Calcium in PDB 8sml: HPAD4 Bound to Inhibitory Fab HI365

All present enzymatic activity of HPAD4 Bound to Inhibitory Fab HI365:
3.5.3.15;

The binding sites of Calcium atom in the HPAD4 Bound to Inhibitory Fab HI365 (pdb code 8sml). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the HPAD4 Bound to Inhibitory Fab HI365, PDB code: 8sml:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:53.3 occ:1.00 OD1 A:ASP176 2.1 57.4 1.0 OD2 A:ASP165 2.1 58.0 1.0 OD1 A:ASP155 2.1 60.0 1.0 OD2 A:ASP157 2.1 53.5 1.0 OD1 A:ASN153 2.4 59.3 1.0 HB2 A:ASP165 2.8 60.9 1.0 CG A:ASP165 3.0 61.5 1.0 CG A:ASP155 3.0 55.3 1.0 CG A:ASP157 3.2 50.9 1.0 CG A:ASP176 3.2 57.6 1.0 H A:ASP157 3.3 57.0 1.0 CB A:ASP165 3.3 60.9 1.0 OD2 A:ASP155 3.3 54.8 1.0 HD22 A:ASN153 3.4 61.4 1.0 HB2 A:ASP157 3.5 49.3 1.0 CG A:ASN153 3.5 60.0 1.0 HB3 A:ASP165 3.5 60.9 1.0 OD2 A:ASP179 3.6 50.3 1.0 HA A:ASP176 3.7 52.1 1.0 CA A:CA702 3.8 67.0 1.0 ND2 A:ASN153 3.8 61.4 1.0 CB A:ASP157 3.9 49.3 1.0 O A:ASP155 3.9 62.7 1.0 OD2 A:ASP176 3.9 60.4 1.0 N A:ASP157 4.1 57.0 1.0 OD1 A:ASP165 4.1 63.1 1.0 HB2 A:ASP179 4.2 47.3 1.0 C A:ASP155 4.2 58.5 1.0 OD1 A:ASP157 4.2 52.7 1.0 H A:ASP155 4.2 59.3 1.0 CB A:ASP176 4.3 52.3 1.0 CB A:ASP155 4.4 54.1 1.0 CG A:ASP179 4.4 52.7 1.0 HB2 A:ASP176 4.4 52.3 1.0 CA A:ASP176 4.5 52.1 1.0 H A:ASP165 4.5 60.8 1.0 HA A:ARG156 4.6 58.9 1.0 CA A:ASP157 4.6 51.7 1.0 HA A:ASN153 4.6 52.5 1.0 CA A:ASP155 4.7 57.0 1.0 N A:ARG156 4.7 56.9 1.0 N A:ASP155 4.7 59.3 1.0 CA A:ASP165 4.8 63.4 1.0 CB A:ASP179 4.8 47.3 1.0 HB3 A:ASP157 4.8 49.3 1.0 CB A:ASN153 4.8 56.1 1.0 HD21 A:ASN153 4.8 61.4 1.0 HB2 A:ASP155 4.9 54.1 1.0 O A:ASP176 4.9 51.1 1.0 C A:ARG156 5.0 58.9 1.0 CA A:ARG156 5.0 58.9 1.0

Calcium binding site 2 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:67.0 occ:1.00 OD2 A:ASP179 2.1 50.3 1.0 OD2 A:ASP155 2.1 54.8 1.0 OD1 A:ASP388 2.3 55.5 1.0 OD1 A:ASP157 2.3 52.7 1.0 OD2 A:ASP157 2.4 53.5 1.0 CG A:ASP157 2.7 50.9 1.0 H A:ASP388 2.9 52.2 1.0 CG A:ASP179 3.0 52.7 1.0 OD1 A:ASP179 3.2 54.9 1.0 CG A:ASP155 3.2 55.3 1.0 CG A:ASP388 3.5 57.1 1.0 HA A:ASP388 3.6 53.6 1.0 N A:ASP388 3.6 52.2 1.0 OD1 A:ASP155 3.7 60.0 1.0 CA A:CA701 3.8 53.3 1.0 HE2 A:LYS362 4.0 54.1 1.0 CA A:ASP388 4.1 53.6 1.0 HA A:ASP176 4.1 52.1 1.0 CB A:ASP157 4.2 49.3 1.0 HA A:PRO387 4.3 52.6 1.0 OD2 A:ASP388 4.3 60.4 1.0 CB A:ASP388 4.3 50.8 1.0 CB A:ASP179 4.3 47.3 1.0 CB A:ASP155 4.4 54.1 1.0 HB2 A:ASP155 4.4 54.1 1.0 HB2 A:ASP179 4.5 47.3 1.0 HB3 A:ASP157 4.6 49.3 1.0 HB2 A:ASP157 4.7 49.3 1.0 C A:PRO387 4.7 49.1 1.0 HB3 A:ASP155 4.7 54.1 1.0 HD12 A:LEU364 4.7 48.8 1.0 OD1 A:ASP176 4.7 57.4 1.0 O A:GLU175 4.8 54.1 1.0 HE3 A:LYS362 4.8 54.1 1.0 HB3 A:GLN178 4.8 58.0 1.0 HA A:ASP157 4.8 51.7 1.0 CE A:LYS362 4.9 54.1 1.0 HB3 A:ASP179 4.9 47.3 1.0 HB3 A:ASP388 4.9 50.8 1.0 HB3 A:PRO387 4.9 56.7 1.0 H A:ASP179 4.9 51.5 1.0 CA A:PRO387 5.0 52.6 1.0

Calcium binding site 3 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:103.1 occ:1.00 O A:ASP165 2.3 65.3 1.0 O A:GLU170 2.3 73.8 1.0 OD1 A:ASP168 2.3 69.7 1.0 OD2 A:ASP168 2.4 70.5 1.0 CG A:ASP168 2.7 70.7 1.0 HB3 A:ASP165 3.3 60.9 1.0 H A:GLU170 3.3 73.8 1.0 C A:ASP165 3.4 64.7 1.0 C A:GLU170 3.5 70.5 1.0 HA A:VAL171 3.6 63.9 1.0 HA A:ASP165 3.8 63.4 1.0 HD21 A:ASN153 3.9 61.4 1.0 OE1 A:GLU252 4.0 56.9 1.0 CA A:ASP165 4.0 63.4 1.0 HG22 A:VAL171 4.0 63.9 1.0 HZ A:PHE214 4.0 65.1 1.0 OD2 A:ASP176 4.0 60.4 1.0 N A:GLU170 4.1 73.8 1.0 HD22 A:ASN153 4.1 61.4 1.0 CB A:ASP165 4.1 60.9 1.0 HA A:CYS166 4.1 61.7 1.0 H A:ASP168 4.1 71.6 1.0 CB A:ASP168 4.2 72.5 1.0 ND2 A:ASN153 4.3 61.4 1.0 OE2 A:GLU252 4.3 57.6 1.0 CA A:GLU170 4.4 68.9 1.0 N A:VAL171 4.4 66.7 1.0 HG23 A:VAL171 4.4 63.9 1.0 N A:CYS166 4.4 61.1 1.0 CA A:VAL171 4.5 63.9 1.0 H A:ASP169 4.5 74.6 1.0 CD A:GLU252 4.6 56.5 1.0 HE1 A:PHE214 4.6 62.9 1.0 CG2 A:VAL171 4.7 63.9 1.0 CZ A:PHE214 4.7 65.1 1.0 HB3 A:ASP168 4.7 72.5 1.0 CA A:CYS166 4.7 61.7 1.0 HB3 A:GLU170 4.8 68.1 1.0 HB2 A:ASP168 4.8 72.5 1.0 HB2 A:ASP165 4.8 60.9 1.0 N A:ASP168 4.9 71.6 1.0 H A:LEU172 4.9 62.0 1.0 N A:ASP169 4.9 74.6 1.0 CA A:ASP168 5.0 76.9 1.0 CG A:ASP165 5.0 61.5 1.0

Calcium binding site 4 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:53.3 occ:1.00 OD1 D:ASP176 2.1 57.4 1.0 OD2 D:ASP165 2.1 58.0 1.0 OD1 D:ASP155 2.1 60.0 1.0 OD2 D:ASP157 2.1 53.5 1.0 OD1 D:ASN153 2.4 59.3 1.0 HB2 D:ASP165 2.8 60.9 1.0 CG D:ASP165 3.0 61.5 1.0 CG D:ASP155 3.0 55.3 1.0 CG D:ASP157 3.2 50.9 1.0 CG D:ASP176 3.2 57.6 1.0 H D:ASP157 3.3 57.0 1.0 CB D:ASP165 3.3 60.9 1.0 OD2 D:ASP155 3.3 54.8 1.0 HD22 D:ASN153 3.4 61.4 1.0 HB2 D:ASP157 3.5 49.3 1.0 CG D:ASN153 3.5 60.0 1.0 HB3 D:ASP165 3.5 60.9 1.0 OD2 D:ASP179 3.6 50.3 1.0 HA D:ASP176 3.7 52.1 1.0 CA D:CA702 3.8 67.0 1.0 ND2 D:ASN153 3.8 61.4 1.0 CB D:ASP157 3.9 49.3 1.0 O D:ASP155 3.9 62.7 1.0 OD2 D:ASP176 3.9 60.4 1.0 N D:ASP157 4.1 57.0 1.0 OD1 D:ASP165 4.1 63.1 1.0 HB2 D:ASP179 4.2 47.3 1.0 C D:ASP155 4.2 58.5 1.0 OD1 D:ASP157 4.2 52.7 1.0 H D:ASP155 4.2 59.3 1.0 CB D:ASP176 4.3 52.3 1.0 CB D:ASP155 4.4 54.1 1.0 CG D:ASP179 4.4 52.7 1.0 HB2 D:ASP176 4.4 52.3 1.0 CA D:ASP176 4.5 52.1 1.0 H D:ASP165 4.5 60.8 1.0 HA D:ARG156 4.6 58.9 1.0 CA D:ASP157 4.6 51.7 1.0 HA D:ASN153 4.6 52.5 1.0 CA D:ASP155 4.7 57.0 1.0 N D:ARG156 4.7 56.9 1.0 N D:ASP155 4.7 59.3 1.0 CA D:ASP165 4.8 63.4 1.0 CB D:ASP179 4.8 47.3 1.0 HB3 D:ASP157 4.8 49.3 1.0 CB D:ASN153 4.8 56.1 1.0 HD21 D:ASN153 4.8 61.4 1.0 HB2 D:ASP155 4.9 54.1 1.0 O D:ASP176 4.9 51.1 1.0 C D:ARG156 5.0 58.9 1.0 CA D:ARG156 5.0 58.9 1.0

Calcium binding site 5 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca702 b:67.0 occ:1.00 OD2 D:ASP179 2.1 50.3 1.0 OD2 D:ASP155 2.1 54.8 1.0 OD1 D:ASP388 2.3 55.5 1.0 OD1 D:ASP157 2.3 52.7 1.0 OD2 D:ASP157 2.4 53.5 1.0 CG D:ASP157 2.7 50.9 1.0 H D:ASP388 2.9 52.2 1.0 CG D:ASP179 2.9 52.7 1.0 OD1 D:ASP179 3.2 54.9 1.0 CG D:ASP155 3.2 55.3 1.0 CG D:ASP388 3.5 57.1 1.0 HA D:ASP388 3.6 53.6 1.0 N D:ASP388 3.6 52.2 1.0 OD1 D:ASP155 3.7 60.0 1.0 CA D:CA701 3.8 53.3 1.0 HE2 D:LYS362 4.0 54.1 1.0 CA D:ASP388 4.1 53.6 1.0 HA D:ASP176 4.1 52.1 1.0 CB D:ASP157 4.2 49.3 1.0 HA D:PRO387 4.3 52.6 1.0 OD2 D:ASP388 4.3 60.4 1.0 CB D:ASP388 4.3 50.8 1.0 CB D:ASP179 4.3 47.3 1.0 CB D:ASP155 4.4 54.1 1.0 HB2 D:ASP155 4.4 54.1 1.0 HB2 D:ASP179 4.5 47.3 1.0 HB3 D:ASP157 4.6 49.3 1.0 HB2 D:ASP157 4.7 49.3 1.0 C D:PRO387 4.7 49.1 1.0 HB3 D:ASP155 4.7 54.1 1.0 HD12 D:LEU364 4.7 48.8 1.0 OD1 D:ASP176 4.7 57.4 1.0 O D:GLU175 4.8 54.1 1.0 HE3 D:LYS362 4.8 54.1 1.0 HB3 D:GLN178 4.8 58.0 1.0 HA D:ASP157 4.8 51.7 1.0 CE D:LYS362 4.9 54.1 1.0 HB3 D:ASP179 4.9 47.3 1.0 HB3 D:ASP388 4.9 50.8 1.0 HB3 D:PRO387 4.9 56.7 1.0 H D:ASP179 4.9 51.5 1.0 CA D:PRO387 5.0 52.6 1.0

Calcium binding site 6 out of 6 in the HPAD4 Bound to Inhibitory Fab HI365


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of HPAD4 Bound to Inhibitory Fab HI365 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca703 b:103.1 occ:1.00 O D:ASP165 2.3 65.3 1.0 O D:GLU170 2.3 73.8 1.0 OD1 D:ASP168 2.3 69.7 1.0 OD2 D:ASP168 2.4 70.5 1.0 CG D:ASP168 2.7 70.7 1.0 HB3 D:ASP165 3.3 60.9 1.0 H D:GLU170 3.3 73.8 1.0 C D:ASP165 3.4 64.7 1.0 C D:GLU170 3.5 70.5 1.0 HA D:VAL171 3.6 63.9 1.0 HA D:ASP165 3.8 63.4 1.0 HD21 D:ASN153 3.9 61.4 1.0 OE1 D:GLU252 4.0 56.9 1.0 CA D:ASP165 4.0 63.4 1.0 HG22 D:VAL171 4.0 63.9 1.0 HZ D:PHE214 4.0 65.1 1.0 OD2 D:ASP176 4.0 60.4 1.0 N D:GLU170 4.1 73.8 1.0 HD22 D:ASN153 4.1 61.4 1.0 CB D:ASP165 4.1 60.9 1.0 HA D:CYS166 4.1 61.7 1.0 H D:ASP168 4.1 71.6 1.0 CB D:ASP168 4.2 72.5 1.0 ND2 D:ASN153 4.3 61.4 1.0 OE2 D:GLU252 4.3 57.6 1.0 CA D:GLU170 4.4 68.9 1.0 N D:VAL171 4.4 66.7 1.0 HG23 D:VAL171 4.4 63.9 1.0 N D:CYS166 4.4 61.1 1.0 CA D:VAL171 4.5 63.9 1.0 H D:ASP169 4.5 74.6 1.0 CD D:GLU252 4.6 56.5 1.0 HE1 D:PHE214 4.6 62.9 1.0 CG2 D:VAL171 4.7 63.9 1.0 CZ D:PHE214 4.7 65.1 1.0 HB3 D:ASP168 4.7 72.5 1.0 CA D:CYS166 4.7 61.7 1.0 HB3 D:GLU170 4.8 68.1 1.0 HB2 D:ASP168 4.8 72.5 1.0 HB2 D:ASP165 4.8 60.9 1.0 N D:ASP168 4.9 71.6 1.0 H D:LEU172 4.9 62.0 1.0 N D:ASP169 4.9 74.6 1.0 CA D:ASP168 5.0 76.9 1.0 CG D:ASP165 5.0 61.5 1.0

X.Zhou, S.Kong, A.Maker, S.G.Remesh, K.K.Leung, K.A.Verba, J.A.Wells. Antibody Discovery Identifies Regulatory Mechanisms of Protein Arginine Deiminase 4 Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01535-8