Calcium in PDB 6ank: Synaptotagmin-7, C2A- and C2B-Domains

The structure of Synaptotagmin-7, C2A- and C2B-Domains, PDB code: 6ank was solved by D.R.Tomchick, J.Rizo, R.Voleti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.46 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.637, 75.059, 70.980, 90.00, 114.51, 90.00
R / Rfree (%)	21.4 / 25.7

The binding sites of Calcium atom in the Synaptotagmin-7, C2A- and C2B-Domains (pdb code 6ank). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Synaptotagmin-7, C2A- and C2B-Domains, PDB code: 6ank:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.3 occ:1.00 O A:TYR226 2.3 60.6 1.0 OD1 A:ASP227 2.4 63.2 1.0 OD2 A:ASP166 2.4 67.8 1.0 OD2 A:ASP172 2.4 40.9 1.0 OD1 A:ASP225 2.4 51.5 1.0 OD1 A:ASP166 2.4 67.8 1.0 OD2 A:ASP225 2.5 53.9 1.0 CG A:ASP166 2.7 72.5 1.0 CG A:ASP225 2.8 52.1 1.0 C A:TYR226 3.4 58.8 1.0 HA A:ASP227 3.4 75.0 1.0 CG A:ASP172 3.4 52.2 1.0 CG A:ASP227 3.5 64.5 1.0 CA A:CA504 3.5 71.5 1.0 H A:ASP172 3.6 56.1 1.0 HB2 A:ASP172 3.6 58.2 1.0 CA A:ASP227 4.0 62.4 1.0 CB A:ASP172 4.0 48.4 1.0 N A:ASP227 4.0 59.1 1.0 HA A:SER171 4.1 69.2 1.0 N A:ASP172 4.2 46.6 1.0 N A:TYR226 4.2 51.1 1.0 CB A:ASP225 4.2 53.2 1.0 OD2 A:ASP227 4.3 64.0 1.0 CB A:ASP166 4.3 76.6 1.0 H A:TYR226 4.4 61.4 1.0 C A:ASP225 4.4 50.6 1.0 OD1 A:ASP172 4.4 53.6 1.0 CB A:ASP227 4.4 61.4 1.0 CA A:TYR226 4.4 53.5 1.0 HB3 A:ASP166 4.6 92.0 1.0 HB3 A:ASP225 4.7 64.0 1.0 HB2 A:ASP166 4.7 92.0 1.0 O A:ASP225 4.7 48.6 1.0 CA A:ASP172 4.7 44.4 1.0 HB2 A:ASP225 4.8 64.0 1.0 H A:ASP227 4.8 71.0 1.0 CA A:ASP225 4.8 50.4 1.0 HB3 A:ASP172 4.8 58.2 1.0 HB2 A:LYS165 4.9 81.1 1.0 HB3 A:ASP227 4.9 73.7 1.0 CA A:SER171 4.9 57.6 1.0 HB3 A:TYR226 4.9 64.3 1.0 C A:SER171 4.9 52.5 1.0 HA A:ASP225 4.9 60.6 1.0

Calcium binding site 2 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:71.5 occ:1.00 OD1 A:ASP166 2.4 67.8 1.0 OD2 A:ASP225 2.4 53.9 1.0 OD2 A:ASP233 2.4 68.7 1.0 OD2 A:ASP227 2.4 64.0 1.0 OD1 A:ASP227 2.4 63.2 1.0 CG A:ASP227 2.7 64.5 1.0 O A:LYS165 2.8 76.3 1.0 O A:HOH653 3.2 46.1 1.0 CG A:ASP233 3.3 66.3 1.0 CA A:CA503 3.5 60.3 1.0 C A:LYS165 3.6 74.4 1.0 CG A:ASP166 3.6 72.5 1.0 CG A:ASP225 3.6 52.1 1.0 HB3 A:LYS165 3.6 81.1 1.0 HA A:ASP166 3.6 96.7 1.0 HB2 A:LYS165 3.7 81.1 1.0 HB2 A:ASP233 3.7 77.0 1.0 OD1 A:ASP233 4.0 67.8 1.0 CB A:LYS165 4.1 67.5 1.0 O A:HOH601 4.1 38.4 1.0 CB A:ASP233 4.1 64.0 1.0 N A:ASP166 4.1 72.9 1.0 CA A:ASP166 4.2 80.5 1.0 HB3 A:ASP225 4.2 64.0 1.0 CB A:ASP227 4.3 61.4 1.0 OD1 A:ASP225 4.4 51.5 1.0 OD2 A:ASP166 4.4 67.8 1.0 CA A:LYS165 4.5 71.0 1.0 CB A:ASP166 4.5 76.6 1.0 H A:ASP233 4.6 75.5 1.0 CB A:ASP225 4.6 53.2 1.0 HB3 A:ASP233 4.6 77.0 1.0 HB3 A:ASP227 4.6 73.7 1.0 HB2 A:ASP227 4.7 73.7 1.0 H A:ASP166 4.8 87.6 1.0 HA A:ASP227 4.9 75.0 1.0 HB3 A:ASP166 4.9 92.0 1.0 HA A:LYS165 5.0 85.3 1.0

Calcium binding site 3 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:36.1 occ:1.00 OD1 A:ASP359 2.3 41.7 1.0 OD2 A:ASP297 2.4 43.9 1.0 OD1 A:ASP357 2.4 33.0 1.0 OD2 A:ASP303 2.4 36.5 1.0 O A:HOH647 2.4 46.7 1.0 OD1 A:ASP297 2.5 44.8 1.0 CG A:ASP297 2.8 43.7 1.0 O A:LYS358 2.8 40.1 1.0 HA A:ASP359 2.8 55.9 1.0 CG A:ASP357 3.2 31.4 1.0 OD2 A:ASP357 3.3 32.9 1.0 C A:LYS358 3.4 38.1 1.0 CG A:ASP303 3.4 35.7 1.0 CG A:ASP359 3.4 42.1 1.0 HB2 A:ASP303 3.5 39.0 1.0 CA A:ASP359 3.5 46.5 1.0 N A:ASP359 3.6 40.7 1.0 H A:ASP303 3.7 38.2 1.0 CB A:ASP303 4.0 32.4 1.0 CB A:ASP359 4.0 44.0 1.0 CA A:CA506 4.1 36.1 1.0 H A:ASP359 4.2 49.0 1.0 N A:ASP303 4.2 31.7 1.0 HA A:SER302 4.2 39.4 1.0 CB A:ASP297 4.3 41.9 1.0 N A:LYS358 4.4 30.3 1.0 OD1 A:ASP303 4.4 36.0 1.0 HB3 A:ASP359 4.4 52.9 1.0 C A:ASP357 4.4 29.8 1.0 OD2 A:ASP359 4.5 41.6 1.0 CA A:LYS358 4.5 35.8 1.0 O A:ASP357 4.5 31.4 1.0 H A:LYS360 4.6 68.2 1.0 CB A:ASP357 4.6 27.9 1.0 H A:LYS358 4.6 36.5 1.0 HB3 A:ASP297 4.6 50.3 1.0 HB2 A:ASP297 4.7 50.3 1.0 CA A:ASP303 4.7 30.9 1.0 HB3 A:ASP303 4.8 39.0 1.0 C A:ASP359 4.8 50.8 1.0 HB2 A:ASP359 4.8 52.9 1.0 C A:SER302 5.0 30.3 1.0 HB3 A:LYS358 5.0 46.8 1.0

Calcium binding site 4 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:36.1 occ:1.00 OD1 A:ASP297 2.3 44.8 1.0 OD2 A:ASP359 2.4 41.6 1.0 OD1 A:ASP359 2.4 41.7 1.0 O A:HOH652 2.4 25.6 1.0 OD2 A:ASP357 2.4 32.9 1.0 O A:MET296 2.4 44.8 1.0 OD2 A:ASP365 2.4 48.3 1.0 CG A:ASP359 2.6 42.1 1.0 HA A:ASP297 3.0 55.0 1.0 C A:MET296 3.0 42.6 1.0 HB3 A:MET296 3.3 50.7 1.0 N A:ASP297 3.4 41.0 1.0 CG A:ASP297 3.5 43.7 1.0 HB2 A:MET296 3.5 50.7 1.0 CA A:ASP297 3.6 45.7 1.0 CG A:ASP365 3.6 47.8 1.0 CG A:ASP357 3.6 31.4 1.0 CB A:MET296 3.7 42.1 1.0 HB2 A:ASP365 3.8 51.9 1.0 CA A:MET296 4.0 40.9 1.0 H A:ASP297 4.0 49.4 1.0 CA A:CA505 4.1 36.1 1.0 CB A:ASP297 4.1 41.9 1.0 CB A:ASP359 4.1 44.0 1.0 OD1 A:ASP357 4.2 33.0 1.0 CB A:ASP365 4.2 43.2 1.0 HB3 A:ASP359 4.3 52.9 1.0 OD2 A:ASP297 4.4 43.9 1.0 OD1 A:ASP365 4.5 50.6 1.0 O A:HOH602 4.5 36.1 1.0 HA A:MET296 4.5 49.2 1.0 HB3 A:ASP297 4.5 50.3 1.0 HB3 A:ASP357 4.5 33.7 1.0 HB2 A:ASP359 4.6 52.9 1.0 H A:ASP365 4.7 61.6 1.0 CB A:ASP357 4.7 27.9 1.0 HB3 A:ASP365 4.7 51.9 1.0 HB2 A:ASP297 4.8 50.3 1.0 HA A:ASP359 4.9 55.9 1.0 C A:ASP297 4.9 47.1 1.0

Calcium binding site 5 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:49.8 occ:1.00 O B:TYR226 2.3 45.7 1.0 OD1 B:ASP227 2.3 51.8 1.0 OD1 B:ASP166 2.4 61.0 1.0 OD2 B:ASP166 2.4 60.6 1.0 OD2 B:ASP172 2.4 49.4 1.0 OD1 B:ASP225 2.4 41.4 1.0 OD2 B:ASP225 2.5 44.1 1.0 CG B:ASP166 2.7 62.8 1.0 CG B:ASP225 2.8 42.7 1.0 C B:TYR226 3.3 46.2 1.0 CG B:ASP172 3.4 47.7 1.0 HB2 B:ASP172 3.4 54.7 1.0 CA B:CA504 3.5 69.3 1.0 CG B:ASP227 3.6 53.4 1.0 H B:ASP172 3.6 58.1 1.0 HA B:ASP227 3.6 63.3 1.0 CB B:ASP172 3.9 45.5 1.0 N B:ASP227 4.0 50.5 1.0 N B:TYR226 4.1 41.0 1.0 N B:ASP172 4.1 48.4 1.0 H B:TYR226 4.2 49.3 1.0 HA B:SER171 4.2 67.5 1.0 CA B:ASP227 4.2 52.6 1.0 CB B:ASP166 4.2 69.5 1.0 CB B:ASP225 4.2 44.6 1.0 CA B:TYR226 4.3 45.3 1.0 OD1 B:ASP172 4.3 45.9 1.0 C B:ASP225 4.4 40.3 1.0 OD2 B:ASP227 4.4 54.1 1.0 CB B:ASP227 4.5 54.5 1.0 HB3 B:ASP166 4.6 83.5 1.0 HB2 B:ASP166 4.6 83.5 1.0 CA B:ASP172 4.6 46.4 1.0 HB3 B:ASP225 4.7 53.6 1.0 HB3 B:ASP172 4.7 54.7 1.0 HB2 B:ASP225 4.7 53.6 1.0 H B:ASP227 4.8 60.7 1.0 O B:ASP225 4.8 36.8 1.0 CA B:ASP225 4.8 41.7 1.0 HB3 B:TYR226 4.8 55.7 1.0 HA B:ASP225 4.9 50.1 1.0 C B:SER171 4.9 51.8 1.0 HB3 B:ASP227 4.9 65.5 1.0 HB2 B:LYS165 4.9 69.6 1.0 HA B:ASP166 4.9 83.6 1.0 CA B:SER171 5.0 56.1 1.0

Calcium binding site 6 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:69.3 occ:1.00 OD2 B:ASP227 2.3 54.1 1.0 OD2 B:ASP225 2.3 44.1 1.0 OD2 B:ASP233 2.3 73.6 1.0 OD1 B:ASP166 2.3 61.0 1.0 OD1 B:ASP227 2.4 51.8 1.0 CG B:ASP227 2.7 53.4 1.0 O B:LYS165 2.8 54.2 1.0 HA B:ASP166 3.5 83.6 1.0 CG B:ASP233 3.5 71.1 1.0 CA B:CA503 3.5 49.8 1.0 CG B:ASP225 3.6 42.7 1.0 CG B:ASP166 3.6 62.8 1.0 C B:LYS165 3.6 58.5 1.0 O B:HOH604 3.6 53.9 1.0 HB3 B:LYS165 3.9 69.6 1.0 HB2 B:ASP233 3.9 76.3 1.0 HB2 B:LYS165 4.0 69.6 1.0 CA B:ASP166 4.1 69.5 1.0 N B:ASP166 4.1 65.8 1.0 HB3 B:ASP225 4.2 53.6 1.0 CB B:ASP227 4.2 54.5 1.0 CB B:LYS165 4.3 57.9 1.0 CB B:ASP233 4.3 63.5 1.0 OD1 B:ASP233 4.3 75.1 1.0 OD1 B:ASP225 4.3 41.4 1.0 CB B:ASP166 4.4 69.5 1.0 OD2 B:ASP166 4.4 60.6 1.0 CB B:ASP225 4.5 44.6 1.0 HB3 B:ASP227 4.6 65.5 1.0 CA B:LYS165 4.6 57.4 1.0 HB2 B:ASP227 4.6 65.5 1.0 H B:ASP233 4.8 72.0 1.0 HB3 B:ASP166 4.8 83.5 1.0 H B:ASP166 4.8 79.1 1.0 HB3 B:ASP233 4.8 76.3 1.0 O B:TYR226 5.0 45.7 1.0 HA B:ASP227 5.0 63.3 1.0

Calcium binding site 7 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:36.7 occ:1.00 OD1 B:ASP297 2.3 48.1 1.0 OD2 B:ASP297 2.4 46.2 1.0 OD1 B:ASP359 2.4 51.0 1.0 OD2 B:ASP303 2.4 35.4 1.0 OD1 B:ASP357 2.5 36.9 1.0 HA B:ASP359 2.7 89.8 1.0 CG B:ASP297 2.7 44.7 1.0 O B:LYS358 2.8 53.1 1.0 CG B:ASP357 3.2 36.7 1.0 C B:LYS358 3.2 55.3 1.0 OD2 B:ASP357 3.3 40.5 1.0 N B:ASP359 3.3 64.2 1.0 CA B:ASP359 3.3 74.8 1.0 CG B:ASP303 3.3 34.9 1.0 HB2 B:ASP303 3.4 39.0 1.0 CG B:ASP359 3.4 57.6 1.0 H B:ASP303 3.4 40.4 1.0 H B:ASP359 3.8 77.1 1.0 CB B:ASP303 3.9 32.4 1.0 CB B:ASP359 3.9 62.0 1.0 N B:ASP303 4.0 33.6 1.0 HA B:SER302 4.0 40.8 1.0 CB B:ASP297 4.2 44.2 1.0 N B:LYS358 4.2 42.5 1.0 CA B:CA506 4.3 44.4 1.0 OD1 B:ASP303 4.3 35.6 1.0 H B:ASP297 4.3 50.1 1.0 CA B:LYS358 4.3 47.0 1.0 C B:ASP357 4.3 38.0 1.0 H B:LYS360 4.4 1.0 1.0 H B:LYS358 4.4 51.1 1.0 OD2 B:ASP359 4.4 54.1 1.0 HB3 B:ASP359 4.5 74.5 1.0 HB3 B:ASP297 4.5 53.2 1.0 O B:ASP357 4.5 35.7 1.0 CA B:ASP303 4.6 30.1 1.0 CB B:ASP357 4.6 35.0 1.0 HB2 B:ASP297 4.6 53.2 1.0 C B:ASP359 4.6 85.2 1.0 HB3 B:ASP303 4.7 39.0 1.0 HB2 B:ASP359 4.7 74.5 1.0 C B:SER302 4.8 33.2 1.0 HB3 B:LYS358 4.8 60.3 1.0 N B:LYS360 4.8 84.1 1.0 CA B:SER302 4.8 33.9 1.0 N B:ASP297 4.9 41.7 1.0 CA B:ASP357 4.9 33.6 1.0 HA B:ASP357 5.0 40.4 1.0 CA B:ASP297 5.0 42.5 1.0

Calcium binding site 8 out of 8 in the Synaptotagmin-7, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Synaptotagmin-7, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:44.4 occ:1.00 N B:ASP297 2.3 41.7 1.0 OD1 B:ASP297 2.4 48.1 1.0 OD2 B:ASP359 2.4 54.1 1.0 OD2 B:ASP357 2.4 40.5 1.0 OD2 B:ASP365 2.4 53.7 1.0 H B:ASP297 2.5 50.1 1.0 OD1 B:ASP359 2.5 51.0 1.0 HA B:ASP297 2.5 51.2 1.0 O B:HOH619 2.5 32.3 1.0 C B:MET296 2.6 43.5 1.0 HB3 B:MET296 2.7 51.4 1.0 CG B:ASP359 2.8 57.6 1.0 HB2 B:MET296 2.9 51.4 1.0 CA B:ASP297 2.9 42.5 1.0 O B:MET296 2.9 47.5 1.0 CB B:MET296 3.1 42.7 1.0 O B:HOH610 3.3 43.9 1.0 CG B:ASP297 3.3 44.7 1.0 CA B:MET296 3.4 44.1 1.0 CG B:ASP357 3.6 36.7 1.0 CG B:ASP365 3.7 47.6 1.0 CB B:ASP297 3.7 44.2 1.0 HA B:MET296 4.0 53.1 1.0 HB2 B:ASP365 4.1 54.9 1.0 C B:ASP297 4.2 41.0 1.0 OD1 B:ASP357 4.2 36.9 1.0 O B:HOH644 4.2 36.5 1.0 HB3 B:ASP297 4.2 53.2 1.0 CA B:CA505 4.3 36.7 1.0 CB B:ASP359 4.3 62.0 1.0 HB2 B:ASP297 4.3 53.2 1.0 H B:MET296 4.4 51.5 1.0 OD2 B:ASP297 4.4 46.2 1.0 CB B:ASP365 4.5 45.7 1.0 N B:MET296 4.5 42.8 1.0 HB3 B:ASP357 4.5 42.1 1.0 CG B:MET296 4.5 47.5 1.0 OD1 B:ASP365 4.6 54.1 1.0 HB3 B:ASP359 4.6 74.5 1.0 CB B:ASP357 4.7 35.0 1.0 HG3 B:MET296 4.7 57.1 1.0 HB2 B:ASP359 4.7 74.5 1.0 H B:ILE298 4.8 51.3 1.0 HB3 B:ASP365 4.9 54.9 1.0 N B:ILE298 4.9 42.7 1.0 O B:ASP297 4.9 42.4 1.0

R.Voleti, D.R.Tomchick, T.C.Sudhof, J.Rizo. Exceptionally Tight Membrane-Binding May Explain the Key Role of the Synaptotagmin-7 C2A Domain in Asynchronous Neurotransmitter Release. Proc. Natl. Acad. Sci. V. 114 E8518 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28923929
DOI: 10.1073/PNAS.1710708114