Magnesium in PDB 9dkm: Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.

The binding sites of Magnesium atom in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. (pdb code 9dkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1., PDB code: 9dkm:

Magnesium binding site 1 out of 1 in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4105 b:20.0 occ:1.00 O3B A:ADP4104 2.1 21.6 1.0 O2B A:ADP4104 2.1 22.2 1.0 OG1 A:THR1803 2.2 14.2 1.0 PB A:ADP4104 2.4 26.0 1.0 OD1 A:ASP1848 2.5 28.1 1.0 OD2 A:ASP1848 2.6 32.7 1.0 CG A:ASP1848 2.9 29.6 1.0 CB A:THR1803 3.4 10.4 1.0 OE2 A:GLU1849 3.4 35.6 1.0 O3A A:ADP4104 3.6 20.4 1.0 O1B A:ADP4104 3.6 19.2 1.0 NH2 A:ARG2209 3.8 21.3 1.0 OG1 A:THR1897 4.2 13.6 1.0 CG2 A:THR1803 4.3 9.3 1.0 N A:THR1803 4.3 11.4 1.0 CB A:ASP1848 4.4 17.1 1.0 CA A:THR1803 4.5 9.6 1.0 CD A:GLU1849 4.5 41.5 1.0 O2A A:ADP4104 4.5 15.4 1.0 PA A:ADP4104 4.6 14.6 1.0 OD2 A:ASP2171 4.9 17.4 1.0 CE A:LYS1802 5.0 12.9 1.0

A.A.Kendrick, K.H.V.Nguyen, W.Ma, E.P.Karasmanis, R.E.Amaro, S.L.Reck-Peterson, A.E.Leschziner. Multiple Steps of Dynein Activation By LIS1 Visualized By Cryo-Em. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 40410592
DOI: 10.1038/S41594-025-01558-W