Calcium in PDB 8r8v: Human PADI4 in Complex with Cyclic Peptide PADI4_11

The binding sites of Calcium atom in the Human PADI4 in Complex with Cyclic Peptide PADI4_11 (pdb code 8r8v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Human PADI4 in Complex with Cyclic Peptide PADI4_11, PDB code: 8r8v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca900 b:51.1 occ:1.00 OE1 A:GLU353 2.4 40.5 1.0 NE2 A:GLN349 2.6 54.1 1.0 O A:LEU410 3.0 36.7 1.0 CD A:GLN349 3.1 54.1 1.0 O A:PHE407 3.2 41.6 1.0 CD A:GLU353 3.2 40.5 1.0 OE1 A:GLN349 3.3 54.1 1.0 OE2 A:GLU353 3.3 40.5 1.0 OE2 A:GLU411 3.6 36.4 1.0 CG A:GLN349 4.1 54.1 1.0 C A:LEU410 4.2 36.7 1.0 C A:PHE407 4.3 41.6 1.0 CB A:LEU410 4.4 36.7 1.0 CB A:PHE407 4.4 41.6 1.0 CD A:GLU411 4.5 36.4 1.0 O A:GLN349 4.7 54.1 1.0 CG A:GLU353 4.7 40.5 1.0 CA A:LEU410 4.8 36.7 1.0 CE1 A:HIS644 4.8 60.3 1.0 CA A:PHE407 4.9 41.6 1.0 NE2 A:HIS644 4.9 60.3 1.0 CG A:LEU410 5.0 36.7 1.0

Calcium binding site 2 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:52.6 occ:1.00 OD1 A:ASP155 2.2 46.1 1.0 OD1 A:ASP176 2.3 54.4 1.0 OD2 A:ASP157 2.3 54.8 1.0 OD2 A:ASP179 2.3 46.0 1.0 OD1 A:ASN153 2.3 40.0 1.0 CG A:ASP155 3.0 46.1 1.0 OD2 A:ASP155 3.0 46.1 1.0 CG A:ASP179 3.2 46.0 1.0 CG A:ASN153 3.3 40.0 1.0 CG A:ASP176 3.4 54.4 1.0 ND2 A:ASN153 3.5 40.0 1.0 CG A:ASP157 3.5 54.8 1.0 CB A:ASP179 3.5 46.0 1.0 CA A:CA902 3.8 44.1 1.0 OD2 A:ASP176 4.1 54.4 1.0 CA A:ASP176 4.2 54.4 1.0 O A:ASP176 4.2 54.4 1.0 CB A:ASP176 4.3 54.4 1.0 OD1 A:ASP157 4.3 54.8 1.0 OD1 A:ASP179 4.4 46.0 1.0 CB A:ASP155 4.5 46.1 1.0 CB A:ASP157 4.5 54.8 1.0 CB A:ASN153 4.6 40.0 1.0 O A:ASP155 4.7 46.1 1.0 CB A:ASP165 4.7 53.8 1.0 C A:ASP176 4.7 54.4 1.0 N A:ASP157 4.8 54.8 1.0 C A:ASP155 4.8 46.1 1.0 N A:ASP155 4.9 46.1 1.0 CA A:ASP179 5.0 46.0 1.0 CA A:ASP155 5.0 46.1 1.0 CA A:ASN153 5.0 40.0 1.0

Calcium binding site 3 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:44.1 occ:1.00 OD2 A:ASP179 2.3 46.0 1.0 OD1 A:ASP157 2.3 54.8 1.0 OD1 A:ASP388 2.3 39.8 1.0 OD2 A:ASP155 2.4 46.1 1.0 OD2 A:ASP157 2.8 54.8 1.0 OD1 A:ASP179 2.9 46.0 1.0 CG A:ASP157 2.9 54.8 1.0 CG A:ASP179 2.9 46.0 1.0 CG A:ASP388 3.5 39.8 1.0 CG A:ASP155 3.6 46.1 1.0 CA A:CA901 3.8 52.6 1.0 N A:ASP388 4.0 39.8 1.0 CA A:ASP388 4.1 39.8 1.0 OD1 A:ASP155 4.2 46.1 1.0 OD2 A:ASP388 4.3 39.8 1.0 CB A:ASP388 4.4 39.8 1.0 CB A:ASP179 4.4 46.0 1.0 CB A:ASP157 4.4 54.8 1.0 CE A:LYS362 4.5 33.5 1.0 CB A:ASP155 4.7 46.1 1.0 O A:GLU175 4.7 57.8 1.0 NZ A:LYS362 4.7 33.5 1.0

Calcium binding site 4 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:46.8 occ:1.00 OD2 A:ASP369 2.3 46.3 1.0 OD1 A:ASP369 2.4 46.3 1.0 CG A:ASP369 2.6 46.3 1.0 OE2 A:GLU351 2.7 50.7 1.0 O A:SER370 3.2 48.9 1.0 OD1 A:ASN373 3.2 61.8 1.0 O A:ARG372 3.5 58.7 1.0 CD A:GLU351 3.9 50.7 1.0 CB A:ASP369 4.1 46.3 1.0 CG A:ASN373 4.1 61.8 1.0 C A:SER370 4.4 48.9 1.0 OE1 A:GLN397 4.5 58.6 1.0 C A:ARG372 4.6 58.7 1.0 CB A:LYS377 4.6 57.5 1.0 CA A:LYS377 4.6 57.5 1.0 N A:SER370 4.7 48.9 1.0 OE1 A:GLU351 4.7 50.7 1.0 C A:ASP369 4.7 46.3 1.0 ND2 A:ASN373 4.8 61.8 1.0 CG A:GLU351 4.8 50.7 1.0 CA A:ASN373 4.8 61.8 1.0 O A:LYS377 4.8 57.5 1.0 CA A:ASP369 4.9 46.3 1.0 CG1 C:VAL9 4.9 59.7 1.0

Calcium binding site 5 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:51.6 occ:1.00 O A:ASP165 2.3 53.8 1.0 O A:GLU170 2.4 59.6 1.0 OD2 A:ASP165 2.4 53.8 1.0 OD1 A:ASP168 3.2 56.6 1.0 C A:ASP165 3.4 53.8 1.0 CG A:ASP165 3.5 53.8 1.0 C A:GLU170 3.6 59.6 1.0 OD2 A:ASP176 3.9 54.4 1.0 CB A:ASP165 4.0 53.8 1.0 CG A:ASP168 4.1 56.6 1.0 CA A:ASP165 4.1 53.8 1.0 CA A:VAL171 4.3 56.8 1.0 CD2 A:LEU172 4.3 59.7 1.0 OE2 A:GLU252 4.3 38.7 1.0 N A:GLU170 4.4 59.6 1.0 N A:VAL171 4.4 56.8 1.0 OD2 A:ASP168 4.4 56.6 1.0 N A:CYS166 4.5 51.5 1.0 OD1 A:ASP165 4.5 53.8 1.0 CA A:GLU170 4.6 59.6 1.0 CA A:CYS166 4.7 51.5 1.0 O A:ASP168 4.8 56.6 1.0 OE1 A:GLU252 4.8 38.7 1.0 CZ A:PHE214 5.0 41.6 1.0

Calcium binding site 6 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca900 b:51.1 occ:1.00 OE1 B:GLU353 2.4 40.5 1.0 NE2 B:GLN349 2.6 54.1 1.0 O B:LEU410 3.0 36.7 1.0 CD B:GLN349 3.1 54.1 1.0 O B:PHE407 3.2 41.6 1.0 CD B:GLU353 3.2 40.5 1.0 OE1 B:GLN349 3.3 54.1 1.0 OE2 B:GLU353 3.3 40.5 1.0 OE2 B:GLU411 3.6 36.4 1.0 CG B:GLN349 4.1 54.1 1.0 C B:LEU410 4.2 36.7 1.0 C B:PHE407 4.3 41.6 1.0 CB B:LEU410 4.4 36.7 1.0 CB B:PHE407 4.4 41.6 1.0 CD B:GLU411 4.5 36.4 1.0 O B:GLN349 4.7 54.1 1.0 CG B:GLU353 4.7 40.5 1.0 CA B:LEU410 4.8 36.7 1.0 CE1 B:HIS644 4.9 60.3 1.0 CA B:PHE407 4.9 41.6 1.0 NE2 B:HIS644 4.9 60.3 1.0 CG B:LEU410 5.0 36.7 1.0

Calcium binding site 7 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:52.6 occ:1.00 OD1 B:ASP155 2.2 46.1 1.0 OD1 B:ASP176 2.3 54.4 1.0 OD2 B:ASP157 2.3 54.8 1.0 OD2 B:ASP179 2.3 46.0 1.0 OD1 B:ASN153 2.3 40.0 1.0 CG B:ASP155 3.0 46.1 1.0 OD2 B:ASP155 3.0 46.1 1.0 CG B:ASP179 3.2 46.0 1.0 CG B:ASN153 3.3 40.0 1.0 CG B:ASP176 3.4 54.4 1.0 ND2 B:ASN153 3.5 40.0 1.0 CG B:ASP157 3.5 54.8 1.0 CB B:ASP179 3.5 46.0 1.0 CA B:CA902 3.8 44.1 1.0 OD2 B:ASP176 4.1 54.4 1.0 CA B:ASP176 4.2 54.4 1.0 O B:ASP176 4.2 54.4 1.0 CB B:ASP176 4.3 54.4 1.0 OD1 B:ASP157 4.3 54.8 1.0 OD1 B:ASP179 4.4 46.0 1.0 CB B:ASP155 4.5 46.1 1.0 CB B:ASP157 4.5 54.8 1.0 CB B:ASN153 4.6 40.0 1.0 O B:ASP155 4.7 46.1 1.0 CB B:ASP165 4.7 53.8 1.0 C B:ASP176 4.7 54.4 1.0 N B:ASP157 4.8 54.8 1.0 C B:ASP155 4.8 46.1 1.0 N B:ASP155 4.9 46.1 1.0 CA B:ASP179 5.0 46.0 1.0 CA B:ASP155 5.0 46.1 1.0 CA B:ASN153 5.0 40.0 1.0

Calcium binding site 8 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:44.1 occ:1.00 OD2 B:ASP179 2.3 46.0 1.0 OD1 B:ASP157 2.3 54.8 1.0 OD1 B:ASP388 2.3 39.8 1.0 OD2 B:ASP155 2.4 46.1 1.0 OD2 B:ASP157 2.8 54.8 1.0 OD1 B:ASP179 2.9 46.0 1.0 CG B:ASP157 2.9 54.8 1.0 CG B:ASP179 2.9 46.0 1.0 CG B:ASP388 3.5 39.8 1.0 CG B:ASP155 3.6 46.1 1.0 CA B:CA901 3.8 52.6 1.0 N B:ASP388 4.0 39.8 1.0 CA B:ASP388 4.1 39.8 1.0 OD1 B:ASP155 4.2 46.1 1.0 OD2 B:ASP388 4.3 39.8 1.0 CB B:ASP388 4.4 39.8 1.0 CB B:ASP179 4.4 46.0 1.0 CB B:ASP157 4.4 54.8 1.0 CE B:LYS362 4.5 33.5 1.0 CB B:ASP155 4.7 46.1 1.0 O B:GLU175 4.7 57.8 1.0 NZ B:LYS362 4.7 33.5 1.0

Calcium binding site 9 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:46.8 occ:1.00 OD2 B:ASP369 2.3 46.3 1.0 OD1 B:ASP369 2.4 46.3 1.0 CG B:ASP369 2.6 46.3 1.0 OE2 B:GLU351 2.7 50.7 1.0 O B:SER370 3.2 48.9 1.0 OD1 B:ASN373 3.2 61.8 1.0 O B:ARG372 3.5 58.7 1.0 CD B:GLU351 3.9 50.7 1.0 CB B:ASP369 4.1 46.3 1.0 CG B:ASN373 4.1 61.8 1.0 C B:SER370 4.4 48.9 1.0 OE1 B:GLN397 4.5 58.6 1.0 C B:ARG372 4.6 58.7 1.0 CB B:LYS377 4.6 57.5 1.0 CA B:LYS377 4.6 57.5 1.0 N B:SER370 4.7 48.9 1.0 OE1 B:GLU351 4.7 50.7 1.0 C B:ASP369 4.7 46.3 1.0 ND2 B:ASN373 4.8 61.8 1.0 CG B:GLU351 4.8 50.7 1.0 CA B:ASN373 4.8 61.8 1.0 O B:LYS377 4.8 57.5 1.0 CA B:ASP369 4.9 46.3 1.0

Calcium binding site 10 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human PADI4 in Complex with Cyclic Peptide PADI4_11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca904 b:51.6 occ:1.00 O B:ASP165 2.3 53.8 1.0 O B:GLU170 2.4 59.6 1.0 OD2 B:ASP165 2.4 53.8 1.0 OD1 B:ASP168 3.2 56.6 1.0 C B:ASP165 3.4 53.8 1.0 CG B:ASP165 3.5 53.8 1.0 C B:GLU170 3.6 59.6 1.0 OD2 B:ASP176 3.9 54.4 1.0 CB B:ASP165 4.0 53.8 1.0 CG B:ASP168 4.1 56.6 1.0 CA B:ASP165 4.1 53.8 1.0 CA B:VAL171 4.3 56.8 1.0 CD2 B:LEU172 4.3 59.7 1.0 OE2 B:GLU252 4.3 38.7 1.0 N B:GLU170 4.4 59.6 1.0 N B:VAL171 4.4 56.8 1.0 OD2 B:ASP168 4.4 56.6 1.0 N B:CYS166 4.5 51.5 1.0 OD1 B:ASP165 4.5 53.8 1.0 CA B:GLU170 4.6 59.6 1.0 CA B:CYS166 4.7 51.5 1.0 O B:ASP168 4.8 56.6 1.0 OE1 B:GLU252 4.8 38.7 1.0 CZ B:PHE214 5.0 41.6 1.0

M.T.Bertran, R.Walmsley, T.Cummings, I.V.Aramburu, D.J.Benton, R.Mora Molina, J.Assalaarachchi, M.Chasampalioti, T.Swanton, D.Joshi, S.Federico, H.Okkenhaug, L.Yu, D.Oxley, S.Walker, V.Papayannopoulos, H.Suga, M.A.Christophorou, L.J.Walport. A Cyclic Peptide Toolkit Reveals Mechanistic Principles of Peptidylarginine Deiminase IV Regulation. Nat Commun V. 15 9746 2024.
ISSN: ESSN 2041-1723
PubMed: 39528459
DOI: 10.1038/S41467-024-53554-1