Calcium in PDB 5n1b: HPAD4 Crystal Complex with Afm-14A

All present enzymatic activity of HPAD4 Crystal Complex with Afm-14A:
3.5.3.15;

The structure of HPAD4 Crystal Complex with Afm-14A, PDB code: 5n1b 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)	42.72 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.580, 60.600, 115.980, 90.00, 124.62, 90.00
R / Rfree (%)	22.2 / 28.4

The binding sites of Calcium atom in the HPAD4 Crystal Complex with Afm-14A (pdb code 5n1b). 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-14A, PDB code: 5n1b:
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-14A


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-14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:9.6 occ:1.00 OE1 A:GLN349 2.4 18.9 1.0 O A:PHE407 2.4 15.5 1.0 OE1 A:GLU353 2.5 11.2 1.0 O A:LEU410 2.5 12.4 1.0 O A:HOH821 2.5 6.8 1.0 OE1 A:GLU411 2.6 13.4 1.0 CD A:GLU411 3.5 12.9 1.0 CD A:GLN349 3.5 19.9 1.0 CD A:GLU353 3.5 11.0 1.0 C A:PHE407 3.6 15.7 1.0 C A:LEU410 3.7 12.1 1.0 OE2 A:GLU411 3.8 13.1 1.0 OE2 A:GLU353 3.9 10.9 1.0 NE2 A:GLN349 4.1 17.9 1.0 N A:GLY408 4.4 15.4 1.0 N A:LEU410 4.4 12.4 1.0 CA A:GLY408 4.5 15.4 1.0 CA A:LEU410 4.5 12.1 1.0 CB A:PHE407 4.5 16.0 1.0 CA A:PHE407 4.6 16.1 1.0 N A:GLU411 4.6 11.9 1.0 CG A:GLU411 4.6 12.3 1.0 CG A:GLN349 4.6 21.5 1.0 CE1 A:HIS644 4.7 22.0 1.0 CB A:LEU410 4.7 12.1 1.0 CA A:GLU411 4.7 11.7 1.0 C A:GLY408 4.7 14.8 1.0 CG A:GLU353 4.8 11.0 1.0 O A:GLN349 4.8 20.4 1.0 O A:GLY408 4.9 15.1 1.0

Calcium binding site 2 out of 5 in the HPAD4 Crystal Complex with Afm-14A


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-14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:25.0 occ:1.00 OD1 A:ASN373 2.3 28.5 1.0 O A:SER370 2.4 20.7 1.0 OE1 A:GLU351 2.4 15.1 1.0 OD1 A:ASP369 2.7 18.4 1.0 CG A:ASP369 3.3 18.3 1.0 OD2 A:ASP369 3.3 18.6 1.0 CG A:ASN373 3.5 29.0 1.0 C A:SER370 3.5 20.5 1.0 CD A:GLU351 3.5 15.6 1.0 N A:ASN373 4.0 27.8 1.0 CG A:GLU351 4.0 15.3 1.0 CA A:ASN373 4.1 28.8 1.0 CA A:PRO371 4.2 24.8 1.0 N A:SER370 4.3 18.7 1.0 N A:PRO371 4.3 22.5 1.0 O A:LYS377 4.3 33.5 1.0 ND2 A:ASN373 4.4 28.5 1.0 C A:PRO371 4.4 27.2 1.0 CB A:ASN373 4.4 28.7 1.0 CA A:SER370 4.5 19.3 1.0 OE1 A:GLN397 4.5 42.8 1.0 OE2 A:GLU351 4.6 15.0 1.0 C A:ASP369 4.6 17.8 1.0 CB A:ASP369 4.6 17.7 1.0 N A:ARG372 4.7 28.4 1.0 CA A:LYS377 4.7 31.6 1.0 CG A:LYS377 4.7 34.5 1.0 O A:GLU351 4.8 14.0 1.0 O A:PRO371 4.9 30.6 1.0 C A:LYS377 5.0 31.0 1.0

Calcium binding site 3 out of 5 in the HPAD4 Crystal Complex with Afm-14A


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-14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:24.6 occ:1.00 OD2 A:ASP165 2.0 29.4 1.0 OD2 A:ASP179 2.2 22.8 1.0 OD1 A:ASP155 2.3 19.9 1.0 OD1 A:ASP176 2.5 23.3 1.0 OD1 A:ASN153 2.5 15.8 1.0 OD2 A:ASP157 2.6 20.9 1.0 CG A:ASP165 3.2 29.1 1.0 CG A:ASP155 3.3 20.4 1.0 CG A:ASP179 3.4 22.6 1.0 OD2 A:ASP155 3.6 20.7 1.0 CG A:ASN153 3.6 15.5 1.0 CG A:ASP157 3.7 22.4 1.0 CG A:ASP176 3.7 23.8 1.0 CA A:CA706 3.7 27.9 1.0 CB A:ASP165 3.8 28.8 1.0 ND2 A:ASN153 4.0 15.4 1.0 CB A:ASP179 4.1 22.8 1.0 CA A:ASP176 4.1 26.6 1.0 CB A:ASP157 4.1 25.1 1.0 O A:ASP176 4.2 25.6 1.0 OD1 A:ASP165 4.2 30.0 1.0 OD1 A:ASP179 4.4 22.4 1.0 CB A:ASP176 4.4 25.2 1.0 N A:ASP157 4.4 26.8 1.0 OD1 A:ASP157 4.7 20.5 1.0 OD2 A:ASP176 4.7 21.5 1.0 C A:ASP176 4.7 26.9 1.0 CB A:ASP155 4.7 19.2 1.0 C A:ASP155 4.8 19.8 1.0 O A:HOH903 4.9 9.8 1.0 CA A:ASP157 4.9 28.1 1.0 CB A:ASN153 4.9 15.5 1.0 O A:ASP155 5.0 18.3 1.0

Calcium binding site 4 out of 5 in the HPAD4 Crystal Complex with Afm-14A


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-14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:27.9 occ:1.00 O A:HOH903 2.1 9.8 1.0 OD2 A:ASP157 2.2 20.9 1.0 OD1 A:ASP388 2.3 27.8 1.0 OD2 A:ASP155 2.5 20.7 1.0 OD2 A:ASP179 2.6 22.8 1.0 OD1 A:ASP157 2.8 20.5 1.0 OD1 A:ASP179 2.8 22.4 1.0 CG A:ASP157 2.9 22.4 1.0 CG A:ASP179 3.1 22.6 1.0 CG A:ASP388 3.5 26.8 1.0 CG A:ASP155 3.6 20.4 1.0 CA A:CA705 3.7 24.6 1.0 N A:ASP388 3.9 26.0 1.0 O A:HOH843 3.9 14.2 1.0 OD1 A:ASP155 4.0 19.9 1.0 CA A:ASP388 4.1 24.7 1.0 CD2 A:LEU364 4.3 17.9 1.0 CB A:ASP157 4.3 25.1 1.0 OD2 A:ASP388 4.4 27.6 1.0 CB A:ASP388 4.4 25.2 1.0 CB A:ASP179 4.6 22.8 1.0 O A:GLU175 4.7 29.2 1.0 CE A:LYS362 4.9 22.2 1.0 NZ A:LYS362 4.9 22.3 1.0 CB A:ASP155 4.9 19.2 1.0 C A:PRO387 5.0 27.8 1.0

Calcium binding site 5 out of 5 in the HPAD4 Crystal Complex with Afm-14A


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-14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:21.1 occ:1.00 O A:HOH851 2.1 15.1 1.0 O A:HOH824 2.3 8.2 1.0 OD1 A:ASP168 2.4 32.1 1.0 O A:GLU170 2.4 28.4 1.0 O A:ASP165 2.5 28.1 1.0 CG A:ASP168 3.4 32.5 1.0 C A:ASP165 3.5 28.1 1.0 C A:GLU170 3.6 31.0 1.0 OD2 A:ASP168 3.7 33.0 1.0 CA A:ASP165 4.0 29.4 1.0 OD2 A:ASP176 4.1 21.5 1.0 CB A:ASP165 4.3 28.8 1.0 N A:GLU170 4.4 34.5 1.0 O A:ASP168 4.4 34.6 1.0 CA A:GLU170 4.5 33.7 1.0 N A:VAL171 4.6 31.2 1.0 N A:CYS166 4.6 26.8 1.0 CA A:VAL171 4.6 33.0 1.0 OE1 A:GLU252 4.7 15.9 1.0 C A:ASP168 4.7 33.8 1.0 CB A:ASP168 4.7 32.0 1.0 N A:ASP168 4.8 30.4 1.0 N A:LEU172 4.9 40.7 1.0 CA A:CYS166 4.9 26.2 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