Magnesium in PDB 6dlu: Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State

All present enzymatic activity of Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State:
3.6.5.5;

The binding sites of Magnesium atom in the Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State (pdb code 6dlu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State, PDB code: 6dlu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:39.8 occ:1.00 O1B B:GCP801 1.9 42.7 1.0 OG1 B:THR65 2.0 37.2 1.0 O2G B:GCP801 2.0 42.7 1.0 CB B:THR65 2.6 37.2 1.0 OG B:SER45 2.8 37.5 1.0 PB B:GCP801 3.0 42.7 1.0 PG B:GCP801 3.0 42.7 1.0 O1G B:GCP801 3.2 42.7 1.0 O2B B:GCP801 3.3 42.7 1.0 C3B B:GCP801 3.5 42.7 1.0 N B:THR65 3.5 37.2 1.0 CA B:THR65 3.6 37.2 1.0 CG2 B:THR65 3.7 37.2 1.0 CB B:SER45 3.8 37.5 1.0 O3A B:GCP801 4.4 42.7 1.0 O3G B:GCP801 4.4 42.7 1.0 N B:SER45 4.4 37.5 1.0 OD2 B:ASP136 4.4 44.3 1.0 O B:PRO58 4.5 40.1 1.0 O1A B:GCP801 4.5 42.7 1.0 OD1 B:ASP136 4.7 44.3 1.0 CB B:VAL64 4.7 35.5 1.0 O B:THR65 4.7 37.2 1.0 C B:THR65 4.7 37.2 1.0 C B:VAL64 4.7 35.5 1.0 CA B:SER45 4.7 37.5 1.0 CE B:LYS44 4.7 36.6 1.0 NZ B:LYS44 4.9 36.6 1.0 PA B:GCP801 4.9 42.7 1.0 CG1 B:VAL64 4.9 35.5 1.0 CG B:ASP136 5.0 44.3 1.0 O2A B:GCP801 5.0 42.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em of the Gmppcp-Bound Human Dynamin-1 Polymer Assembled on the Membrane in the Constricted State within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg802 b:38.3 occ:1.00 OG1 P:THR65 2.0 39.2 1.0 OG P:SER45 2.1 37.9 1.0 O2B P:GCP801 2.3 49.8 1.0 O1G P:GCP801 2.8 49.8 1.0 CB P:THR65 3.1 39.2 1.0 CB P:SER45 3.2 37.9 1.0 PB P:GCP801 3.6 49.8 1.0 O P:PRO58 3.8 42.0 1.0 PG P:GCP801 3.8 49.8 1.0 OD2 P:ASP136 3.9 38.4 1.0 CG2 P:THR65 4.0 39.2 1.0 O3G P:GCP801 4.1 49.8 1.0 O1B P:GCP801 4.1 49.8 1.0 N P:SER45 4.1 37.9 1.0 C3B P:GCP801 4.2 49.8 1.0 N P:THR65 4.2 39.2 1.0 CA P:THR65 4.2 39.2 1.0 CA P:SER45 4.2 37.9 1.0 O2A P:GCP801 4.3 49.8 1.0 OD1 P:ASP136 4.4 38.4 1.0 CG P:ASP136 4.6 38.4 1.0 NZ P:LYS44 4.6 54.9 1.0 CE P:LYS44 4.7 54.9 1.0 O3A P:GCP801 4.8 49.8 1.0 C P:PRO58 5.0 42.0 1.0

L.Kong, K.A.Sochacki, H.Wang, S.Fang, B.Canagarajah, A.D.Kehr, W.J.Rice, M.P.Strub, J.W.Taraska, J.E.Hinshaw. Cryo-Em of the Dynamin Polymer Assembled on Lipid Membrane. Nature V. 560 258 2018.
ISSN: ESSN 1476-4687
PubMed: 30069048
DOI: 10.1038/S41586-018-0378-6