Calcium in PDB 7a1r: Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r was solved by G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.908, 57.532, 84.57, 90, 90, 90
R / Rfree (%)	17 / 19.1

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) also contains other interesting chemical elements:

Chlorine	(Cl)	7 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) (pdb code 7a1r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:15.0 occ:1.00 OD1 A:ASN547 2.3 16.0 1.0 OD2 A:ASP498 2.4 15.1 1.0 O A:LYS546 2.4 15.9 1.0 OD1 A:ASP545 2.4 16.3 1.0 O A:HOH832 2.4 19.9 1.0 OE2 A:GLU492 2.5 17.9 1.0 OE1 A:GLU492 2.5 19.3 1.0 CD A:GLU492 2.9 16.6 1.0 CG A:ASP545 3.2 15.2 1.0 C A:LYS546 3.4 14.8 1.0 OD2 A:ASP545 3.5 17.5 1.0 CG A:ASN547 3.5 13.8 1.0 CG A:ASP498 3.5 13.9 1.0 CA A:ASN547 4.0 16.1 1.0 CA A:CA602 4.0 14.8 0.9 N A:ASN547 4.1 14.0 1.0 CB A:ASP498 4.1 13.6 1.0 N A:ASP498 4.2 11.8 1.0 CB A:ASN547 4.3 15.8 1.0 O A:HOH817 4.3 25.6 1.0 N A:LYS546 4.3 13.4 1.0 CG A:GLU492 4.4 15.8 1.0 O A:HOH825 4.4 27.2 1.0 C A:ASP545 4.4 14.4 1.0 ND2 A:ASN547 4.4 16.3 1.0 CA A:LYS546 4.5 13.4 1.0 CB A:ASP545 4.5 13.0 1.0 OD1 A:ASP498 4.5 16.2 1.0 CA A:SER497 4.6 13.1 1.0 O A:HOH728 4.6 22.5 1.0 O A:HOH772 4.6 32.1 1.0 O A:HOH845 4.7 31.0 1.0 O A:ASP545 4.7 14.4 1.0 C A:SER497 4.8 12.8 1.0 CA A:ASP498 4.8 11.6 1.0 O A:HOH735 4.9 21.2 1.0 CA A:ASP545 4.9 13.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:14.8 occ:0.92 O A:HOH817 2.3 25.6 1.0 O A:HOH708 2.4 25.1 1.0 O A:HOH828 2.4 20.3 1.0 OE2 A:GLU492 2.4 17.9 1.0 O A:VAL496 2.4 17.1 1.0 OD1 A:ASP498 2.5 16.2 1.0 OD2 A:ASP498 2.6 15.1 1.0 CG A:ASP498 2.9 13.9 1.0 CD A:GLU492 3.5 16.6 1.0 C A:VAL496 3.5 14.2 1.0 CA A:CA601 4.0 15.0 1.0 O A:HOH832 4.1 19.9 1.0 CG A:GLU492 4.1 15.8 1.0 C A:SER497 4.2 12.8 1.0 CA A:SER497 4.3 13.1 1.0 N A:VAL496 4.3 18.7 1.0 O A:HOH845 4.3 31.0 1.0 N A:SER497 4.3 15.6 1.0 CB A:ASP498 4.4 13.6 1.0 OG A:SER517 4.4 24.3 0.7 O A:HOH804 4.4 25.2 1.0 O A:HOH837 4.4 32.0 1.0 OE1 A:GLU492 4.4 19.3 1.0 N A:ASP498 4.5 11.8 1.0 O A:HOH885 4.5 43.6 1.0 O A:HOH862 4.5 36.2 1.0 O A:SER497 4.5 15.1 1.0 CA A:VAL496 4.6 13.7 1.0 N A:SER517 4.6 15.2 1.0 CA A:SER517 4.7 16.5 0.3 CA A:SER517 4.7 19.7 0.7 CB A:SER517 4.9 13.7 0.3 CA A:ASP498 4.9 11.6 1.0 CB A:SER517 5.0 18.9 0.7 CB A:GLU492 5.0 17.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:16.5 occ:1.00 OD1 B:ASN547 2.3 17.9 1.0 O B:HOH720 2.3 21.1 1.0 OD2 B:ASP498 2.4 16.7 1.0 O B:LYS546 2.4 16.6 1.0 OD1 B:ASP545 2.4 16.6 1.0 OE1 B:GLU492 2.4 22.6 1.0 OE2 B:GLU492 2.6 26.2 1.0 CD B:GLU492 2.9 19.6 1.0 CG B:ASP545 3.2 16.1 1.0 C B:LYS546 3.4 15.8 1.0 CG B:ASN547 3.5 18.0 1.0 OD2 B:ASP545 3.5 18.5 1.0 CG B:ASP498 3.5 12.8 1.0 CA B:ASN547 4.0 18.8 1.0 CA B:CA602 4.0 19.4 1.0 N B:ASN547 4.1 16.6 1.0 CB B:ASP498 4.1 14.4 1.0 N B:ASP498 4.2 14.2 1.0 CB B:ASN547 4.3 18.1 1.0 CG B:GLU492 4.4 24.3 1.0 N B:LYS546 4.4 15.8 1.0 O B:HOH830 4.4 31.5 1.0 OXT B:ACT603 4.4 28.2 1.0 O B:HOH831 4.4 34.1 1.0 ND2 B:ASN547 4.4 20.9 1.0 C B:ASP545 4.5 18.7 1.0 CA B:LYS546 4.5 14.4 1.0 OD1 B:ASP498 4.5 16.9 1.0 O B:HOH725 4.6 24.5 1.0 CB B:ASP545 4.6 13.0 1.0 CA B:SER497 4.7 15.4 1.0 O B:ASP545 4.7 17.6 1.0 CA B:ASP498 4.8 15.0 1.0 C B:SER497 4.8 16.1 1.0 CH3 B:ACT603 4.9 28.5 1.0 CA B:ASP545 5.0 15.1 1.0 O B:HOH723 5.0 30.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:19.4 occ:1.00 O B:HOH705 2.3 30.2 1.0 O B:HOH830 2.3 31.5 1.0 O B:VAL496 2.4 17.3 1.0 O B:HOH801 2.4 25.3 1.0 OE1 B:GLU492 2.4 22.6 1.0 OD1 B:ASP498 2.5 16.9 1.0 OD2 B:ASP498 2.6 16.7 1.0 CG B:ASP498 2.9 12.8 1.0 C B:VAL496 3.5 17.3 1.0 CD B:GLU492 3.5 19.6 1.0 CA B:CA601 4.0 16.5 1.0 CG B:GLU492 4.1 24.3 1.0 O B:HOH720 4.2 21.1 1.0 C B:SER497 4.2 16.1 1.0 OG B:SER517 4.3 28.9 0.7 N B:VAL496 4.3 18.7 1.0 CA B:SER497 4.4 15.4 1.0 CB B:ASP498 4.4 14.4 1.0 N B:SER497 4.4 16.6 1.0 O B:HOH773 4.4 27.9 1.0 N B:ASP498 4.5 14.2 1.0 O B:SER497 4.5 15.9 1.0 O B:HOH838 4.5 40.0 1.0 OE2 B:GLU492 4.5 26.2 1.0 CA B:VAL496 4.5 19.7 1.0 O B:HOH846 4.5 46.8 1.0 N B:SER517 4.6 16.6 1.0 CA B:SER517 4.7 20.0 0.3 CA B:SER517 4.7 20.9 0.7 O B:HOH782 4.8 44.7 1.0 CB B:SER517 4.9 20.5 0.3 CA B:ASP498 4.9 15.0 1.0 CB B:SER517 4.9 22.1 0.7 CB B:GLU492 5.0 22.3 1.0

E.Stepinac, N.Landrein, D.Skwarzynska, P.Wojcik, J.Lesigang, I.Lucic, C.Y.He, M.Bonhivers, D.R.Robinson, G.Dong. Structural Studies of the Shortest Extended Synaptotagmin with Only Two C2 Domains From Trypanosoma Brucei . Iscience V. 24 02422 2021.
ISSN: ESSN 2589-0042
PubMed: 33997700
DOI: 10.1016/J.ISCI.2021.102422