Calcium in PDB 4v11: Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84

The structure of Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84, PDB code: 4v11 was solved by N.Zhang, S.L.Gordon, M.J.Fritsch, N.Esoof, D.Campbell, R.Gourlay, S.Velupillai, T.Macartney, M.Peggie, D.M.F.Vanaalten, M.A.Cousin, D.R.Alessi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.279 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.049, 41.432, 48.014, 90.00, 96.59, 90.00
R / Rfree (%)	15.12 / 19.56

The binding sites of Calcium atom in the Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84 (pdb code 4v11). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84, PDB code: 4v11:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1423 b:6.1 occ:1.00 O A:TYR365 2.3 7.2 1.0 OD1 A:ASP366 2.3 8.8 1.0 OD1 A:ASP364 2.4 5.7 1.0 OD2 A:ASP310 2.4 8.9 1.0 OD2 A:ASP304 2.4 8.3 1.0 O A:HOH2024 2.4 9.0 1.0 OD1 A:ASP304 2.6 5.6 1.0 CG A:ASP304 2.8 7.4 1.0 OD2 A:ASP364 3.0 8.0 1.0 CG A:ASP364 3.0 7.2 1.0 C A:TYR365 3.4 8.0 1.0 CG A:ASP310 3.4 9.1 1.0 CG A:ASP366 3.6 13.2 1.0 CA A:CA1424 3.7 7.5 1.0 CB A:ASP310 3.9 4.4 1.0 CA A:ASP366 4.1 8.0 1.0 N A:ASP310 4.1 4.3 1.0 N A:ASP366 4.1 6.7 1.0 O A:HOH2025 4.2 11.7 1.0 CB A:ASP304 4.3 7.7 1.0 N A:TYR365 4.4 4.8 1.0 C A:ASP364 4.4 7.2 1.0 CB A:ASP366 4.4 7.5 1.0 O A:HOH2086 4.4 21.0 1.0 OD2 A:ASP366 4.5 11.1 1.0 CB A:ASP364 4.5 5.5 1.0 CA A:TYR365 4.5 6.2 1.0 OD1 A:ASP310 4.5 6.4 1.0 O A:ASP364 4.6 5.2 1.0 CA A:ASP310 4.6 4.3 1.0 C A:SER309 4.7 4.5 1.0 O A:HOH2104 4.7 32.6 1.0 CA A:SER309 4.8 5.0 1.0 O A:HOH2081 4.9 16.6 1.0 CA A:ASP364 4.9 5.5 1.0

Calcium binding site 2 out of 3 in the Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1424 b:7.5 occ:1.00 OD2 A:ASP364 2.3 8.0 1.0 OD1 A:ASP304 2.4 5.6 1.0 O A:HOH2023 2.4 18.7 1.0 OD2 A:ASP366 2.5 11.1 1.0 O A:MET303 2.5 10.0 1.0 O A:HOH2022 2.5 15.3 1.0 OD1 A:ASP366 2.6 8.8 1.0 O A:HOH2081 2.8 16.6 1.0 CG A:ASP366 2.9 13.2 1.0 C A:MET303 3.5 8.1 1.0 CG A:ASP364 3.5 7.2 1.0 CG A:ASP304 3.5 7.4 1.0 O A:HOH2083 3.6 4.7 1.0 CA A:CA1423 3.7 6.1 1.0 CA A:ASP304 4.1 6.2 1.0 CB A:MET303 4.1 9.4 1.0 N A:ASP304 4.2 8.3 1.0 OD1 A:ASP364 4.2 5.7 1.0 OD2 A:ASP304 4.4 8.3 1.0 CB A:ASP366 4.4 7.5 1.0 CB A:ASP304 4.4 7.7 1.0 CA A:MET303 4.5 6.4 1.0 CB A:ASP364 4.5 5.5 1.0 OD2 A:ASP372 4.5 17.2 1.0 O A:HOH2084 4.6 14.3 1.0 O A:HOH2026 4.7 21.8 1.0 O A:HOH2024 4.8 9.0 1.0 O A:ASP364 4.8 5.2 1.0 O A:HOH2088 4.9 27.6 1.0 O A:LYS370 5.0 6.0 1.0

Calcium binding site 3 out of 3 in the Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Synaptotagmin-1 with SV2A Peptide Phosphorylated at THR84 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1425 b:29.2 occ:1.00 O A:HOH2042 2.7 8.0 1.0 O A:HOH2138 2.7 9.8 1.0 O A:HOH2137 2.8 25.2 1.0 N A:LYS326 3.2 3.7 1.0 O A:LYS326 3.5 8.7 1.0 CA A:LYS325 3.7 4.0 1.0 CG A:LYS326 3.8 4.8 1.0 C A:LYS325 3.9 5.2 1.0 CB A:LYS325 4.1 5.3 1.0 CA A:LYS326 4.2 4.1 1.0 C A:LYS326 4.2 10.0 1.0 CD A:LYS325 4.3 10.2 1.0 CB A:LYS326 4.6 6.6 1.0 O A:HOH2039 4.6 23.7 1.0 OD2 B:ASP82 4.7 10.8 1.0 O A:LEU324 4.8 7.5 1.0 CG A:LYS325 4.8 5.5 1.0 N A:LYS325 4.9 6.3 1.0 CE A:LYS326 4.9 7.0 1.0 CD A:LYS326 5.0 7.7 1.0

N.Zhang, S.L.Gordon, M.J.Fritsch, N.Esoof, D.G.Campbell, R.Gourlay, S.Velupillai, T.Macartney, M.Peggie, D.M.F.Van Aalten, M.A.Cousin, D.R.Alessi. Phosphorylation of Synaptic Vesicle Protein 2A at THR84 By Casein Kinase 1 Family Kinases Controls the Specific Retrieval of Synaptotagmin-1. J.Neurosci. V. 35 2492 2015.
ISSN: ISSN 0270-6474
PubMed: 25673844
DOI: 10.1523/JNEUROSCI.4248-14.2015