Calcium in PDB 4x8g: Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199

All present enzymatic activity of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199:
3.5.3.15;

The structure of Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199, PDB code: 4x8g was solved by H.D.Lewis, B.D.Bax, C.-W.Chung, O.Polyakova, J.Thorpe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 3.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.990, 62.250, 116.750, 90.00, 124.71, 90.00
R / Rfree (%)	19.8 / 23

The binding sites of Calcium atom in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199 (pdb code 4x8g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199, PDB code: 4x8g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199


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 Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:1.0 occ:1.00 O A:LEU410 2.5 0.8 1.0 OE1 A:GLU411 2.5 0.8 1.0 O A:HOH819 2.5 0.8 1.0 O A:PHE407 2.5 0.7 1.0 O A:HOH818 2.6 0.4 1.0 OE1 A:GLU353 2.9 0.5 1.0 CD A:GLU411 3.4 0.3 1.0 C A:LEU410 3.6 0.9 1.0 CD A:GLU353 3.7 1.0 1.0 C A:PHE407 3.7 0.1 1.0 CG A:GLU411 3.8 0.4 1.0 OE2 A:GLU353 3.8 0.5 1.0 CA A:GLY408 4.0 0.9 1.0 O A:GLY408 4.3 0.7 1.0 C A:GLY408 4.3 0.0 1.0 N A:GLY408 4.3 0.2 1.0 N A:LEU410 4.4 0.7 1.0 CA A:LEU410 4.5 0.2 1.0 N A:GLU411 4.5 0.2 1.0 OE2 A:GLU411 4.5 0.2 1.0 CA A:GLU411 4.6 0.1 1.0 CB A:GLU411 4.8 0.3 1.0 CB A:LEU410 4.8 0.9 1.0 CA A:PHE407 4.9 0.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199


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 Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:0.1 occ:1.00 OD1 A:ASP176 2.4 1.0 1.0 OD2 A:ASP157 2.4 0.1 1.0 OD1 A:ASP155 2.4 0.4 1.0 OD2 A:ASP179 2.5 0.7 1.0 OD1 A:ASN153 2.6 0.5 1.0 OD2 A:ASP165 2.6 0.0 1.0 CG A:ASP155 3.2 0.7 1.0 OD2 A:ASP155 3.3 0.1 1.0 CG A:ASP179 3.5 1.0 1.0 CG A:ASP176 3.6 0.5 1.0 CG A:ASN153 3.6 0.5 1.0 CG A:ASP157 3.7 0.6 1.0 CG A:ASP165 3.7 0.6 1.0 CB A:ASP179 3.9 1.0 1.0 ND2 A:ASN153 4.0 0.9 1.0 CB A:ASP165 4.1 0.7 1.0 OD2 A:ASP176 4.4 0.1 1.0 OD1 A:ASP157 4.4 0.2 1.0 CB A:ASP176 4.4 0.0 1.0 CA A:ASP176 4.4 0.5 1.0 O A:ASP176 4.5 0.5 1.0 CA A:CA703 4.5 0.6 1.0 OD1 A:ASP179 4.5 0.2 1.0 CB A:ASP157 4.6 0.6 1.0 CB A:ASP155 4.7 0.1 1.0 N A:ASP157 4.7 0.4 1.0 OD1 A:ASP165 4.8 0.1 1.0 C A:ASP155 4.8 0.8 1.0 CB A:ASN153 5.0 0.8 1.0 O A:ASP155 5.0 1.0 1.0 C A:ASP176 5.0 0.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199


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 Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:0.6 occ:1.00 OD2 A:ASP179 2.5 0.7 1.0 OD1 A:ASP157 2.6 0.2 1.0 OD1 A:ASP388 2.6 0.5 1.0 OD1 A:ASP179 2.6 0.2 1.0 CG A:ASP179 2.9 1.0 1.0 NZ A:LYS362 3.0 0.5 1.0 OD2 A:ASP155 3.3 0.1 1.0 CG A:ASP157 3.3 0.6 1.0 OD2 A:ASP157 3.4 0.1 1.0 CG A:ASP388 3.8 0.7 1.0 O A:GLU175 4.0 0.9 1.0 CE A:LYS362 4.1 0.1 1.0 N A:ASP388 4.2 0.3 1.0 CD2 A:LEU364 4.3 0.1 1.0 CA A:ASP388 4.4 0.8 1.0 CB A:ASP179 4.4 1.0 1.0 CG A:ASP155 4.5 0.7 1.0 CA A:CA702 4.5 0.1 1.0 OD2 A:ASP388 4.6 0.1 1.0 CB A:ASP388 4.8 0.9 1.0 CB A:ASP157 4.8 0.6 1.0 OD1 A:ASP155 4.9 0.4 1.0 N A:ASP179 5.0 0.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199


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 Human Peptidylarginine Deiminase TYPE4 (PAD4) in Complex with GSK199 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:1.0 occ:1.00 O A:ASP165 2.4 0.1 1.0 O A:HOH821 2.5 0.8 1.0 O A:GLU170 2.5 0.3 1.0 O A:HOH813 2.6 0.4 1.0 O A:HOH822 2.7 0.8 1.0 OD2 A:ASP168 2.8 0.3 1.0 OD1 A:ASP168 3.2 0.5 1.0 CG A:ASP168 3.2 0.2 1.0 C A:ASP165 3.5 0.2 1.0 C A:GLU170 3.7 0.8 1.0 N A:GLU170 4.0 0.7 1.0 CA A:ASP165 4.1 0.9 1.0 O A:ASP168 4.2 0.7 1.0 CB A:ASP165 4.4 0.7 1.0 C A:ASP168 4.4 0.8 1.0 CA A:GLU170 4.4 0.0 1.0 CB A:ASP168 4.6 0.3 1.0 OD2 A:ASP176 4.6 0.1 1.0 N A:CYS166 4.6 0.4 1.0 N A:VAL171 4.7 0.2 1.0 OE2 A:GLU252 4.7 0.7 1.0 OE1 A:GLU252 4.7 0.1 1.0 N A:ASP168 4.8 0.8 1.0 CZ A:PHE214 4.8 0.6 1.0 CA A:VAL171 4.8 0.7 1.0 ND2 A:ASN153 4.9 0.9 1.0 CA A:ASP168 4.9 0.1 1.0 N A:ASP169 4.9 0.5 1.0 CA A:CYS166 4.9 0.9 1.0

H.D.Lewis, J.Liddle, J.E.Coote, S.J.Atkinson, M.D.Barker, B.D.Bax, K.L.Bicker, R.P.Bingham, M.Campbell, Y.H.Chen, C.W.Chung, P.D.Craggs, R.P.Davis, D.Eberhard, G.Joberty, K.E.Lind, K.Locke, C.Maller, K.Martinod, C.Patten, O.Polyakova, C.E.Rise, M.Rudiger, R.J.Sheppard, D.J.Slade, P.Thomas, J.Thorpe, G.Yao, G.Drewes, D.D.Wagner, P.R.Thompson, R.K.Prinjha, D.M.Wilson. Inhibition of PAD4 Activity Is Sufficient to Disrupt Mouse and Human Net Formation. Nat.Chem.Biol. 2015.
ISSN: ESSN 1552-4469
PubMed: 25622091
DOI: 10.1038/NCHEMBIO.1735