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Cadmium in PDB 5t0s: Synaptotagmin 1 C2B Domain, Cadmium-Bound

Protein crystallography data

The structure of Synaptotagmin 1 C2B Domain, Cadmium-Bound, PDB code: 5t0s 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) 36.54 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.992, 41.948, 80.657, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.8

Other elements in 5t0s:

The structure of Synaptotagmin 1 C2B Domain, Cadmium-Bound also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Synaptotagmin 1 C2B Domain, Cadmium-Bound (pdb code 5t0s). 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 C2B Domain, Cadmium-Bound, PDB code: 5t0s:

Cadmium binding site 1 out of 1 in 5t0s

Go back to Cadmium Binding Sites List in 5t0s
Cadmium binding site 1 out of 1 in the Synaptotagmin 1 C2B 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 C2B Domain, Cadmium-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:17.5
occ:0.46
O A:HOH695 2.3 32.0 1.0
OD1 A:ASP363 2.5 17.0 1.0
O A:TYR364 2.6 19.3 1.0
OD2 A:ASP309 2.7 24.6 1.0
OD2 A:ASP303 2.7 39.9 1.0
OD2 A:ASP363 2.8 25.1 1.0
OD1 A:ASP303 2.8 38.4 1.0
CG A:ASP363 3.0 18.6 1.0
CG A:ASP303 3.1 38.8 1.0
CG A:ASP309 3.4 20.4 1.0
C A:TYR364 3.6 20.3 1.0
CB A:ASP309 3.8 19.3 1.0
N A:ASP309 3.9 17.9 1.0
CA A:ASP365 4.1 31.1 1.0
CB A:ASP365 4.3 34.9 1.0
N A:ASP365 4.3 23.9 1.0
O A:HOH678 4.4 38.6 1.0
OD1 A:ASP309 4.4 20.2 1.0
OD1 A:ASP365 4.4 38.3 1.0
CB A:ASP363 4.4 13.3 1.0
N A:TYR364 4.5 13.8 1.0
CA A:ASP309 4.5 16.5 1.0
CB A:ASP303 4.6 36.4 1.0
C A:ASP363 4.6 14.6 1.0
C A:SER308 4.7 18.8 1.0
CA A:TYR364 4.7 16.6 1.0
CG A:ASP365 4.8 37.2 1.0
O A:HOH627 4.8 32.1 1.0
CA A:SER308 4.8 17.7 1.0
CA A:ASP363 5.0 13.0 1.0

Reference:

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
Page generated: Sat Dec 12 08:27:38 2020

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