Calcium in PDB 6fgd: 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;

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

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

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Gephyrin E Domain in Complex with Artemether, PDB code: 6fgd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Gephyrin E Domain in Complex with Artemether


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca801 b:20.7 occ:1.00 O2A A:ADP829 2.3 20.3 1.0 O A:HOH1012 2.3 18.8 1.0 O A:HOH1023 2.4 32.2 1.0 O A:HOH1076 2.4 20.4 1.0 O A:HOH1044 2.4 16.8 1.0 O A:HOH966 2.4 22.2 1.0 O A:HOH1105 2.4 20.2 1.0 PA A:ADP829 3.5 20.7 1.0 H A:GLY573 3.5 21.9 1.0 O1A A:ADP829 3.9 21.1 1.0 HA2 A:GLY507 4.0 21.2 1.0 O5' A:ADP829 4.0 19.5 1.0 H2' A:ADP829 4.0 21.2 1.0 HA3 A:GLY507 4.1 21.2 1.0 H8 A:ADP829 4.1 19.1 1.0 OE2 A:GLU509 4.1 20.5 1.0 N A:GLY573 4.2 18.3 1.0 HA2 A:GLY573 4.2 24.3 1.0 OD1 A:ASP549 4.2 23.5 1.0 CA A:CA802 4.3 29.4 1.0 OD1 A:ASP580 4.3 33.4 1.0 OE1 A:GLU509 4.3 18.8 1.0 O A:THR506 4.5 18.0 1.0 HA3 A:GLY572 4.5 20.1 1.0 OD2 A:ASP549 4.5 22.3 1.0 CA A:GLY507 4.5 17.7 1.0 CA A:GLY573 4.6 20.2 1.0 CD A:GLU509 4.7 19.4 1.0 CG A:ASP549 4.8 23.0 1.0 HA2 A:GLY572 4.8 20.1 1.0 O3A A:ADP829 4.8 22.7 1.0 HA3 A:GLY573 4.8 24.3 1.0 CA A:GLY572 5.0 16.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Gephyrin E Domain in Complex with Artemether


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Gephyrin E Domain in Complex with Artemether within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:29.4 occ:1.00 O1A A:ADP829 2.2 21.1 1.0 O A:HOH1144 2.3 32.9 1.0 O1B A:ADP829 2.4 28.4 1.0 O A:HOH1023 2.4 32.2 1.0 OD2 A:ASP580 2.7 32.8 1.0 OD1 A:ASP580 2.8 33.4 1.0 CG A:ASP580 3.1 32.0 1.0 HB2 A:SER575 3.2 37.3 1.0 PA A:ADP829 3.3 20.7 1.0 O2A A:ADP829 3.6 20.3 1.0 PB A:ADP829 3.6 27.1 1.0 O3A A:ADP829 3.9 22.7 1.0 H A:SER575 3.9 29.7 1.0 HA2 A:GLY573 4.0 24.3 1.0 H A:GLY573 4.0 21.9 1.0 HA3 A:GLY577 4.1 49.2 1.0 O A:HOH976 4.1 42.1 1.0 O A:HOH1190 4.1 36.2 1.0 O A:HOH966 4.1 22.2 1.0 CB A:SER575 4.2 31.1 1.0 H A:GLY577 4.2 52.5 0.5 H A:GLY577 4.2 52.5 0.5 O3B A:ADP829 4.3 28.7 1.0 CA A:CA801 4.3 20.7 1.0 O5' A:ADP829 4.6 19.5 1.0 CB A:ASP580 4.6 31.7 1.0 HG A:SER575 4.6 38.8 1.0 H5'2 A:ADP829 4.6 22.1 1.0 HB3 A:SER575 4.7 37.3 1.0 N A:SER575 4.7 24.7 1.0 N A:GLY573 4.7 18.3 1.0 OG A:SER575 4.7 32.3 1.0 CA A:GLY573 4.8 20.2 1.0 O2B A:ADP829 4.8 30.5 1.0 H A:VAL574 4.9 25.6 1.0 N A:GLY577 4.9 43.7 1.0 O A:HOH1076 4.9 20.4 1.0 HB3 A:ASP580 4.9 38.1 1.0 CA A:GLY577 4.9 41.0 1.0 CA A:SER575 4.9 29.3 1.0

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