Calcium in PDB 5cch: Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)

The structure of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form), PDB code: 5cch was solved by Q.Zhou, M.Zhao, A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, W.I.Weis, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 3.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.073, 171.626, 146.942, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 28.9

The binding sites of Calcium atom in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) (pdb code 5cch). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form), PDB code: 5cch:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:0.2 occ:1.00 O E:TYR364 2.9 0.2 1.0 OD1 E:ASP363 2.9 0.7 1.0 OG E:SER308 3.0 0.6 1.0 OD1 E:ASP365 3.1 0.0 1.0 OD2 E:ASP365 3.2 0.8 1.0 CB E:ASP303 3.2 0.1 1.0 OD2 E:ASP309 3.3 0.9 1.0 CG E:ASP365 3.4 0.5 1.0 OD2 E:ASP363 3.4 0.1 1.0 OD2 E:ASP303 3.4 0.3 1.0 CG E:ASP363 3.5 0.3 1.0 CG E:ASP303 3.5 0.4 1.0 CA E:CA502 3.6 0.7 1.0 C E:TYR364 4.1 0.3 1.0 CG E:ASP309 4.1 0.5 1.0 O E:SER308 4.2 1.0 1.0 OD1 E:ASP309 4.2 0.1 1.0 CA E:ASP303 4.3 1.0 1.0 CB E:SER308 4.3 0.4 1.0 O E:MET302 4.4 0.5 1.0 OD1 E:ASP303 4.5 0.4 1.0 CB E:ASP365 4.5 0.7 1.0 CA E:ASP365 4.5 0.3 1.0 N E:ASP303 4.7 0.7 1.0 C E:SER308 4.7 0.1 1.0 C E:MET302 4.8 0.8 1.0 N E:ASP365 4.8 0.5 1.0 CA E:SER308 4.9 0.5 1.0 N E:SER308 4.9 0.5 1.0

Calcium binding site 2 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:0.7 occ:1.00 O E:MET302 2.1 0.5 1.0 OD2 E:ASP363 2.9 0.1 1.0 OD2 E:ASP365 3.0 0.8 1.0 OD1 E:ASP365 3.1 0.0 1.0 C E:MET302 3.2 0.8 1.0 CG E:ASP365 3.4 0.5 1.0 CA E:CA501 3.6 0.2 1.0 CA E:ASP303 3.9 1.0 1.0 N E:ASP303 3.9 0.7 1.0 CG E:ASP363 4.0 0.3 1.0 CB E:ASP303 4.1 0.1 1.0 CB E:MET302 4.2 0.4 1.0 CA E:MET302 4.4 0.2 1.0 OD1 E:ASP363 4.5 0.7 1.0 OD2 E:ASP371 4.6 0.5 1.0 CG E:ASP303 4.7 0.4 1.0 OD1 E:ASP303 4.8 0.4 1.0 CB E:ASP365 4.9 0.7 1.0

Calcium binding site 3 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca503 b:1.0 occ:1.00 O E:PHE231 2.6 0.4 1.0 OD2 E:ASP172 2.6 0.1 1.0 OD2 E:ASP178 2.9 0.7 1.0 OD1 E:ASP232 2.9 0.7 1.0 CG E:ASP172 3.2 0.3 1.0 CG E:ASP232 3.5 0.7 1.0 OD1 E:ASP172 3.5 0.6 1.0 C E:PHE231 3.7 0.3 1.0 OD1 E:ASP230 3.9 0.0 1.0 OD2 E:ASP232 3.9 0.5 1.0 CG E:ASP178 3.9 0.6 1.0 CA E:ASP232 3.9 0.5 1.0 CB E:ASP172 4.3 0.7 1.0 CB E:ASP232 4.3 1.0 1.0 CB E:ASP178 4.3 0.3 1.0 N E:ASP232 4.3 0.1 1.0 CG E:ASP230 4.7 0.3 1.0 OD2 E:ASP230 4.8 0.4 1.0 N E:ASP178 4.8 0.9 1.0 CA E:PHE231 4.9 0.5 1.0

Calcium binding site 4 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca501 b:0.3 occ:1.00 CA F:CA502 2.2 0.2 1.0 OD1 F:ASP172 2.4 0.1 1.0 OD2 F:ASP232 2.6 0.8 1.0 OD1 F:ASP232 2.6 0.8 1.0 OD1 F:ASP230 2.6 0.8 1.0 OD2 F:ASP230 2.8 0.3 1.0 CG F:ASP232 2.8 0.3 1.0 O F:PHE231 2.8 0.1 1.0 CG F:ASP230 2.9 0.1 1.0 CG F:ASP172 3.1 0.6 1.0 OD2 F:ASP172 3.1 0.5 1.0 C F:PHE231 3.8 0.0 1.0 CB F:ASP232 4.1 0.2 1.0 CB F:ASP230 4.2 0.1 1.0 CA F:ASP232 4.3 0.9 1.0 N F:ASP232 4.4 0.7 1.0 O F:ASP230 4.4 0.3 1.0 OD2 F:ASP178 4.4 0.3 1.0 C F:ASP230 4.4 0.3 1.0 CB F:ASP172 4.4 0.3 1.0 N F:PHE231 4.6 0.9 1.0 CA F:PHE231 4.8 0.5 1.0 CA F:ASP230 4.9 0.8 1.0 CA F:ASP172 4.9 0.4 1.0 N F:ASP178 5.0 0.3 1.0

Calcium binding site 5 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca502 b:0.2 occ:1.00 CA F:CA501 2.2 0.3 1.0 OD2 F:ASP178 2.4 0.3 1.0 OD2 F:ASP172 2.4 0.5 1.0 O F:PHE231 2.5 0.1 1.0 CG F:ASP172 3.1 0.6 1.0 OD1 F:ASP172 3.4 0.1 1.0 CG F:ASP178 3.4 0.6 1.0 OD1 F:ASP230 3.5 0.8 1.0 OD1 F:ASP232 3.6 0.8 1.0 C F:PHE231 3.8 0.0 1.0 CB F:ASP178 3.9 0.7 1.0 CG F:ASP232 4.0 0.3 1.0 N F:ASP178 4.2 0.3 1.0 OD2 F:ASP232 4.3 0.8 1.0 CB F:ASP172 4.3 0.3 1.0 CG F:ASP230 4.4 0.1 1.0 CA F:ASP232 4.4 0.9 1.0 OD1 F:ASP178 4.5 0.4 1.0 N F:ASP232 4.5 0.7 1.0 OD2 F:ASP230 4.5 0.3 1.0 CA F:ASP178 4.7 0.9 1.0 NH2 F:ARG199 4.7 0.2 1.0 CA F:PHE231 4.8 0.5 1.0 CB F:ASP232 4.8 0.2 1.0 N F:PHE231 4.9 0.9 1.0 C F:SER177 5.0 0.4 1.0

Calcium binding site 6 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca503 b:0.9 occ:1.00 O F:TYR364 2.4 0.0 1.0 OD2 F:ASP309 2.5 0.4 1.0 CG F:ASP309 3.1 0.2 1.0 CB F:ASP309 3.1 0.3 1.0 CA F:CA504 3.4 0.3 1.0 N F:ASP309 3.4 0.4 1.0 CD2 F:TYR364 3.4 0.2 1.0 C F:TYR364 3.5 0.8 1.0 CA F:ASP309 3.8 0.4 1.0 CB F:TYR364 4.1 0.7 1.0 C F:SER308 4.1 0.8 1.0 OD1 F:ASP309 4.1 0.3 1.0 CG F:TYR364 4.2 0.1 1.0 CA F:TYR364 4.2 0.3 1.0 CE2 F:TYR364 4.3 0.6 1.0 OD1 F:ASP363 4.3 0.9 1.0 O F:ASP309 4.3 0.6 1.0 OD1 F:ASP365 4.4 0.7 1.0 N F:ASP365 4.4 0.8 1.0 CA F:SER308 4.5 0.4 1.0 C F:ASP309 4.6 0.5 1.0 N F:TYR364 4.6 0.8 1.0 CA F:ASP365 4.6 0.4 1.0 O F:SER308 4.9 0.3 1.0

Calcium binding site 7 out of 7 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Short Unit Cell Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca504 b:0.3 occ:1.00 OD2 F:ASP363 2.5 0.7 1.0 OD1 F:ASP363 2.6 0.9 1.0 OD1 F:ASP365 2.9 0.7 1.0 CG F:ASP363 2.9 0.2 1.0 O F:TYR364 3.2 0.0 1.0 CA F:CA503 3.4 0.9 1.0 CG F:ASP365 4.0 0.5 1.0 CA F:SER308 4.2 0.4 1.0 C F:TYR364 4.3 0.8 1.0 OG F:SER308 4.3 0.4 1.0 CB F:SER308 4.4 0.7 1.0 N F:ASP309 4.4 0.4 1.0 CB F:ASP363 4.4 0.6 1.0 OD2 F:ASP365 4.5 0.3 1.0 C F:SER308 4.8 0.8 1.0 N F:TYR364 4.9 0.8 1.0 C F:ASP363 4.9 0.3 1.0

Q.Zhou, Y.Lai, T.Bacaj, M.Zhao, A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, A.S.Brewster, N.K.Sauter, A.E.Cohen, S.M.Soltis, R.Alonso-Mori, M.Chollet, H.T.Lemke, R.A.Pfuetzner, U.B.Choi, W.I.Weis, J.Diao, T.C.Sudhof, A.T.Brunger. Architecture of the Synaptotagmin-Snare Machinery For Neuronal Exocytosis. Nature V. 525 62 2015.
ISSN: ESSN 1476-4687
PubMed: 26280336
DOI: 10.1038/NATURE14975