Calcium in PDB 6anj: Synaptotagmin-7, C2A Domain

The structure of Synaptotagmin-7, C2A Domain, PDB code: 6anj 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)	27.65 / 1.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	55.302, 55.302, 89.805, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 18.1

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

Calcium binding site 1 out of 3 in the Synaptotagmin-7, C2A Domain


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 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:7.8 occ:1.00 O A:TYR226 2.3 8.6 1.0 OD2 A:ASP166 2.4 8.3 1.0 OD1 A:ASP225 2.4 8.9 1.0 OD1 A:ASP227 2.4 11.0 1.0 OD2 A:ASP172 2.4 7.8 1.0 OD1 A:ASP166 2.5 8.7 1.0 CG A:ASP166 2.8 8.0 1.0 OD2 A:ASP225 2.8 10.9 1.0 CG A:ASP225 2.9 9.3 1.0 HA A:ASP227 3.3 6.8 1.0 C A:TYR226 3.4 8.2 1.0 CG A:ASP172 3.5 10.1 1.0 HB2 A:ASP172 3.5 10.8 1.0 CG A:ASP227 3.7 8.5 1.0 H A:ASP172 3.7 7.4 1.0 CA A:CA302 3.7 7.2 1.0 HH11 A:ARG228 3.8 23.4 1.0 CA A:ASP227 4.0 5.7 1.0 CB A:ASP172 4.0 9.0 1.0 HH12 A:ARG228 4.0 23.4 1.0 N A:ASP227 4.1 9.6 1.0 HA A:SER171 4.1 7.8 1.0 N A:ASP172 4.2 6.2 1.0 NH1 A:ARG228 4.2 19.5 1.0 CB A:ASP166 4.3 10.4 1.0 O A:HOH416 4.3 12.3 1.0 N A:TYR226 4.3 7.1 1.0 CB A:ASP225 4.4 6.6 1.0 CB A:ASP227 4.4 8.3 1.0 CA A:TYR226 4.5 4.7 1.0 C A:ASP225 4.5 9.9 1.0 OD1 A:ASP172 4.5 10.9 1.0 H A:TYR226 4.5 8.5 1.0 OD2 A:ASP227 4.6 10.8 1.0 HB3 A:ASP166 4.6 12.4 1.0 HB2 A:ASP166 4.7 12.4 1.0 O A:ASP225 4.8 7.4 1.0 CA A:ASP172 4.8 8.2 1.0 HB3 A:TYR226 4.8 6.5 1.0 HB3 A:ASP172 4.8 10.8 1.0 HB3 A:ASP225 4.9 7.9 1.0 H A:ASP227 4.9 11.5 1.0 C A:SER171 4.9 7.2 1.0 HB2 A:ASP225 4.9 7.9 1.0 CA A:SER171 4.9 6.5 1.0 CA A:ASP225 5.0 6.3 1.0

Calcium binding site 2 out of 3 in the Synaptotagmin-7, C2A Domain


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 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:7.2 occ:1.00 OD2 A:ASP233 2.3 22.2 1.0 OD2 A:ASP225 2.3 10.9 1.0 OD1 A:ASP166 2.3 8.7 1.0 O A:LYS165 2.4 8.0 1.0 OD1 A:ASP227 2.5 11.0 1.0 O A:HOH401 2.5 36.2 1.0 OD2 A:ASP227 2.5 10.8 1.0 CG A:ASP227 2.8 8.5 1.0 C A:LYS165 3.4 7.0 1.0 CG A:ASP233 3.4 14.4 1.0 HA A:ASP166 3.4 12.3 1.0 CG A:ASP166 3.5 8.0 1.0 CG A:ASP225 3.6 9.3 1.0 HB3 A:LYS165 3.7 15.3 1.0 CA A:CA301 3.7 7.8 1.0 HB2 A:LYS165 3.9 15.3 1.0 HB2 A:ASP233 4.1 12.9 1.0 CA A:ASP166 4.1 10.3 1.0 N A:ASP166 4.1 8.0 1.0 CA A:CA303 4.1 11.8 1.0 OD1 A:ASP233 4.1 11.7 1.0 CB A:LYS165 4.2 12.8 1.0 O A:HOH520 4.2 25.0 1.0 HB3 A:ASP225 4.3 7.9 1.0 OD1 A:ASP225 4.3 8.9 1.0 OD2 A:ASP166 4.3 8.3 1.0 CB A:ASP227 4.4 8.3 1.0 CB A:ASP233 4.4 10.7 1.0 CB A:ASP166 4.4 10.4 1.0 CA A:LYS165 4.4 10.3 1.0 CB A:ASP225 4.6 6.6 1.0 O A:HOH494 4.6 21.2 1.0 HB3 A:ASP227 4.7 10.0 1.0 HB2 A:ASP227 4.7 10.0 1.0 HB3 A:ASP166 4.8 12.4 1.0 H A:ASP166 4.9 9.6 1.0 HB3 A:ASP233 4.9 12.9 1.0 HA A:LYS165 4.9 12.4 1.0 HA A:ASP227 4.9 6.8 1.0 H A:ASP233 4.9 12.1 1.0 H31 A:TBU305 4.9 26.1 1.0

Calcium binding site 3 out of 3 in the Synaptotagmin-7, C2A Domain


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 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:11.8 occ:1.00 OD2 A:ASP227 2.3 10.8 1.0 OD1 A:ASP233 2.3 11.7 1.0 O A:HOH494 2.4 21.2 1.0 O A:HOH544 2.4 17.9 1.0 OG A:SER230 2.4 13.6 1.0 O A:ARG231 2.4 14.7 1.0 O A:HOH401 2.6 36.2 1.0 CG A:ASP233 3.2 14.4 1.0 OD2 A:ASP233 3.3 22.2 1.0 CG A:ASP227 3.5 8.5 1.0 HB2 A:SER230 3.5 23.6 1.0 CB A:SER230 3.5 19.7 1.0 C A:ARG231 3.6 10.1 1.0 HB2 A:ASP227 3.7 10.0 1.0 CB A:ASP227 4.0 8.3 1.0 N A:ARG231 4.0 16.2 1.0 HB3 A:ASP227 4.0 10.0 1.0 C A:SER230 4.1 14.9 1.0 H A:ARG231 4.1 19.4 1.0 CA A:CA302 4.1 7.2 1.0 O A:HOH581 4.1 40.4 1.0 HB3 A:SER230 4.2 23.6 1.0 O A:HOH437 4.3 29.5 1.0 CA A:ARG231 4.4 15.7 1.0 O A:HOH554 4.4 44.8 1.0 HA A:ASN232 4.4 9.2 1.0 CA A:SER230 4.4 18.3 1.0 C A:ASN232 4.5 10.2 1.0 O A:HOH431 4.5 23.0 1.0 O A:SER230 4.5 14.2 1.0 OD1 A:ASP227 4.5 11.0 1.0 CB A:ASP233 4.5 10.7 1.0 N A:ASP233 4.5 10.1 1.0 HB2 A:ARG231 4.6 20.6 1.0 N A:ASN232 4.6 10.3 1.0 HA A:ASP233 4.7 10.8 1.0 O A:ASN232 4.7 13.4 1.0 H A:ASP233 4.7 12.1 1.0 CA A:ASN232 4.7 7.7 1.0 O A:HOH536 4.9 41.5 1.0 CA A:ASP233 4.9 9.0 1.0 H A:SER230 4.9 14.9 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