Cadmium in PDB 5t0r: Synaptotagmin 1 C2A Domain, Cadmium-Bound

The structure of Synaptotagmin 1 C2A Domain, Cadmium-Bound, PDB code: 5t0r was solved by A.B.Taylor, P.J.Hart, T.I.Igumenova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.07 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.064, 63.276, 76.143, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.9

The binding sites of Cadmium atom in the Synaptotagmin 1 C2A Domain, Cadmium-Bound (pdb code 5t0r). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Synaptotagmin 1 C2A Domain, Cadmium-Bound, PDB code: 5t0r:

Cadmium binding site 1 out of 1 in the Synaptotagmin 1 C2A Domain, Cadmium-Bound


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Synaptotagmin 1 C2A Domain, Cadmium-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:22.8 occ:1.00 OD2 A:ASP178 2.4 21.7 1.0 OD2 A:ASP172 2.4 25.5 1.0 OD1 A:ASP230 2.4 20.1 1.0 O A:PHE231 2.5 18.0 1.0 O A:HOH403 2.6 25.4 1.0 OD2 A:ASP230 2.6 24.5 1.0 CG A:ASP230 2.8 22.5 1.0 OD1 A:ASP172 2.9 28.3 1.0 CG A:ASP172 3.0 27.1 1.0 CG A:ASP178 3.3 22.4 1.0 C A:PHE231 3.6 23.9 1.0 CB A:ASP178 3.7 20.1 1.0 N A:ASP178 3.9 17.0 1.0 O A:HOH401 4.0 28.4 1.0 CB A:ASP230 4.3 18.3 1.0 OD2 A:ASP232 4.3 28.4 1.0 N A:PHE231 4.4 17.2 1.0 CA A:ASP178 4.4 18.5 1.0 OD1 A:ASP178 4.4 18.4 1.0 CB A:ASP232 4.4 22.1 1.0 N A:ASP232 4.5 21.4 1.0 CA A:ASP232 4.5 22.1 1.0 CB A:ASP172 4.5 23.6 1.0 CA A:PHE231 4.6 20.3 1.0 C A:ASP230 4.6 16.5 1.0 O A:HOH510 4.6 37.3 1.0 C A:SER177 4.6 21.7 1.0 O A:HOH521 4.7 38.0 1.0 CA A:SER177 4.8 21.9 1.0 O A:HOH513 4.9 36.5 1.0 CA A:ASP230 4.9 19.0 1.0 CG A:ASP232 4.9 24.8 1.0

S.Katti, S.B.Nyenhuis, B.Her, A.K.Srivastava, A.B.Taylor, P.J.Hart, D.S.Cafiso, T.I.Igumenova. Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions. Biochemistry V. 56 3283 2017.
ISSN: ISSN 1520-4995
PubMed: 28574251
DOI: 10.1021/ACS.BIOCHEM.7B00188