Calcium in PDB 4n2e: Crystal Structure of Protein Arginine Deiminase 2 (D123N, 10 Mm CA2+)

All present enzymatic activity of Crystal Structure of Protein Arginine Deiminase 2 (D123N, 10 Mm CA2+):
3.5.3.15;

The structure of Crystal Structure of Protein Arginine Deiminase 2 (D123N, 10 Mm CA2+), PDB code: 4n2e 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)	38.42 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.386, 51.917, 76.587, 90.00, 105.63, 90.00
R / Rfree (%)	16.9 / 20.8

The binding sites of Calcium atom in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 10 Mm CA2+) (pdb code 4n2e). 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 (D123N, 10 Mm CA2+), PDB code: 4n2e:
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 (D123N, 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 (D123N, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:30.2 occ:1.00 OD1 A:ASN123 2.2 26.8 1.0 OD1 A:ASP125 2.2 26.7 1.0 O A:HOH1386 2.3 33.1 1.0 O A:VAL129 2.3 29.8 1.0 OE1 A:GLU131 2.3 21.3 1.0 OD1 A:ASP127 2.3 38.7 1.0 CG A:ASP127 3.2 39.0 1.0 CG A:ASP125 3.2 30.4 1.0 CG A:ASN123 3.2 25.7 1.0 CD A:GLU131 3.3 27.1 1.0 C A:VAL129 3.4 29.7 1.0 OD2 A:ASP125 3.5 38.8 1.0 OD2 A:ASP127 3.5 38.9 1.0 CB A:ASN123 3.8 21.6 1.0 N A:VAL129 3.9 35.9 1.0 OE2 A:GLU131 3.9 21.6 1.0 CA A:ASN123 4.0 21.6 1.0 N A:GLU131 4.0 24.3 1.0 N A:ASP127 4.1 29.5 1.0 CA A:VAL129 4.1 34.5 1.0 ND2 A:ASN123 4.3 24.6 1.0 CB A:GLU131 4.3 28.8 1.0 CB A:ASP127 4.4 35.4 1.0 N A:VAL130 4.4 31.6 1.0 N A:ASP125 4.4 18.7 1.0 CG A:GLU131 4.4 21.5 1.0 CB A:VAL129 4.4 40.3 1.0 N A:ARG126 4.5 21.0 0.7 N A:ARG126 4.5 22.2 0.3 CB A:ASP125 4.5 23.6 1.0 CA A:VAL130 4.5 27.7 1.0 C A:ASN123 4.5 23.9 1.0 CA A:ASP127 4.6 35.7 1.0 N A:GLY128 4.6 40.6 1.0 C A:ASP125 4.7 23.9 1.0 CA A:ASP125 4.7 22.1 1.0 N A:ALA124 4.7 17.7 1.0 C A:VAL130 4.7 31.5 1.0 CA A:GLU131 4.8 26.6 1.0 C A:ASP127 4.9 42.4 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:21.0 occ:1.00 O A:LYS171 2.3 25.4 1.0 OD1 A:ASP169 2.3 23.2 1.0 O A:ASP166 2.3 21.1 1.0 O A:HOH875 2.4 24.2 1.0 O A:HOH920 2.4 24.9 1.0 O A:HOH833 2.4 19.7 1.0 O A:HOH996 2.5 29.5 1.0 C A:ASP166 3.4 22.6 1.0 CG A:ASP169 3.4 29.3 1.0 C A:LYS171 3.5 29.8 1.0 OD2 A:ASP169 3.8 34.7 1.0 CA A:ASP166 4.0 24.8 1.0 N A:LYS171 4.2 25.9 1.0 CB A:ASP166 4.3 24.8 1.0 OD2 A:ASP177 4.3 26.3 1.0 O A:ASP169 4.3 23.8 1.0 O A:HOH1111 4.4 33.9 1.0 CA A:LYS171 4.4 24.8 1.0 N A:VAL172 4.5 28.1 1.0 N A:CYS167 4.5 22.8 1.0 CA A:VAL172 4.6 30.3 1.0 C A:ASP169 4.6 25.0 1.0 O A:HOH1116 4.6 49.0 1.0 OE1 A:GLU253 4.6 24.4 1.0 CB A:ASP169 4.7 26.4 1.0 CG2 A:VAL172 4.8 20.3 1.0 N A:ASP169 4.8 28.1 1.0 CA A:CYS167 4.8 20.3 1.0 OE2 A:GLU253 4.9 23.2 1.0 CA A:ASP169 4.9 24.2 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:17.7 occ:1.00 OD2 A:ASP180 2.3 18.2 1.0 OD2 A:ASP166 2.3 26.7 1.0 OD1 A:ASN154 2.3 16.4 1.0 OD1 A:ASP156 2.3 18.5 1.0 OD1 A:ASP177 2.3 23.6 1.0 OE2 A:GLU158 2.4 24.7 1.0 CG A:ASP156 3.2 21.9 1.0 CG A:ASN154 3.3 17.3 1.0 CG A:ASP166 3.4 31.6 1.0 CD A:GLU158 3.4 29.4 1.0 OD2 A:ASP156 3.4 20.2 1.0 CG A:ASP180 3.4 21.7 1.0 CG A:ASP177 3.6 29.3 1.0 ND2 A:ASN154 3.6 20.9 1.0 CG A:GLU158 3.6 30.9 1.0 CA A:CA708 3.7 20.1 1.0 CB A:ASP166 3.9 24.8 1.0 CB A:ASP180 4.1 20.2 1.0 CA A:ASP177 4.3 22.4 1.0 OD2 A:ASP177 4.4 26.3 1.0 OD1 A:ASP180 4.4 18.9 1.0 CB A:ASP177 4.4 22.9 1.0 OD1 A:ASP166 4.4 24.5 1.0 O A:ASP177 4.5 20.3 1.0 OE1 A:GLU158 4.6 27.6 1.0 O A:ASP156 4.6 22.5 1.0 CB A:ASP156 4.6 18.9 1.0 C A:ASP156 4.6 22.9 1.0 CB A:ASN154 4.7 17.6 1.0 N A:ASP156 4.8 17.6 1.0 C A:ASP177 4.9 24.8 1.0 CA A:ASP156 4.9 19.0 1.0 N A:GLU158 4.9 28.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:20.1 occ:1.00 OD2 A:ASP156 2.3 20.2 1.0 OD1 A:ASP389 2.4 25.0 1.0 OD2 A:ASP180 2.4 18.2 1.0 O A:HOH912 2.4 18.1 1.0 O A:HOH852 2.5 21.3 1.0 OE2 A:GLU158 2.5 24.7 1.0 OD1 A:ASP180 2.6 18.9 1.0 CG A:ASP180 2.9 21.7 1.0 CG A:ASP156 3.4 21.9 1.0 CD A:GLU158 3.5 29.4 1.0 CG A:ASP389 3.5 29.7 1.0 NZ A:LYS363 3.7 36.0 1.0 OE1 A:GLU158 3.7 27.6 1.0 CA A:CA707 3.7 17.7 1.0 OD1 A:ASP156 3.8 18.5 1.0 N A:ASP389 3.9 23.6 1.0 OD2 A:ASP389 4.2 39.6 1.0 CA A:ASP389 4.2 21.6 1.0 CB A:ASP180 4.4 20.2 1.0 CB A:ASP389 4.5 23.5 1.0 O A:GLU176 4.6 23.3 1.0 CE2 A:PHE365 4.6 24.2 1.0 CB A:ASP156 4.7 18.9 1.0 CD2 A:PHE365 4.8 20.4 1.0 CG A:GLU158 4.8 30.9 1.0 O A:HOH995 4.9 37.0 1.0 C A:PRO388 4.9 25.9 1.0 CE A:LYS363 4.9 38.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Protein Arginine Deiminase 2 (D123N, 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 (D123N, 10 Mm CA2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:17.1 occ:1.00 O A:PHE408 2.3 15.3 1.0 O A:HOH1280 2.3 30.6 1.0 O A:LEU411 2.4 17.4 1.0 OE1 A:GLU354 2.4 17.2 1.0 OE2 A:GLU412 2.5 21.4 1.0 O A:HOH823 2.5 21.7 1.0 OE1 A:GLN350 2.7 18.3 0.5 CD A:GLU412 3.3 27.4 1.0 C A:PHE408 3.4 17.9 1.0 CD A:GLU354 3.5 24.7 1.0 C A:LEU411 3.6 13.1 1.0 CD A:GLN350 3.8 37.6 0.5 OE2 A:GLU354 3.8 25.6 1.0 OE1 A:GLU412 3.9 30.7 1.0 CB A:PHE408 4.3 13.7 1.0 N A:GLY409 4.3 15.5 1.0 NE2 A:GLN350 4.3 18.2 0.5 CG A:GLU412 4.3 21.6 1.0 CA A:GLY409 4.3 16.7 1.0 N A:LEU411 4.4 13.8 1.0 CA A:PHE408 4.4 13.2 1.0 CA A:LEU411 4.4 14.4 1.0 O A:GLN350 4.5 28.8 1.0 CB A:LEU411 4.5 10.8 1.0 N A:GLU412 4.6 13.7 1.0 C A:GLY409 4.7 17.9 1.0 CA A:GLU412 4.7 14.1 1.0 O A:HOH1144 4.8 40.5 1.0 CG A:GLU354 4.8 16.8 1.0 O A:HOH1071 4.9 39.8 1.0 O A:GLY409 5.0 16.7 1.0 CG A:GLN350 5.0 36.6 0.5

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