Calcium in PDB 5n0z: HPAD4 Crystal Complex with Afm-41A

All present enzymatic activity of HPAD4 Crystal Complex with Afm-41A:
3.5.3.15;

The structure of HPAD4 Crystal Complex with Afm-41A, PDB code: 5n0z 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)	55.79 / 2.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.150, 60.940, 115.320, 90.00, 124.68, 90.00
R / Rfree (%)	18 / 22.9

The binding sites of Calcium atom in the HPAD4 Crystal Complex with Afm-41A (pdb code 5n0z). 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-41A, PDB code: 5n0z:
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-41A


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-41A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:43.4 occ:1.00 O A:PHE407 2.3 36.7 1.0 OE1 A:GLN349 2.4 42.7 1.0 OE1 A:GLU353 2.5 39.0 1.0 O A:LEU410 2.5 32.4 1.0 OE1 A:GLU411 2.5 38.1 1.0 O A:HOH943 2.6 39.6 1.0 O A:HOH822 2.7 32.9 1.0 CD A:GLN349 3.5 40.5 1.0 C A:PHE407 3.5 39.6 1.0 CD A:GLU353 3.5 39.0 1.0 CD A:GLU411 3.6 38.0 1.0 C A:LEU410 3.7 32.4 1.0 OE2 A:GLU353 3.9 39.2 1.0 OE2 A:GLU411 4.2 48.4 1.0 NE2 A:GLN349 4.2 37.0 1.0 CA A:GLY408 4.3 40.2 1.0 N A:GLY408 4.3 38.0 1.0 N A:LEU410 4.4 34.6 1.0 CA A:LEU410 4.5 31.6 1.0 O A:HOH904 4.5 38.3 1.0 CA A:PHE407 4.5 41.0 1.0 CB A:PHE407 4.5 42.6 1.0 CG A:GLU411 4.6 36.0 1.0 CG A:GLN349 4.6 44.0 1.0 C A:GLY408 4.6 41.8 1.0 CB A:LEU410 4.6 32.5 1.0 N A:GLU411 4.6 33.2 1.0 CE1 A:HIS644 4.7 55.1 1.0 CA A:GLU411 4.8 31.3 1.0 O A:GLN349 4.8 48.4 1.0 O A:HOH902 4.8 29.7 1.0 CG A:GLU353 4.9 38.0 1.0 O A:GLY408 4.9 41.3 1.0

Calcium binding site 2 out of 5 in the HPAD4 Crystal Complex with Afm-41A


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-41A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:60.3 occ:1.00 O A:HOH808 2.2 67.7 1.0 OD1 A:ASN373 2.3 53.2 1.0 O A:HOH924 2.3 46.5 1.0 O A:SER370 2.3 51.2 1.0 OE1 A:GLU351 2.5 46.0 1.0 OD1 A:ASP369 2.5 49.5 1.0 CG A:ASP369 3.3 53.5 1.0 OD2 A:ASP369 3.5 56.8 1.0 C A:SER370 3.5 48.0 1.0 CG A:ASN373 3.6 58.0 1.0 CD A:GLU351 3.6 48.2 1.0 N A:ASN373 4.0 62.7 1.0 CG A:GLU351 4.0 45.2 1.0 CA A:ASN373 4.2 63.4 1.0 CA A:PRO371 4.2 52.0 1.0 O A:LYS377 4.3 74.0 1.0 N A:SER370 4.3 46.9 1.0 N A:PRO371 4.3 46.6 1.0 OE1 A:GLN397 4.4 67.7 1.0 C A:ASP369 4.4 45.5 1.0 ND2 A:ASN373 4.5 50.6 1.0 C A:PRO371 4.5 53.9 1.0 CB A:ASN373 4.5 57.3 1.0 CA A:SER370 4.5 47.6 1.0 O A:ASP369 4.6 46.0 1.0 CA A:LYS377 4.6 69.2 1.0 CB A:ASP369 4.6 51.1 1.0 N A:ARG372 4.7 60.9 1.0 OE2 A:GLU351 4.7 50.0 1.0 O A:GLU351 4.8 46.5 1.0 C A:LYS377 4.9 70.5 1.0

Calcium binding site 3 out of 5 in the HPAD4 Crystal Complex with Afm-41A


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-41A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:63.2 occ:1.00 OD2 A:ASP165 2.1 57.5 1.0 OD2 A:ASP179 2.3 43.3 1.0 OD1 A:ASP155 2.4 54.8 1.0 OD1 A:ASP176 2.5 58.7 1.0 OD1 A:ASN153 2.6 64.1 1.0 OD2 A:ASP157 2.8 66.3 1.0 CG A:ASP165 3.2 60.4 1.0 CG A:ASP155 3.3 55.8 1.0 CG A:ASP179 3.4 47.4 1.0 CG A:ASN153 3.5 55.2 1.0 OD2 A:ASP155 3.6 50.7 1.0 CG A:ASP157 3.6 63.7 1.0 CG A:ASP176 3.7 61.1 1.0 ND2 A:ASN153 3.8 57.0 1.0 CB A:ASP179 3.8 47.7 1.0 CB A:ASP165 3.9 60.5 1.0 CA A:CA706 3.9 59.9 1.0 CB A:ASP157 4.1 67.7 1.0 CA A:ASP176 4.2 63.6 1.0 OD1 A:ASP165 4.2 62.1 1.0 O A:ASP176 4.3 56.0 1.0 CB A:ASP176 4.4 63.8 1.0 OD1 A:ASP179 4.5 46.0 1.0 OD1 A:ASP157 4.5 60.7 1.0 O A:ASP155 4.6 58.3 1.0 OD2 A:ASP176 4.6 55.1 1.0 N A:ASP157 4.6 73.2 1.0 C A:ASP176 4.7 60.4 1.0 CB A:ASP155 4.7 55.1 1.0 O A:HOH901 4.8 48.1 1.0 C A:ASP155 4.8 62.4 1.0 CB A:ASN153 4.8 53.5 1.0

Calcium binding site 4 out of 5 in the HPAD4 Crystal Complex with Afm-41A


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-41A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:59.9 occ:1.00 OD2 A:ASP155 2.3 50.7 1.0 OD1 A:ASP388 2.3 66.0 1.0 OD2 A:ASP179 2.4 43.3 1.0 O A:HOH901 2.4 48.1 1.0 OD2 A:ASP157 2.6 66.3 1.0 OD1 A:ASP179 2.7 46.0 1.0 CG A:ASP179 2.9 47.4 1.0 OD1 A:ASP157 3.0 60.7 1.0 CG A:ASP157 3.2 63.7 1.0 CG A:ASP155 3.5 55.8 1.0 CG A:ASP388 3.5 61.6 1.0 N A:ASP388 3.8 58.3 1.0 CA A:ASP388 3.8 58.6 1.0 CA A:CA705 3.9 63.2 1.0 OD1 A:ASP155 3.9 54.8 1.0 CB A:ASP388 4.3 57.8 1.0 OD2 A:ASP388 4.4 65.4 1.0 O A:HOH974 4.4 50.5 1.0 CB A:ASP179 4.4 47.7 1.0 CD2 A:LEU364 4.4 49.7 1.0 CB A:ASP157 4.6 67.7 1.0 NZ A:LYS362 4.7 64.5 1.0 CB A:ASP155 4.7 55.1 1.0

Calcium binding site 5 out of 5 in the HPAD4 Crystal Complex with Afm-41A


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-41A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:78.5 occ:1.00 O A:HOH825 2.0 53.4 1.0 O A:GLU170 2.3 65.9 1.0 O A:ASP165 2.3 78.5 1.0 OD1 A:ASP168 2.4 66.8 1.0 O A:HOH858 2.5 48.4 1.0 O A:HOH905 2.5 62.9 1.0 C A:ASP165 3.4 66.9 1.0 CG A:ASP168 3.4 69.2 1.0 C A:GLU170 3.5 63.4 1.0 OD2 A:ASP168 3.6 69.5 1.0 OD2 A:ASP176 4.0 55.1 1.0 CA A:ASP165 4.1 63.6 1.0 N A:GLU170 4.2 68.8 1.0 O A:HOH945 4.2 49.3 1.0 CB A:ASP165 4.3 60.5 1.0 N A:CYS166 4.3 64.7 1.0 CA A:GLU170 4.4 64.8 1.0 N A:VAL171 4.4 63.2 1.0 O A:ASP168 4.5 68.5 1.0 CA A:VAL171 4.6 65.4 1.0 CA A:CYS166 4.6 60.6 1.0 OE1 A:GLU252 4.6 46.0 1.0 C A:ASP168 4.8 71.7 1.0 CB A:ASP168 4.8 68.3 1.0 N A:ASP168 4.9 64.9 1.0 OE2 A:GLU252 5.0 42.7 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