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Sodium in PDB 7a1r: Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)

Protein crystallography data

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r was solved by G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.908, 57.532, 84.57, 90, 90, 90
R / Rfree (%) 17 / 19.1

Other elements in 7a1r:

The structure of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) (pdb code 7a1r). 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 Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt), PDB code: 7a1r:

Sodium binding site 1 out of 1 in 7a1r

Go back to Sodium Binding Sites List in 7a1r
Sodium binding site 1 out of 1 in the Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the C2B Domain of Trypanosoma Brucei Extended Synaptotagmin (E-Syt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:45.8
occ:1.00
OG A:SER586 3.7 14.1 0.5
O A:HOH746 3.8 35.8 1.0
CB A:GLN483 3.8 17.2 1.0
NH2 A:ARG574 3.8 64.9 1.0
OE1 A:GLN483 3.9 22.4 1.0
CD A:GLN483 3.9 21.4 1.0
CZ A:ARG574 4.1 62.0 1.0
NE2 A:GLN483 4.1 19.5 1.0
NE A:ARG574 4.2 56.1 1.0
CG A:GLN483 4.5 20.8 1.0
CB A:GLU588 4.5 23.4 1.0
C A:LEU587 4.6 21.9 1.0
O A:LEU587 4.6 23.8 1.0
CG A:ARG574 4.7 47.5 1.0
N A:GLU588 4.7 18.2 1.0
O A:HOH710 4.7 43.4 1.0
NH1 A:ARG574 4.8 52.0 1.0
N A:LEU587 4.9 15.7 1.0
C A:SER586 5.0 14.6 1.0

Reference:

E.Stepinac, N.Landrein, D.Skwarzynska, P.Wojcik, J.Lesigang, I.Lucic, C.Y.He, M.Bonhivers, D.R.Robinson, G.Dong. Structural Studies of the Shortest Extended Synaptotagmin with Only Two C2 Domains From Trypanosoma Brucei . Iscience V. 24 02422 2021.
ISSN: ESSN 2589-0042
PubMed: 33997700
DOI: 10.1016/J.ISCI.2021.102422
Page generated: Mon Jul 12 15:54:42 2021

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