Calcium in PDB 7u4q: Human Synaptotagmin-1 C2A Y181F CA2+ Bound

The structure of Human Synaptotagmin-1 C2A Y181F CA2+ Bound, PDB code: 7u4q was solved by M.J.Dominguez, S.Karmakar, K.L.Fuson, R.B.Sutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.06 / 1.56
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	99.81, 99.81, 77.31, 90, 90, 90
R / Rfree (%)	16.4 / 18.9

The binding sites of Calcium atom in the Human Synaptotagmin-1 C2A Y181F CA2+ Bound (pdb code 7u4q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Synaptotagmin-1 C2A Y181F CA2+ Bound, PDB code: 7u4q:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Synaptotagmin-1 C2A Y181F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Synaptotagmin-1 C2A Y181F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.8 occ:0.71 O A:HOH473 2.3 45.5 1.0 OD1 A:ASP233 2.4 52.5 1.0 OD2 A:ASP179 2.5 40.5 1.0 OD2 A:ASP173 2.5 34.3 0.7 O A:PHE232 2.5 41.6 0.0 OD1 A:ASP173 2.6 36.8 0.7 O A:PHE232 2.6 45.3 1.0 OD1 A:ASP231 2.6 33.5 1.0 CG A:ASP173 2.9 35.2 0.7 HB2 A:ASP179 3.1 30.4 1.0 CG A:ASP231 3.3 32.4 1.0 OD2 A:ASP231 3.3 34.8 1.0 CG A:ASP179 3.3 32.8 1.0 H A:ASP179 3.5 28.6 1.0 HA A:ASP233 3.6 47.9 1.0 CG A:ASP233 3.7 54.2 1.0 C A:PHE232 3.7 41.0 0.0 CA A:CA302 3.7 36.3 0.6 C A:PHE232 3.7 40.1 1.0 CB A:ASP179 3.7 30.4 1.0 HB2 A:ASP173 3.9 43.1 0.3 HB3 A:ASP173 3.9 43.1 0.3 N A:ASP179 4.0 28.6 1.0 O A:HOH401 4.1 49.6 1.0 HA A:SER178 4.2 27.6 1.0 CA A:ASP233 4.3 47.9 1.0 OD1 A:ASP179 4.3 33.5 1.0 CB A:ASP173 4.4 43.1 0.3 CB A:ASP173 4.4 35.2 0.7 N A:ASP233 4.4 43.5 1.0 HB3 A:ASP179 4.5 30.4 1.0 CA A:ASP179 4.5 28.8 1.0 OD2 A:ASP233 4.5 62.8 1.0 HD1 A:PHE232 4.5 40.5 0.0 N A:PHE232 4.6 34.6 1.0 CB A:ASP233 4.6 50.6 1.0 N A:PHE232 4.6 37.2 0.0 HB3 A:ASP173 4.7 43.1 0.7 C A:SER178 4.7 27.6 1.0 H A:PHE232 4.7 37.2 1.0 CB A:ASP231 4.7 35.2 1.0 CA A:PHE232 4.8 38.1 1.0 CA A:PHE232 4.8 39.5 0.0 C A:ASP231 4.8 34.7 1.0 HB3 A:PHE232 4.8 39.9 1.0 H A:PHE232 4.8 37.2 0.0 HB2 A:ASP173 4.8 43.1 0.7 HB3 A:PHE232 4.9 39.9 0.0 CA A:SER178 4.9 27.6 1.0 O A:HOH455 4.9 50.5 1.0

Calcium binding site 2 out of 3 in the Human Synaptotagmin-1 C2A Y181F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Synaptotagmin-1 C2A Y181F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:36.3 occ:0.60 O A:HOH455 2.1 50.5 1.0 OD2 A:ASP231 2.3 34.8 1.0 OD1 A:ASP173 2.5 36.8 0.7 OD2 A:ASP233 2.6 62.8 1.0 OD1 A:ASP233 2.7 52.5 1.0 OD2 A:ASP239 2.7 46.9 1.0 O A:LEU172 2.8 43.3 1.0 CG A:ASP233 3.0 54.2 1.0 CG A:ASP231 3.4 32.4 1.0 HB3 A:LEU172 3.5 35.9 1.0 C A:LEU172 3.6 37.2 1.0 CG A:ASP173 3.7 35.2 0.7 CA A:CA301 3.7 35.8 0.7 HB2 A:LEU172 3.8 35.9 1.0 HA A:ASP173 3.8 42.1 0.7 CG A:ASP239 3.9 67.8 1.0 HA A:ASP173 4.0 42.1 0.3 CB A:LEU172 4.1 35.9 1.0 OD1 A:ASP231 4.1 33.5 1.0 HB2 A:ASP239 4.2 59.7 1.0 HB2 A:ASP173 4.2 43.1 0.3 N A:ASP173 4.3 34.2 0.7 N A:ASP173 4.3 39.5 0.3 HB3 A:ASP231 4.3 35.2 1.0 CA A:CA303 4.4 59.4 0.6 HB3 A:ASP173 4.4 43.1 0.3 OD2 A:ASP173 4.4 34.3 0.7 CA A:ASP173 4.4 34.5 0.7 CA A:ASP173 4.5 42.1 0.3 CA A:LEU172 4.5 34.8 1.0 O A:HOH473 4.5 45.5 1.0 CB A:ASP231 4.5 35.2 1.0 CB A:ASP233 4.6 50.6 1.0 CB A:ASP173 4.6 43.1 0.3 CB A:ASP173 4.6 35.2 0.7 CB A:ASP239 4.6 59.7 1.0 OD1 A:ASP239 4.7 67.1 1.0 HB3 A:ASP233 4.9 50.6 1.0 O A:HOH471 5.0 61.2 1.0 HB2 A:ASP233 5.0 50.6 1.0 H A:ASP173 5.0 39.5 0.7

Calcium binding site 3 out of 3 in the Human Synaptotagmin-1 C2A Y181F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Synaptotagmin-1 C2A Y181F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:59.4 occ:0.57 O A:HOH471 2.4 61.2 1.0 OD2 A:ASP233 2.4 62.8 1.0 OG A:SER236 2.6 84.3 1.0 O A:LYS237 2.8 66.6 1.0 OD1 A:ASP239 2.9 67.1 1.0 HB2 A:SER236 3.2 83.2 1.0 OD2 A:ASP239 3.3 46.9 1.0 CG A:ASP239 3.3 67.8 1.0 CG A:ASP233 3.5 54.2 1.0 CB A:SER236 3.5 83.2 1.0 HB2 A:ASP233 3.5 50.6 1.0 CB A:ASP233 3.8 50.6 1.0 HB3 A:ASP233 3.8 50.6 1.0 C A:LYS237 4.0 71.2 1.0 HB3 A:SER236 4.1 83.2 1.0 N A:LYS237 4.3 90.5 1.0 H A:ASP239 4.3 54.0 1.0 C A:SER236 4.3 90.8 1.0 CA A:CA302 4.4 36.3 0.6 H A:LYS237 4.4 90.5 1.0 HA A:HIS238 4.4 57.9 1.0 N A:ASP239 4.4 54.0 1.0 CA A:SER236 4.5 90.0 1.0 OD1 A:ASP233 4.6 52.5 1.0 CB A:ASP239 4.6 59.7 1.0 O A:HOH455 4.6 50.5 1.0 O A:SER236 4.7 71.1 1.0 CA A:LYS237 4.8 85.3 1.0 HA A:ASP239 4.8 49.0 1.0 C A:HIS238 4.8 54.6 1.0 HB2 A:ASP239 4.9 59.7 1.0 CA A:ASP239 4.9 49.0 1.0 HB3 A:LYS237 4.9 89.6 1.0 CA A:HIS238 4.9 57.9 1.0 N A:HIS238 4.9 65.2 1.0

M.J.Dominguez, S.Karmakar, K.L.Fuson, R.B.Sutton. Human Synaptotagmin-1 C2A Y181F CA2+ Bound To Be Published.