Calcium in PDB 5n0y: HPAD4 Crystal Complex with Afm-30A

All present enzymatic activity of HPAD4 Crystal Complex with Afm-30A:
3.5.3.15;

The structure of HPAD4 Crystal Complex with Afm-30A, PDB code: 5n0y was solved by E.Beaumont, P.Kerry, P.Thompson, A.Muth, V.Subramanian, M.Nagar, H.Srinath, K.Clancy, S.Parelkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.10 / 2.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.556, 60.929, 115.656, 90.00, 124.69, 90.00
R / Rfree (%)	17.8 / 22.7

The binding sites of Calcium atom in the HPAD4 Crystal Complex with Afm-30A (pdb code 5n0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the HPAD4 Crystal Complex with Afm-30A, PDB code: 5n0y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the HPAD4 Crystal Complex with Afm-30A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HPAD4 Crystal Complex with Afm-30A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:31.4 occ:1.00 O A:PHE407 2.3 26.4 1.0 OE1 A:GLN349 2.4 38.8 1.0 OE1 A:GLU411 2.4 35.7 1.0 OE1 A:GLU353 2.4 32.9 1.0 O A:LEU410 2.5 28.1 1.0 O A:HOH893 2.6 36.0 1.0 O A:HOH827 2.6 27.0 1.0 C A:PHE407 3.4 28.9 1.0 CD A:GLN349 3.5 36.7 1.0 CD A:GLU411 3.5 38.3 1.0 CD A:GLU353 3.5 35.8 1.0 C A:LEU410 3.7 27.9 1.0 OE2 A:GLU353 3.9 41.3 1.0 CA A:GLY408 4.1 32.1 1.0 N A:GLY408 4.2 30.1 1.0 OE2 A:GLU411 4.3 39.9 1.0 NE2 A:GLN349 4.3 36.9 1.0 CB A:PHE407 4.4 30.8 1.0 O A:HOH933 4.4 44.6 1.0 N A:LEU410 4.5 27.6 1.0 CG A:GLU411 4.5 34.0 1.0 CA A:PHE407 4.5 28.7 1.0 CA A:LEU410 4.5 28.4 1.0 CG A:GLN349 4.5 38.7 1.0 C A:GLY408 4.6 32.3 1.0 CE1 A:HIS644 4.6 38.2 1.0 N A:GLU411 4.7 28.4 1.0 O A:GLN349 4.7 36.0 1.0 CB A:LEU410 4.7 29.8 1.0 O A:HOH899 4.7 27.9 1.0 CA A:GLU411 4.8 25.8 1.0 CG A:GLU353 4.8 31.7 1.0 O A:GLY408 4.9 32.2 1.0

Calcium binding site 2 out of 5 in the HPAD4 Crystal Complex with Afm-30A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HPAD4 Crystal Complex with Afm-30A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:47.2 occ:1.00 OD1 A:ASP369 2.2 45.1 1.0 O A:SER370 2.3 38.0 1.0 O A:HOH805 2.4 45.0 1.0 OD1 A:ASN373 2.4 42.1 1.0 OE1 A:GLU351 2.5 40.3 1.0 O A:HOH913 2.5 38.0 1.0 CG A:ASP369 3.2 49.2 1.0 C A:SER370 3.4 38.9 1.0 OD2 A:ASP369 3.5 52.0 1.0 CD A:GLU351 3.6 41.8 1.0 CG A:ASN373 3.6 49.3 1.0 N A:ASN373 3.9 51.2 1.0 N A:SER370 4.0 37.6 1.0 CG A:GLU351 4.1 40.1 1.0 CA A:ASN373 4.2 53.3 1.0 CA A:PRO371 4.3 41.9 1.0 C A:ASP369 4.3 39.3 1.0 N A:PRO371 4.3 40.0 1.0 CA A:SER370 4.3 37.3 1.0 O A:LYS377 4.4 61.8 1.0 OE1 A:GLN397 4.4 55.5 1.0 CB A:ASP369 4.4 44.9 1.0 C A:PRO371 4.5 42.9 1.0 CB A:ASN373 4.5 45.0 1.0 ND2 A:ASN373 4.5 44.2 1.0 O A:GLU351 4.6 35.3 1.0 OE2 A:GLU351 4.6 41.8 1.0 N A:ARG372 4.6 49.4 1.0 CA A:LYS377 4.7 58.2 1.0 O A:ASP369 4.7 41.0 1.0 CA A:ASP369 4.8 38.0 1.0 C A:ARG372 5.0 50.5 1.0

Calcium binding site 3 out of 5 in the HPAD4 Crystal Complex with Afm-30A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of HPAD4 Crystal Complex with Afm-30A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:46.2 occ:1.00 OD2 A:ASP165 2.0 44.6 1.0 OD2 A:ASP179 2.1 41.9 1.0 OD1 A:ASP176 2.4 47.3 1.0 OD1 A:ASP155 2.4 44.2 1.0 OD1 A:ASN153 2.5 58.6 1.0 OD2 A:ASP157 2.6 56.1 1.0 CG A:ASP165 3.2 42.5 1.0 CG A:ASP179 3.3 37.0 1.0 CG A:ASP155 3.3 45.2 1.0 CG A:ASN153 3.5 48.3 1.0 OD2 A:ASP155 3.5 42.7 1.0 CG A:ASP157 3.6 55.1 1.0 CG A:ASP176 3.6 49.5 1.0 CB A:ASP165 3.7 39.8 1.0 ND2 A:ASN153 3.8 45.9 1.0 CA A:CA705 3.8 47.9 1.0 CB A:ASP179 3.9 40.7 1.0 CB A:ASP157 4.1 54.9 1.0 CA A:ASP176 4.1 48.8 1.0 OD1 A:ASP165 4.3 41.8 1.0 O A:ASP176 4.3 50.2 1.0 CB A:ASP176 4.3 48.6 1.0 OD1 A:ASP179 4.3 36.0 1.0 N A:ASP157 4.4 61.3 1.0 OD2 A:ASP176 4.5 49.8 1.0 OD1 A:ASP157 4.5 51.8 1.0 C A:ASP176 4.7 51.3 1.0 CB A:ASP155 4.7 43.5 1.0 C A:ASP155 4.8 48.5 1.0 O A:HOH932 4.8 43.1 1.0 O A:ASP155 4.8 44.7 1.0 CB A:ASN153 4.8 45.2 1.0 CA A:ASP157 4.9 62.0 1.0

Calcium binding site 4 out of 5 in the HPAD4 Crystal Complex with Afm-30A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of HPAD4 Crystal Complex with Afm-30A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:47.9 occ:1.00 O A:HOH932 2.2 43.1 1.0 OD1 A:ASP388 2.3 56.4 1.0 OD2 A:ASP155 2.5 42.7 1.0 OD2 A:ASP157 2.5 56.1 1.0 OD2 A:ASP179 2.5 41.9 1.0 OD1 A:ASP179 2.6 36.0 1.0 OD1 A:ASP157 2.9 51.8 1.0 CG A:ASP179 2.9 37.0 1.0 CG A:ASP157 3.0 55.1 1.0 CG A:ASP388 3.5 50.1 1.0 CG A:ASP155 3.6 45.2 1.0 CA A:CA704 3.8 46.2 1.0 N A:ASP388 4.0 47.0 1.0 OD1 A:ASP155 4.1 44.2 1.0 CA A:ASP388 4.1 47.0 1.0 O A:HOH1011 4.2 51.6 1.0 OD2 A:ASP388 4.2 58.9 1.0 CB A:ASP179 4.4 40.7 1.0 CB A:ASP388 4.4 41.8 1.0 CB A:ASP157 4.5 54.9 1.0 NZ A:LYS362 4.7 51.4 1.0 CB A:ASP155 4.9 43.5 1.0 O A:GLU175 4.9 50.9 1.0 CE A:LYS362 4.9 49.1 1.0

Calcium binding site 5 out of 5 in the HPAD4 Crystal Complex with Afm-30A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of HPAD4 Crystal Complex with Afm-30A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:49.9 occ:1.00 OD1 A:ASP168 2.2 47.6 1.0 O A:GLU170 2.2 45.7 1.0 O A:ASP165 2.3 56.7 1.0 O A:HOH970 2.3 56.1 1.0 O A:HOH845 2.4 43.6 1.0 O A:HOH804 2.4 44.5 1.0 CG A:ASP168 3.2 50.9 1.0 C A:ASP165 3.4 50.5 1.0 OD2 A:ASP168 3.4 55.1 1.0 C A:GLU170 3.4 49.7 1.0 N A:GLU170 4.1 53.9 1.0 OD2 A:ASP176 4.2 49.8 1.0 O A:HOH992 4.2 60.1 1.0 CA A:ASP165 4.2 42.4 1.0 O A:ASP168 4.2 58.9 1.0 N A:VAL171 4.4 47.1 1.0 CA A:GLU170 4.4 52.8 1.0 N A:CYS166 4.4 44.6 1.0 CB A:ASP165 4.5 39.8 1.0 CA A:CYS166 4.5 42.0 1.0 CA A:VAL171 4.5 48.7 1.0 CB A:ASP168 4.5 45.9 1.0 C A:ASP168 4.6 57.6 1.0 N A:ASP168 4.6 46.4 1.0 OE1 A:GLU252 4.7 39.9 1.0 OE2 A:GLU252 4.8 36.2 1.0 CA A:ASP168 4.8 51.4 1.0 N A:LEU172 5.0 63.2 1.0

A.Muth, V.Subramanian, E.Beaumont, M.Nagar, P.Kerry, P.Mcewan, H.Srinath, K.Clancy, S.Parelkar, P.R.Thompson. Development of A Selective Inhibitor of Protein Arginine Deiminase 2. J. Med. Chem. V. 60 3198 2017.
ISSN: ISSN 1520-4804
PubMed: 28328217
DOI: 10.1021/ACS.JMEDCHEM.7B00274