C A:ASP123 4.5 29.5 1.0 CA A:VAL130 4.5 31.8 1.0 N A:GLY128 4.5 38.9 1.0 C A:ASP125 4.7 30.4 1.0 N A:ALA124 4.7 23.7 1.0 C A:VAL130 4.7 35.5 1.0 CB A:VAL129 4.7 49.4 1.0 CA A:ASP125 4.7 28.0 1.0 C A:ASP127 4.7 39.0 1.0 CA A:GLU131 4.8 33.1 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