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Sodium in PDB 6fgd: Crystal Structure of Gephyrin E Domain in Complex with Artemether

Enzymatic activity of Crystal Structure of Gephyrin E Domain in Complex with Artemether

All present enzymatic activity of Crystal Structure of Gephyrin E Domain in Complex with Artemether:
2.10.1.1; 2.7.7.75;

Protein crystallography data

The structure of Crystal Structure of Gephyrin E Domain in Complex with Artemether, PDB code: 6fgd was solved by V.B.Kasaragod, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.58 / 1.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.152, 99.455, 111.965, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.8

Other elements in 6fgd:

The structure of Crystal Structure of Gephyrin E Domain in Complex with Artemether also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Gephyrin E Domain in Complex with Artemether (pdb code 6fgd). 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 Gephyrin E Domain in Complex with Artemether, PDB code: 6fgd:

Sodium binding site 1 out of 1 in 6fgd

Go back to Sodium Binding Sites List in 6fgd
Sodium binding site 1 out of 1 in the Crystal Structure of Gephyrin E Domain in Complex with Artemether


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 Gephyrin E Domain in Complex with Artemether within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na828

b:32.6
occ:1.00
HG A:SER630 2.1 28.6 1.0
O A:HOH1310 2.5 51.8 1.0
O A:HOH1191 2.8 32.5 1.0
OG A:SER630 2.9 23.9 1.0
HB3 A:PRO625 2.9 22.7 0.0
HB3 A:PRO625 3.0 22.4 1.0
O A:HOH1140 3.0 22.7 1.0
H A:GLY604 3.1 25.1 1.0
HB3 A:SER630 3.2 23.9 1.0
HD2 A:PRO606 3.2 25.2 1.0
HB2 A:PRO625 3.2 22.4 1.0
HB2 A:PRO625 3.3 22.7 0.0
CB A:SER630 3.4 19.9 1.0
CB A:PRO625 3.5 18.9 0.0
CB A:PRO625 3.5 18.7 1.0
HB2 A:SER630 3.5 23.9 1.0
HD3 A:PRO606 3.6 25.2 1.0
HG2 A:PRO625 3.6 23.3 0.0
HA2 A:GLY604 3.6 25.4 1.0
HB3 A:ASN627 3.6 26.5 1.0
HG2 A:PRO625 3.7 24.6 1.0
N A:GLY604 3.8 20.9 1.0
CD A:PRO606 3.8 21.0 1.0
H A:LEU605 3.9 24.7 1.0
CG A:PRO625 3.9 19.4 0.0
CG A:PRO625 4.0 20.5 1.0
HB2 A:PRO603 4.0 28.8 1.0
HG3 A:PRO625 4.0 23.3 0.0
HG3 A:PRO606 4.1 24.5 1.0
HG3 A:PRO625 4.1 24.6 1.0
CA A:GLY604 4.1 21.1 1.0
O A:HOH1281 4.2 54.0 1.0
CG A:PRO606 4.3 20.4 1.0
HG2 A:PRO606 4.3 24.5 1.0
N A:LEU605 4.3 20.6 1.0
HB2 A:ASN627 4.4 26.5 1.0
H A:ASN627 4.4 19.9 1.0
CB A:ASN627 4.4 22.1 1.0
C A:GLY604 4.6 20.4 1.0
O A:HOH1288 4.7 32.1 1.0
O A:HOH1126 4.7 52.5 1.0
CB A:PRO603 4.8 24.0 1.0
C A:PRO603 4.9 22.3 1.0
CA A:PRO625 4.9 18.1 0.0
CA A:PRO625 4.9 16.3 1.0
CA A:SER630 4.9 17.8 1.0
O3B A:ADP829 4.9 28.7 1.0
HA A:PRO603 5.0 26.0 1.0
HA3 A:GLY604 5.0 25.4 1.0

Reference:

V.B.Kasaragod, T.J.Hausrat, N.Schaefer, M.Kuhn, N.R.Christensen, I.Tessmer, H.M.Maric, K.L.Madsen, C.Sotriffer, C.Villmann, M.Kneussel, H.Schindelin. Elucidating the Molecular Basis For Inhibitory Neurotransmission Regulation By Artemisinins. Neuron V. 101 673 2019.
ISSN: ISSN 1097-4199
PubMed: 30704910
DOI: 10.1016/J.NEURON.2019.01.001
Page generated: Tue Dec 15 12:15:09 2020

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