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Sodium 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:

Cadmium (Cd) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Synaptotagmin 1 C2B Domain, Cadmium-Bound (pdb code 5t0s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Synaptotagmin 1 C2B Domain, Cadmium-Bound, PDB code: 5t0s:

Sodium binding site 1 out of 1 in 5t0s

Go back to Sodium Binding Sites List in 5t0s
Sodium binding site 1 out of 1 in the Synaptotagmin 1 C2B Domain, Cadmium-Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Synaptotagmin 1 C2B Domain, Cadmium-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:17.4
occ:1.00
O A:HOH779 2.5 46.9 1.0
OE2 A:GLU386 2.7 12.8 1.0
O A:HOH730 2.8 11.2 1.0
OG1 A:THR383 2.9 15.7 1.0
O A:HOH761 3.0 24.3 1.0
O A:HOH642 3.1 36.3 1.0
O A:THR383 3.1 9.3 1.0
CD A:GLU386 3.7 10.7 1.0
O A:HOH666 3.7 21.2 1.0
C A:THR383 3.7 9.3 1.0
CG A:GLU386 4.0 8.3 1.0
O A:HOH671 4.1 24.8 1.0
N A:THR383 4.1 9.3 1.0
CB A:GLU386 4.1 9.4 1.0
CB A:THR383 4.1 12.2 1.0
O A:HOH713 4.2 12.3 1.0
CA A:THR383 4.2 10.1 1.0
O A:HOH781 4.3 12.2 1.0
O A:HOH636 4.6 14.3 1.0
N A:GLY384 4.6 11.2 1.0
O A:HOH778 4.7 37.4 1.0
N A:GLU386 4.8 9.6 1.0
OE1 A:GLU386 4.8 11.8 1.0
O A:HOH790 4.9 12.1 1.0
CA A:GLY384 4.9 11.3 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: Tue Dec 15 11:35:06 2020

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