Calcium in PDB 5n0m: HPAD4 Crystal Complex with Bb-F-Amidine

All present enzymatic activity of HPAD4 Crystal Complex with Bb-F-Amidine:
3.5.3.15;

The structure of HPAD4 Crystal Complex with Bb-F-Amidine, PDB code: 5n0m 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)	60.71 / 2.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.910, 61.300, 115.750, 90.00, 124.83, 90.00
R / Rfree (%)	18.7 / 24

The binding sites of Calcium atom in the HPAD4 Crystal Complex with Bb-F-Amidine (pdb code 5n0m). 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 Bb-F-Amidine, PDB code: 5n0m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the HPAD4 Crystal Complex with Bb-F-Amidine


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 Bb-F-Amidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:40.4 occ:1.00 O A:HOH860 2.1 45.4 1.0 O A:PHE407 2.2 32.6 1.0 OE1 A:GLU353 2.4 45.2 1.0 OE1 A:GLN349 2.4 47.4 1.0 OE1 A:GLU411 2.4 43.0 1.0 O A:LEU410 2.6 31.1 1.0 O A:HOH826 2.7 39.8 1.0 C A:PHE407 3.3 36.3 1.0 CD A:GLU411 3.5 49.3 1.0 CD A:GLU353 3.5 47.1 1.0 CD A:GLN349 3.5 45.2 1.0 C A:LEU410 3.7 29.3 1.0 OE2 A:GLU353 4.0 49.1 1.0 CA A:GLY408 4.1 36.8 1.0 N A:GLY408 4.1 36.8 1.0 OE2 A:GLU411 4.1 49.2 1.0 NE2 A:GLN349 4.3 42.4 1.0 N A:LEU410 4.3 31.1 1.0 CB A:PHE407 4.4 38.2 1.0 CA A:PHE407 4.4 36.5 1.0 CA A:LEU410 4.4 30.1 1.0 CB A:LEU410 4.5 31.3 1.0 C A:GLY408 4.6 37.6 1.0 CG A:GLN349 4.6 47.1 1.0 CG A:GLU411 4.6 46.0 1.0 CE1 A:HIS644 4.6 53.2 1.0 N A:GLU411 4.7 30.6 1.0 O A:GLN349 4.7 45.7 1.0 CG A:GLU353 4.8 40.8 1.0 CA A:GLU411 4.9 30.1 1.0 O A:GLY408 4.9 37.1 1.0

Calcium binding site 2 out of 5 in the HPAD4 Crystal Complex with Bb-F-Amidine


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 Bb-F-Amidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:57.6 occ:1.00 O A:HOH866 2.2 63.2 1.0 OD1 A:ASN373 2.3 46.0 1.0 O A:SER370 2.3 48.0 1.0 OD1 A:ASP369 2.5 56.1 1.0 OE1 A:GLU351 2.5 50.7 1.0 O A:HOH841 2.6 43.6 1.0 CG A:ASP369 3.3 56.3 1.0 C A:SER370 3.4 45.9 1.0 OD2 A:ASP369 3.5 59.2 1.0 CG A:ASN373 3.5 57.9 1.0 CD A:GLU351 3.6 51.1 1.0 N A:ASN373 3.9 56.0 1.0 CG A:GLU351 4.0 48.0 1.0 CA A:ASN373 4.1 62.6 1.0 CA A:PRO371 4.2 51.1 1.0 N A:SER370 4.2 46.5 1.0 N A:PRO371 4.3 48.1 1.0 ND2 A:ASN373 4.4 56.5 1.0 C A:ASP369 4.4 46.0 1.0 CB A:ASN373 4.4 55.1 1.0 CA A:SER370 4.4 43.7 1.0 C A:PRO371 4.5 54.1 1.0 OE1 A:GLN397 4.5 84.0 1.0 O A:LYS377 4.5 76.4 1.0 CB A:ASP369 4.6 50.2 1.0 O A:GLU351 4.6 38.9 1.0 OE2 A:GLU351 4.6 57.8 1.0 N A:ARG372 4.7 56.4 1.0 O A:ASP369 4.7 45.6 1.0 CA A:LYS377 4.7 72.2 1.0 CA A:ASP369 4.9 45.5 1.0

Calcium binding site 3 out of 5 in the HPAD4 Crystal Complex with Bb-F-Amidine


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 Bb-F-Amidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:53.4 occ:1.00 OD2 A:ASP165 2.1 44.6 1.0 OD2 A:ASP179 2.2 49.3 1.0 OD1 A:ASP155 2.4 48.2 1.0 OD1 A:ASN153 2.5 60.0 1.0 OD1 A:ASP176 2.6 57.1 1.0 OD2 A:ASP157 3.0 65.3 1.0 CG A:ASP165 3.3 49.1 1.0 CG A:ASP155 3.3 53.8 1.0 CG A:ASP179 3.4 50.3 1.0 OD2 A:ASP155 3.5 48.1 1.0 CG A:ASN153 3.5 55.5 1.0 CG A:ASP176 3.7 64.4 1.0 CB A:ASP165 3.8 49.9 1.0 ND2 A:ASN153 3.8 48.1 1.0 CA A:CA706 3.9 61.3 1.0 CG A:ASP157 3.9 66.1 1.0 CB A:ASP179 4.0 48.9 1.0 CB A:ASP157 4.1 66.6 1.0 CA A:ASP176 4.1 64.8 1.0 O A:ASP176 4.3 58.4 1.0 OD1 A:ASP165 4.3 52.8 1.0 CB A:ASP176 4.4 64.4 1.0 N A:ASP157 4.4 72.3 1.0 OD1 A:ASP179 4.5 45.9 1.0 OD2 A:ASP176 4.6 63.5 1.0 C A:ASP176 4.7 63.4 1.0 O A:ASP155 4.7 51.9 1.0 CB A:ASP155 4.7 51.4 1.0 C A:ASP155 4.8 56.5 1.0 CB A:ASN153 4.9 51.5 1.0 CA A:ASP157 4.9 74.4 1.0 O A:HOH879 4.9 55.8 1.0

Calcium binding site 4 out of 5 in the HPAD4 Crystal Complex with Bb-F-Amidine


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 Bb-F-Amidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:61.3 occ:1.00 OD1 A:ASP388 2.1 85.5 1.0 OD2 A:ASP157 2.1 65.3 1.0 O A:HOH879 2.3 55.8 1.0 OD2 A:ASP155 2.4 48.1 1.0 OD2 A:ASP179 2.5 49.3 1.0 OD1 A:ASP179 2.7 45.9 1.0 CG A:ASP179 2.9 50.3 1.0 CG A:ASP157 3.0 66.1 1.0 OD1 A:ASP157 3.3 67.0 1.0 CG A:ASP388 3.3 68.4 1.0 CG A:ASP155 3.5 53.8 1.0 CA A:CA705 3.9 53.4 1.0 N A:ASP388 3.9 55.4 1.0 CA A:ASP388 4.0 56.2 1.0 O A:HOH917 4.0 60.2 1.0 OD1 A:ASP155 4.0 48.2 1.0 OD2 A:ASP388 4.1 72.2 1.0 CB A:ASP388 4.3 55.8 1.0 CB A:ASP179 4.4 48.9 1.0 CB A:ASP157 4.4 66.6 1.0 CD2 A:LEU364 4.7 52.0 1.0 CB A:ASP155 4.8 51.4 1.0 CE A:LYS362 4.8 54.2 1.0 NZ A:LYS362 4.9 58.6 1.0 O A:GLU175 4.9 62.0 1.0

Calcium binding site 5 out of 5 in the HPAD4 Crystal Complex with Bb-F-Amidine


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 Bb-F-Amidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:61.3 occ:1.00 O A:HOH830 2.2 46.6 1.0 O A:ASP165 2.3 67.7 1.0 O A:GLU170 2.3 62.1 1.0 OD1 A:ASP168 2.3 69.5 1.0 O A:HOH944 2.3 67.1 1.0 O A:HOH871 2.4 52.5 1.0 CG A:ASP168 3.2 67.9 1.0 C A:ASP165 3.3 54.9 1.0 OD2 A:ASP168 3.4 77.0 1.0 C A:GLU170 3.5 67.4 1.0 OD2 A:ASP176 4.0 63.5 1.0 CA A:ASP165 4.1 47.1 1.0 N A:GLU170 4.1 74.8 1.0 N A:CYS166 4.3 55.5 1.0 CB A:ASP165 4.3 49.9 1.0 O A:ASP168 4.4 74.0 1.0 N A:VAL171 4.4 63.3 1.0 CA A:GLU170 4.4 74.9 1.0 CA A:CYS166 4.5 52.6 1.0 CA A:VAL171 4.5 64.0 1.0 CB A:ASP168 4.6 64.8 1.0 C A:ASP168 4.6 72.6 1.0 N A:ASP168 4.7 58.7 1.0 OE1 A:GLU252 4.9 48.7 1.0 CA A:ASP168 4.9 69.9 1.0 N A:LEU172 4.9 78.6 1.0 OE2 A:GLU252 4.9 41.4 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