Calcium in PDB 7plp: Human Teneurin-4 C-Rich Domain

The structure of Human Teneurin-4 C-Rich Domain, PDB code: 7plp was solved by J.W.Beugelink, D.H.Meijer, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.19 / 1.40
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	66.343, 66.343, 66.343, 90, 90, 90
R / Rfree (%)	15.5 / 17.1

The structure of Human Teneurin-4 C-Rich Domain also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Iron	(Fe)	1 atom

The binding sites of Calcium atom in the Human Teneurin-4 C-Rich Domain (pdb code 7plp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Human Teneurin-4 C-Rich Domain, PDB code: 7plp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:14.5 occ:1.00 O A:ALA12 2.2 16.8 1.0 OD1 A:ASP26 2.3 15.3 1.0 OD1 A:ASN19 2.3 14.5 1.0 OE2 A:GLU10 2.3 14.5 1.0 O A:LYS17 2.3 14.7 1.0 OD1 A:ASP15 2.3 15.1 1.0 CD A:GLU10 3.2 14.2 1.0 CG A:ASP15 3.4 17.0 1.0 CG A:ASN19 3.4 15.2 1.0 C A:ALA12 3.4 15.4 1.0 C A:LYS17 3.5 14.8 1.0 CG A:ASP26 3.5 15.5 1.0 CG A:GLU10 3.8 15.5 1.0 N A:LYS17 3.9 14.6 1.0 OD2 A:ASP15 3.9 18.0 1.0 ND2 A:ASN19 4.0 16.9 1.0 N A:ASP26 4.1 14.4 1.0 OE1 A:GLU10 4.1 15.8 1.0 CA A:LYS17 4.2 14.4 1.0 CA A:CYS13 4.3 17.4 1.0 OD2 A:ASP26 4.3 16.3 1.0 N A:CYS13 4.3 16.5 1.0 CA A:ASP26 4.3 14.8 1.0 N A:ASP15 4.3 17.1 1.0 N A:ASN19 4.4 14.3 1.0 CB A:ALA12 4.4 16.7 1.0 CA A:ALA12 4.5 16.5 1.0 N A:SER16 4.5 15.2 1.0 CB A:ASP26 4.5 14.2 1.0 N A:ASP18 4.5 14.1 1.0 CB A:LYS17 4.6 19.2 1.0 CB A:ASP15 4.6 17.5 1.0 C A:CYS13 4.6 18.0 1.0 CB A:ASN19 4.6 14.1 1.0 N A:GLY14 4.7 18.3 1.0 CA A:ASP15 4.8 16.8 1.0 C A:ASP15 4.8 15.9 1.0 CA A:ASP18 4.8 14.3 1.0 CG1 A:VAL25 4.8 17.8 1.0 C A:SER16 4.9 16.2 1.0 N A:ALA12 4.9 17.0 1.0

Calcium binding site 2 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:15.6 occ:1.00 OD1 A:ASP20 2.3 16.1 1.0 O A:LEU24 2.3 17.3 1.0 OD2 A:ASP29 2.3 16.0 1.0 OE1 A:GLU10 2.3 15.8 1.0 OD1 A:ASP18 2.3 16.5 1.0 OD1 A:ASP22 2.3 16.7 1.0 CG A:ASP22 3.3 18.8 1.0 CG A:ASP20 3.3 16.2 1.0 CG A:ASP29 3.3 16.9 1.0 C A:LEU24 3.4 17.6 1.0 CG A:ASP18 3.5 15.8 1.0 CD A:GLU10 3.5 14.2 1.0 OD2 A:ASP22 3.7 19.1 1.0 CB A:ASP29 3.8 16.8 1.0 OD2 A:ASP20 3.8 17.1 1.0 N A:LEU24 4.0 18.3 1.0 CB A:GLU10 4.1 15.5 1.0 CA A:LEU24 4.1 17.6 1.0 CA A:CA103 4.1 17.3 1.0 CA A:ASP18 4.2 14.3 1.0 CB A:LEU24 4.2 17.9 1.0 N A:ASP22 4.2 17.1 1.0 CB A:ASP18 4.3 14.7 1.0 OD2 A:ASP18 4.3 18.7 1.0 N A:ASP20 4.3 15.5 1.0 OE2 A:GLU10 4.3 14.5 1.0 CG A:GLU10 4.4 15.5 1.0 C A:ASP18 4.4 13.9 1.0 OD1 A:ASP29 4.4 17.8 1.0 CB A:ASP22 4.5 19.5 1.0 N A:ASN19 4.5 14.3 1.0 N A:VAL25 4.5 16.3 1.0 CB A:ASP20 4.6 15.4 1.0 N A:GLY21 4.6 16.5 1.0 CA A:ASP22 4.7 18.2 1.0 CA A:VAL25 4.8 14.6 1.0 N A:GLY23 4.8 19.6 1.0 CA A:ASP20 4.8 15.1 1.0 C A:ASP20 4.9 15.4 1.0 C A:ASP22 4.9 19.5 1.0

Calcium binding site 3 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:17.3 occ:1.00 OD2 A:ASP22 2.3 19.1 1.0 OD2 A:ASP31 2.3 19.6 1.0 OD2 A:ASP20 2.3 17.1 1.0 O A:HOH222 2.4 26.3 1.0 O A:HOH212 2.4 21.2 1.0 OD1 A:ASP29 2.5 17.8 1.0 OD2 A:ASP29 2.5 16.0 1.0 CG A:ASP29 2.8 16.9 1.0 CG A:ASP31 3.2 18.7 1.0 CG A:ASP22 3.3 18.8 1.0 CG A:ASP20 3.4 16.2 1.0 OD1 A:ASP31 3.7 24.7 1.0 OD1 A:ASP20 3.7 16.1 1.0 OD1 A:ASP22 3.9 16.7 1.0 CA A:CA102 4.1 15.6 1.0 CB A:ASP31 4.2 16.8 1.0 CB A:ASP22 4.3 19.5 1.0 CB A:ASP29 4.3 16.8 1.0 N A:GLU10 4.3 15.1 1.0 O A:HOH215 4.3 55.5 1.0 O A:HOH224 4.4 58.9 1.0 CA A:MET9 4.6 17.0 0.5 O A:SER8 4.6 17.7 1.0 CB A:ASP20 4.7 15.4 1.0 CA A:MET9 4.7 15.8 0.5 CB A:GLU10 4.7 15.5 1.0 N A:ASP31 4.8 18.4 1.0

Calcium binding site 4 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:15.5 occ:1.00 OD2 B:ASP22 2.3 17.9 1.0 OD2 B:ASP20 2.3 16.2 1.0 OD2 B:ASP31 2.3 16.6 1.0 O B:HOH216 2.4 18.5 1.0 O B:HOH224 2.4 23.1 1.0 OD2 B:ASP29 2.5 14.3 1.0 OD1 B:ASP29 2.5 16.4 1.0 CG B:ASP29 2.8 13.6 1.0 CG B:ASP31 3.2 18.0 1.0 CG B:ASP22 3.3 16.5 1.0 CG B:ASP20 3.3 14.3 1.0 OD1 B:ASP20 3.7 15.9 1.0 OD1 B:ASP31 3.8 23.1 1.0 OD1 B:ASP22 3.9 15.4 1.0 O B:HOH218 4.1 49.6 1.0 CA B:CA102 4.1 14.0 1.0 O B:HOH217 4.2 45.4 1.0 CB B:ASP31 4.2 16.7 1.0 N B:GLU10 4.3 14.4 1.0 CB B:ASP29 4.3 13.6 1.0 CB B:ASP22 4.4 18.0 1.0 O B:HOH231 4.6 54.7 1.0 CA B:MET9 4.6 16.5 0.5 O B:SER8 4.6 17.3 1.0 CB B:GLU10 4.6 14.5 1.0 CB B:ASP20 4.7 14.8 1.0 CA B:MET9 4.7 17.6 0.5 N B:ASP31 4.9 15.5 1.0 C B:MET9 5.0 15.7 0.5

Calcium binding site 5 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:14.0 occ:1.00 OD1 B:ASP20 2.3 15.9 1.0 O B:LEU24 2.3 15.7 1.0 OD2 B:ASP29 2.3 14.3 1.0 OE1 B:GLU10 2.3 14.7 1.0 OD1 B:ASP18 2.3 16.3 1.0 OD1 B:ASP22 2.3 15.4 1.0 CG B:ASP22 3.3 16.5 1.0 CG B:ASP20 3.3 14.3 1.0 C B:LEU24 3.4 14.6 1.0 CG B:ASP29 3.4 13.6 1.0 CD B:GLU10 3.5 13.3 1.0 CG B:ASP18 3.5 14.8 1.0 OD2 B:ASP22 3.7 17.9 1.0 OD2 B:ASP20 3.8 16.2 1.0 CB B:ASP29 3.9 13.6 1.0 N B:LEU24 3.9 15.7 1.0 CA B:LEU24 4.0 14.5 1.0 CB B:GLU10 4.0 14.5 1.0 CB B:LEU24 4.0 15.4 1.0 CA B:CA101 4.1 15.5 1.0 CA B:ASP18 4.2 14.5 1.0 CB B:ASP18 4.3 14.7 1.0 N B:ASP20 4.3 13.9 1.0 OE2 B:GLU10 4.3 12.0 1.0 N B:ASP22 4.3 17.2 1.0 CG B:GLU10 4.4 13.4 1.0 C B:ASP18 4.4 13.8 1.0 OD2 B:ASP18 4.4 16.8 1.0 N B:ASN19 4.4 13.4 1.0 OD1 B:ASP29 4.5 16.4 1.0 N B:VAL25 4.5 14.3 1.0 CB B:ASP22 4.5 18.0 1.0 N B:GLY21 4.5 16.5 1.0 CB B:ASP20 4.6 14.8 1.0 N B:GLY23 4.8 15.8 1.0 CA B:VAL25 4.8 13.7 1.0 CA B:ASP20 4.8 14.5 1.0 CA B:ASP22 4.8 17.1 1.0 C B:ASP20 4.9 16.8 1.0 C B:ASP22 5.0 16.4 1.0 CG B:LEU24 5.0 18.5 1.0

Calcium binding site 6 out of 6 in the Human Teneurin-4 C-Rich Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Teneurin-4 C-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:13.6 occ:1.00 O B:ALA12 2.2 15.9 1.0 OD1 B:ASN19 2.3 14.4 1.0 OD1 B:ASP26 2.3 13.4 1.0 O B:LYS17 2.3 14.5 1.0 OD1 B:ASP15 2.3 14.8 1.0 OE2 B:GLU10 2.3 12.0 1.0 CD B:GLU10 3.2 13.3 1.0 CG B:ASP15 3.4 15.5 1.0 CG B:ASN19 3.4 14.4 1.0 C B:LYS17 3.4 13.9 1.0 C B:ALA12 3.5 13.8 1.0 CG B:ASP26 3.5 13.7 1.0 CG B:GLU10 3.9 13.4 1.0 N B:LYS17 3.9 13.8 1.0 OD2 B:ASP15 3.9 16.3 1.0 N B:ASP26 4.0 13.7 1.0 ND2 B:ASN19 4.1 15.1 1.0 OE1 B:GLU10 4.1 14.7 1.0 CA B:LYS17 4.1 13.9 1.0 CA B:CYS13 4.3 14.9 1.0 OD2 B:ASP26 4.3 15.3 1.0 CA B:ASP26 4.3 13.3 1.0 N B:CYS13 4.3 14.5 1.0 N B:ASP15 4.4 14.6 1.0 N B:ASN19 4.4 13.4 1.0 CB B:ALA12 4.4 15.8 1.0 CB B:LYS17 4.4 15.5 1.0 CA B:ALA12 4.5 13.8 1.0 CB B:ASP26 4.5 14.0 1.0 N B:ASP18 4.5 13.0 1.0 N B:SER16 4.6 14.7 1.0 CB B:ASP15 4.6 15.7 1.0 CB B:ASN19 4.6 14.4 1.0 C B:CYS13 4.6 15.3 1.0 N B:GLY14 4.7 14.0 1.0 CA B:ASP15 4.8 15.1 1.0 CG1 B:VAL25 4.8 15.5 1.0 CA B:ASP18 4.8 14.5 1.0 C B:ASP15 4.9 13.9 1.0 N B:ALA12 5.0 14.1 1.0 C B:SER16 5.0 14.8 1.0

D.H.Meijer, C.P.Frias, J.W.Beugelink, Y.N.Deurloo, B.J.C.Janssen. TENEURIN4 Dimer Structures Reveal A Calcium-Stabilized Compact Conformation Supporting Homomeric Trans-Interactions. Embo J. V. 41 07505 2022.
ISSN: ESSN 1460-2075
PubMed: 35099835
DOI: 10.15252/EMBJ.2020107505