Calcium in PDB 8r8u: Human PADI4 in Complex with Cyclic Peptide PADI4_3

The binding sites of Calcium atom in the Human PADI4 in Complex with Cyclic Peptide PADI4_3 (pdb code 8r8u). 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_3, PDB code: 8r8u:
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_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca900 b:19.9 occ:1.00 OE1 A:GLU353 2.4 28.6 1.0 NE2 A:GLN349 2.4 32.0 1.0 O A:LEU410 2.5 20.7 1.0 OE1 A:GLU411 2.7 33.9 1.0 O A:PHE407 2.7 23.1 1.0 CD A:GLU353 3.4 25.6 1.0 CD A:GLU411 3.5 39.9 1.0 CD A:GLN349 3.7 29.6 1.0 C A:LEU410 3.7 19.3 1.0 OE2 A:GLU353 3.7 32.5 1.0 C A:PHE407 4.0 20.7 1.0 OE2 A:GLU411 4.1 42.8 1.0 CG A:GLU411 4.4 27.5 1.0 CA A:GLY408 4.4 21.8 1.0 OE1 A:GLN349 4.5 27.7 1.0 CG A:GLN349 4.5 26.6 1.0 N A:LEU410 4.6 18.7 1.0 CA A:LEU410 4.6 18.1 1.0 N A:GLU411 4.6 18.8 1.0 CA A:GLU411 4.7 18.2 1.0 N A:GLY408 4.7 22.6 1.0 CG A:GLU353 4.7 19.7 1.0 C A:GLY408 4.8 22.5 1.0 CB A:LEU410 4.8 18.1 1.0 O A:GLY408 5.0 22.5 1.0 CB A:PHE407 5.0 20.4 1.0

Calcium binding site 2 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:30.2 occ:1.00 OD1 A:ASN153 2.3 31.4 1.0 OD2 A:ASP157 2.3 33.7 1.0 OD2 A:ASP165 2.4 34.6 1.0 OD1 A:ASP155 2.4 38.0 1.0 OD2 A:ASP179 2.6 28.8 1.0 OD1 A:ASP176 2.6 41.9 1.0 CG A:ASP155 3.1 31.8 1.0 OD2 A:ASP155 3.2 31.1 1.0 CG A:ASN153 3.3 30.0 1.0 CG A:ASP165 3.4 36.7 1.0 CG A:ASP157 3.5 34.5 1.0 CG A:ASP179 3.6 32.1 1.0 CB A:ASP165 3.7 30.4 1.0 ND2 A:ASN153 3.7 31.6 1.0 CG A:ASP176 3.8 45.5 1.0 CA A:CA902 4.0 31.8 1.0 CB A:ASP179 4.1 30.4 1.0 CB A:ASP157 4.1 35.6 1.0 CA A:ASP176 4.4 42.1 1.0 OD1 A:ASP157 4.5 34.2 1.0 OD1 A:ASP165 4.5 42.4 1.0 CB A:ASP155 4.5 25.9 1.0 O A:ASP176 4.5 38.2 1.0 OD2 A:ASP176 4.6 47.9 1.0 CB A:ASP176 4.6 45.3 1.0 N A:ASP157 4.6 40.3 1.0 OD1 A:ASP179 4.6 41.1 1.0 O A:ASP155 4.7 35.4 1.0 CB A:ASN153 4.7 27.8 1.0 C A:ASP155 4.8 31.0 1.0 N A:ASP155 4.9 27.7 1.0 CA A:ASN153 4.9 24.1 1.0 C A:ASP176 5.0 38.9 1.0 CA A:ASP155 5.0 25.1 1.0 CA A:ASP157 5.0 38.2 1.0

Calcium binding site 3 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:31.8 occ:1.00 OD2 A:ASP179 2.4 28.8 1.0 OD1 A:ASP388 2.5 40.9 1.0 OD2 A:ASP157 2.7 33.7 1.0 OD1 A:ASP179 2.8 41.1 1.0 OD1 A:ASP157 2.9 34.2 1.0 CG A:ASP179 3.0 32.1 1.0 OD2 A:ASP155 3.0 31.1 1.0 CG A:ASP157 3.2 34.5 1.0 CG A:ASP388 3.7 39.4 1.0 CA A:CA901 4.0 30.2 1.0 O A:GLU175 4.0 47.7 1.0 CG A:ASP155 4.1 31.8 1.0 N A:ASP388 4.4 24.7 1.0 CE A:LYS362 4.4 33.5 1.0 OD2 A:ASP388 4.4 43.3 1.0 NZ A:LYS362 4.4 39.7 1.0 CB A:ASP179 4.5 30.4 1.0 CA A:ASP388 4.5 24.1 1.0 CB A:ASP157 4.6 35.6 1.0 OD1 A:ASP155 4.7 38.0 1.0 CB A:ASP388 4.7 27.4 1.0 C A:GLU175 4.8 46.5 1.0 N A:ASP179 5.0 30.9 1.0

Calcium binding site 4 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:34.4 occ:1.00 OD2 A:ASP369 2.3 34.1 1.0 OE2 A:GLU351 2.4 30.1 1.0 OD1 A:ASN373 2.5 31.7 1.0 O A:SER370 2.9 26.1 1.0 O A:ARG372 3.0 42.0 1.0 CG A:ASP369 3.0 33.1 1.0 OD1 A:ASP369 3.1 37.8 1.0 CD A:GLU351 3.6 31.9 1.0 CG A:ASN373 3.7 33.3 1.0 C A:ARG372 4.0 36.6 1.0 C A:SER370 4.1 29.7 1.0 CA A:LYS377 4.1 33.1 1.0 CA A:ASN373 4.3 32.8 1.0 O A:LYS377 4.3 39.9 1.0 OE1 A:GLU351 4.3 33.2 1.0 N A:SER370 4.4 27.9 1.0 CB A:ASP369 4.4 24.9 1.0 CB A:LYS377 4.4 36.0 1.0 CB A:ASN373 4.4 34.5 1.0 CG A:GLU351 4.6 29.7 1.0 N A:ASN373 4.6 33.0 1.0 O A:GLU351 4.6 25.7 1.0 ND2 A:ASN373 4.7 35.3 1.0 C A:ASP369 4.7 27.4 1.0 C A:LYS377 4.7 39.7 1.0 CA A:SER370 4.8 26.2 1.0 OE1 A:GLN397 4.8 47.7 1.0 C A:PRO371 4.9 31.8 1.0 CA A:ASP369 4.9 23.1 1.0 O A:PRO371 5.0 34.0 1.0

Calcium binding site 5 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:33.2 occ:1.00 OD1 A:ASP168 2.3 55.1 1.0 O A:ASP165 2.4 45.0 1.0 O A:GLU170 2.5 55.5 1.0 O A:ASP168 3.4 50.1 1.0 CG A:ASP168 3.6 54.5 1.0 C A:ASP165 3.6 38.3 1.0 C A:GLU170 3.7 49.9 1.0 OD2 A:ASP176 3.9 47.9 1.0 OD2 A:ASP168 4.2 53.1 1.0 C A:ASP168 4.2 49.4 1.0 N A:GLU170 4.3 50.2 1.0 CA A:ASP165 4.4 33.4 1.0 N A:VAL171 4.5 47.4 1.0 CA A:VAL171 4.5 45.6 1.0 N A:CYS166 4.6 37.1 1.0 CB A:ASP165 4.6 30.4 1.0 CA A:GLU170 4.6 50.2 1.0 CB A:ASP168 4.7 53.2 1.0 OE2 A:GLU252 4.7 36.4 1.0 N A:ASP168 4.7 49.1 1.0 CA A:CYS166 4.8 37.0 1.0 CA A:ASP168 4.8 47.1 1.0 OE1 A:GLU252 4.9 39.0 1.0 CZ A:PHE214 4.9 33.3 1.0

Calcium binding site 6 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca900 b:19.9 occ:1.00 OE1 B:GLU353 2.4 28.6 1.0 NE2 B:GLN349 2.4 32.0 1.0 O B:LEU410 2.5 20.7 1.0 OE1 B:GLU411 2.7 33.9 1.0 O B:PHE407 2.7 23.1 1.0 CD B:GLU353 3.4 25.6 1.0 CD B:GLU411 3.5 39.9 1.0 CD B:GLN349 3.7 29.6 1.0 C B:LEU410 3.7 19.3 1.0 OE2 B:GLU353 3.7 32.5 1.0 C B:PHE407 4.0 20.7 1.0 OE2 B:GLU411 4.1 42.8 1.0 CG B:GLU411 4.4 27.5 1.0 CA B:GLY408 4.4 21.8 1.0 OE1 B:GLN349 4.5 27.7 1.0 CG B:GLN349 4.5 26.6 1.0 N B:LEU410 4.6 18.7 1.0 CA B:LEU410 4.6 18.1 1.0 N B:GLU411 4.6 18.8 1.0 CA B:GLU411 4.7 18.2 1.0 N B:GLY408 4.7 22.6 1.0 CG B:GLU353 4.7 19.7 1.0 C B:GLY408 4.8 22.5 1.0 CB B:LEU410 4.8 18.1 1.0 O B:GLY408 5.0 22.5 1.0 CB B:PHE407 5.0 20.4 1.0

Calcium binding site 7 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:30.2 occ:1.00 OD1 B:ASN153 2.3 31.4 1.0 OD2 B:ASP157 2.3 33.7 1.0 OD2 B:ASP165 2.4 34.6 1.0 OD1 B:ASP155 2.4 38.0 1.0 OD2 B:ASP179 2.6 28.8 1.0 OD1 B:ASP176 2.6 41.9 1.0 CG B:ASP155 3.1 31.8 1.0 OD2 B:ASP155 3.2 31.1 1.0 CG B:ASN153 3.3 30.0 1.0 CG B:ASP165 3.4 36.7 1.0 CG B:ASP157 3.5 34.5 1.0 CG B:ASP179 3.6 32.1 1.0 CB B:ASP165 3.7 30.4 1.0 ND2 B:ASN153 3.7 31.6 1.0 CG B:ASP176 3.8 45.5 1.0 CA B:CA902 4.0 31.8 1.0 CB B:ASP179 4.1 30.4 1.0 CB B:ASP157 4.1 35.6 1.0 CA B:ASP176 4.4 42.1 1.0 OD1 B:ASP157 4.5 34.2 1.0 OD1 B:ASP165 4.5 42.4 1.0 CB B:ASP155 4.5 25.9 1.0 O B:ASP176 4.5 38.2 1.0 OD2 B:ASP176 4.6 47.9 1.0 CB B:ASP176 4.6 45.3 1.0 N B:ASP157 4.6 40.3 1.0 OD1 B:ASP179 4.6 41.1 1.0 O B:ASP155 4.7 35.4 1.0 CB B:ASN153 4.7 27.8 1.0 C B:ASP155 4.8 31.0 1.0 N B:ASP155 4.9 27.7 1.0 CA B:ASN153 4.9 24.1 1.0 C B:ASP176 5.0 38.9 1.0 CA B:ASP155 5.0 25.1 1.0 CA B:ASP157 5.0 38.2 1.0

Calcium binding site 8 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:31.8 occ:1.00 OD2 B:ASP179 2.4 28.8 1.0 OD1 B:ASP388 2.5 40.9 1.0 OD2 B:ASP157 2.7 33.7 1.0 OD1 B:ASP179 2.8 41.1 1.0 OD1 B:ASP157 2.9 34.2 1.0 CG B:ASP179 3.0 32.1 1.0 OD2 B:ASP155 3.0 31.1 1.0 CG B:ASP157 3.2 34.5 1.0 CG B:ASP388 3.7 39.4 1.0 CA B:CA901 4.0 30.2 1.0 O B:GLU175 4.0 47.7 1.0 CG B:ASP155 4.1 31.8 1.0 N B:ASP388 4.4 24.7 1.0 CE B:LYS362 4.4 33.5 1.0 OD2 B:ASP388 4.4 43.3 1.0 NZ B:LYS362 4.4 39.7 1.0 CB B:ASP179 4.5 30.4 1.0 CA B:ASP388 4.5 24.1 1.0 CB B:ASP157 4.6 35.6 1.0 OD1 B:ASP155 4.7 38.0 1.0 CB B:ASP388 4.7 27.4 1.0 C B:GLU175 4.8 46.5 1.0 N B:ASP179 5.0 30.9 1.0

Calcium binding site 9 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:34.4 occ:1.00 OD2 B:ASP369 2.3 34.1 1.0 OE2 B:GLU351 2.4 30.1 1.0 OD1 B:ASN373 2.5 31.7 1.0 O B:SER370 2.9 26.1 1.0 O B:ARG372 3.0 42.0 1.0 CG B:ASP369 3.0 33.1 1.0 OD1 B:ASP369 3.1 37.8 1.0 CD B:GLU351 3.6 31.9 1.0 CG B:ASN373 3.7 33.3 1.0 C B:ARG372 4.0 36.6 1.0 C B:SER370 4.1 29.7 1.0 CA B:LYS377 4.1 33.1 1.0 CA B:ASN373 4.3 32.8 1.0 O B:LYS377 4.3 39.9 1.0 OE1 B:GLU351 4.3 33.2 1.0 N B:SER370 4.4 27.9 1.0 CB B:ASP369 4.4 24.9 1.0 CB B:LYS377 4.4 36.0 1.0 CB B:ASN373 4.4 34.5 1.0 CG B:GLU351 4.6 29.7 1.0 N B:ASN373 4.6 33.0 1.0 O B:GLU351 4.6 25.7 1.0 ND2 B:ASN373 4.7 35.3 1.0 C B:ASP369 4.7 27.4 1.0 C B:LYS377 4.7 39.7 1.0 CA B:SER370 4.8 26.2 1.0 OE1 B:GLN397 4.8 47.7 1.0 C B:PRO371 4.9 31.8 1.0 CA B:ASP369 4.9 23.1 1.0 O B:PRO371 5.0 34.0 1.0

Calcium binding site 10 out of 10 in the Human PADI4 in Complex with Cyclic Peptide PADI4_3


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_3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca904 b:33.2 occ:1.00 OD1 B:ASP168 2.3 55.1 1.0 O B:ASP165 2.4 45.0 1.0 O B:GLU170 2.5 55.5 1.0 O B:ASP168 3.4 50.1 1.0 CG B:ASP168 3.6 54.5 1.0 C B:ASP165 3.6 38.3 1.0 C B:GLU170 3.7 49.9 1.0 OD2 B:ASP176 3.9 47.9 1.0 OD2 B:ASP168 4.2 53.1 1.0 C B:ASP168 4.2 49.4 1.0 N B:GLU170 4.3 50.2 1.0 CA B:ASP165 4.4 33.4 1.0 N B:VAL171 4.5 47.4 1.0 CA B:VAL171 4.5 45.6 1.0 N B:CYS166 4.6 37.1 1.0 CB B:ASP165 4.6 30.4 1.0 CA B:GLU170 4.6 50.2 1.0 CB B:ASP168 4.6 53.2 1.0 OE2 B:GLU252 4.7 36.4 1.0 N B:ASP168 4.7 49.1 1.0 CA B:CYS166 4.8 37.0 1.0 CA B:ASP168 4.8 47.1 1.0 OE1 B:GLU252 4.9 39.0 1.0 CZ B:PHE214 4.9 33.3 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