Calcium in PDB 1byn: Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I

The binding sites of Calcium atom in the Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I (pdb code 1byn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I, PDB code: 1byn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca272 b:0.0 occ:1.00 HA A:ASP232 2.6 0.0 1.0 O A:PHE231 2.8 0.0 1.0 OD1 A:ASP172 2.8 0.0 1.0 OD1 A:ASP230 2.8 0.0 1.0 OD2 A:ASP178 2.8 0.0 1.0 OD1 A:ASP232 2.8 0.0 1.0 OD2 A:ASP172 2.8 0.0 1.0 CG A:ASP172 3.2 0.0 1.0 CG A:ASP232 3.5 0.0 1.0 CA A:ASP232 3.6 0.0 1.0 C A:PHE231 3.6 0.0 1.0 HB2 A:ASP178 3.6 0.0 1.0 CA A:CA273 3.7 0.0 1.0 CG A:ASP230 3.8 0.0 1.0 CG A:ASP178 3.9 0.0 1.0 N A:ASP232 3.9 0.0 1.0 CB A:ASP232 4.1 0.0 1.0 H A:ASP178 4.2 0.0 1.0 OD2 A:ASP230 4.2 0.0 1.0 OD2 A:ASP232 4.2 0.0 1.0 CB A:ASP178 4.3 0.0 1.0 HB3 A:ASP232 4.5 0.0 1.0 CB A:ASP172 4.6 0.0 1.0 N A:ASP178 4.7 0.0 1.0 C A:ASP232 4.7 0.0 1.0 HA A:SER177 4.8 0.0 1.0 N A:PHE231 4.8 0.0 1.0 H A:ASP232 4.8 0.0 1.0 CA A:PHE231 4.8 0.0 1.0 HZ1 A:LYS200 4.9 0.0 1.0 H A:PHE231 4.9 0.0 1.0 OD1 A:ASP178 4.9 0.0 1.0 HB2 A:ASP172 5.0 0.0 1.0

Calcium binding site 2 out of 3 in the Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca273 b:0.0 occ:1.00 HB2 A:LEU171 2.7 0.0 1.0 HB2 A:ASP238 2.8 0.0 1.0 O A:LEU171 2.8 0.0 1.0 OD1 A:ASP232 2.8 0.0 1.0 OD2 A:ASP238 2.8 0.0 1.0 OD1 A:ASP172 2.8 0.0 1.0 OD2 A:ASP232 2.8 0.0 1.0 OD2 A:ASP230 2.8 0.0 1.0 CG A:ASP230 3.0 0.0 1.0 HB3 A:ASP230 3.0 0.0 1.0 CG A:ASP232 3.2 0.0 1.0 OD1 A:ASP230 3.3 0.0 1.0 HB3 A:LEU171 3.4 0.0 1.0 CB A:LEU171 3.5 0.0 1.0 CB A:ASP230 3.5 0.0 1.0 C A:LEU171 3.6 0.0 1.0 CG A:ASP238 3.6 0.0 1.0 CB A:ASP238 3.6 0.0 1.0 CG A:ASP172 3.7 0.0 1.0 CA A:CA272 3.7 0.0 1.0 H A:ASP238 4.0 0.0 1.0 HB2 A:ASP230 4.1 0.0 1.0 OD2 A:ASP172 4.1 0.0 1.0 HD11 A:LEU171 4.1 0.0 1.0 CA A:LEU171 4.2 0.0 1.0 HB3 A:ASP238 4.2 0.0 1.0 N A:ASP172 4.5 0.0 1.0 HA A:ASP172 4.6 0.0 1.0 CA A:CA274 4.6 0.0 1.0 CB A:ASP232 4.7 0.0 1.0 N A:ASP238 4.7 0.0 1.0 HD12 A:LEU171 4.7 0.0 1.0 CD1 A:LEU171 4.7 0.0 1.0 CA A:ASP238 4.7 0.0 1.0 CG A:LEU171 4.7 0.0 1.0 OD1 A:ASP238 4.8 0.0 1.0 CB A:ASP172 4.8 0.0 1.0 O A:ASP238 4.8 0.0 1.0 O A:ASP230 4.8 0.0 1.0 CA A:ASP230 4.8 0.0 1.0 H A:LEU171 4.9 0.0 1.0 CA A:ASP172 4.9 0.0 1.0 C A:ASP230 4.9 0.0 1.0 HA A:ASP232 5.0 0.0 1.0 HA A:SER177 5.0 0.0 1.0

Calcium binding site 3 out of 3 in the Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Solution Structure of the Calcium-Bound First C2-Domain of Synaptotagmin I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca274 b:0.0 occ:1.00 HG A:SER235 2.4 0.0 1.0 O A:LYS236 2.8 0.0 1.0 OD2 A:ASP238 2.8 0.0 1.0 OD1 A:ASP238 2.8 0.0 1.0 OD2 A:ASP232 2.8 0.0 1.0 OG A:SER235 2.8 0.0 1.0 CG A:ASP232 3.0 0.0 1.0 CG A:ASP238 3.1 0.0 1.0 HB2 A:ASP232 3.4 0.0 1.0 HB3 A:ASP232 3.4 0.0 1.0 CB A:ASP232 3.6 0.0 1.0 OD1 A:ASP232 3.6 0.0 1.0 H A:ASP238 3.8 0.0 1.0 C A:LYS236 3.9 0.0 1.0 HB2 A:SER235 4.0 0.0 1.0 CB A:SER235 4.0 0.0 1.0 HA A:HIS237 4.1 0.0 1.0 N A:ASP238 4.4 0.0 1.0 CB A:ASP238 4.4 0.0 1.0 H A:LYS236 4.5 0.0 1.0 N A:LYS236 4.5 0.0 1.0 CA A:CA273 4.6 0.0 1.0 HB2 A:ASP238 4.7 0.0 1.0 C A:SER235 4.7 0.0 1.0 HB3 A:SER235 4.7 0.0 1.0 CA A:HIS237 4.8 0.0 1.0 N A:HIS237 4.8 0.0 1.0 CA A:LYS236 4.8 0.0 1.0 HB2 A:LYS236 4.9 0.0 1.0 CA A:ASP238 4.9 0.0 1.0 C A:HIS237 4.9 0.0 1.0 CA A:SER235 5.0 0.0 1.0

X.Shao, I.Fernandez, T.C.Sudhof, J.Rizo. Solution Structures of the CA2+-Free and CA2+-Bound C2A Domain of Synaptotagmin I: Does CA2+ Induce A Conformational Change? Biochemistry V. 37 16106 1998.
ISSN: ISSN 0006-2960
PubMed: 9819203
DOI: 10.1021/BI981789H