Magnesium in PDB 8vh5: Cryo-Em Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State

All present enzymatic activity of Cryo-Em Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State:
2.7.11.1;

The binding sites of Magnesium atom in the Cryo-Em Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State (pdb code 8vh5). 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 Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State, PDB code: 8vh5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer 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 Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:161.0 occ:1.00 O2B B:GNP302 2.0 126.7 1.0 O1A B:GNP302 2.1 126.7 1.0 OG1 B:THR56 2.1 146.1 1.0 O2G B:GNP302 2.2 126.7 1.0 PB B:GNP302 2.4 126.7 1.0 N3B B:GNP302 2.4 126.7 1.0 PA B:GNP302 2.4 126.7 1.0 O2A B:GNP302 2.5 126.7 1.0 CB B:THR56 2.5 146.1 1.0 PG B:GNP302 2.6 126.7 1.0 O3A B:GNP302 2.8 126.7 1.0 N B:THR56 3.0 146.1 1.0 O3G B:GNP302 3.1 126.7 1.0 CA B:THR56 3.3 146.1 1.0 CG2 B:THR56 3.8 146.1 1.0 O1B B:GNP302 3.8 126.7 1.0 O5' B:GNP302 4.0 126.7 1.0 O1G B:GNP302 4.0 126.7 1.0 C B:THR56 4.2 146.1 1.0 N B:SER57 4.2 148.1 1.0 N B:LYS55 4.2 142.0 1.0 C B:LYS55 4.2 142.0 1.0 NZ B:LYS55 4.3 142.0 1.0 OG1 B:THR74 4.5 123.7 1.0 N B:THR74 4.5 123.7 1.0 CA B:SER73 4.6 140.0 1.0 CA B:LYS55 4.6 142.0 1.0 C B:GLY54 4.7 156.9 1.0 OD1 B:ASP97 4.7 114.8 1.0 OD2 B:ASP97 4.7 114.8 1.0 N B:GLY54 4.8 156.9 1.0 O B:LYS72 4.8 168.8 1.0 CA B:GLY54 4.8 156.9 1.0 CB B:LYS55 4.8 142.0 1.0 SG B:CYS71 4.9 183.2 1.0 C5' B:GNP302 4.9 126.7 1.0 CG2 B:THR74 5.0 123.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer 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 Structure of RAB12-LRRK2 Complex in the LRRK2 Dimer State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:188.4 occ:1.00 O2B D:GNP302 2.0 155.0 1.0 O1A D:GNP302 2.1 155.0 1.0 OG1 D:THR56 2.1 185.9 1.0 O2G D:GNP302 2.2 155.0 1.0 PB D:GNP302 2.4 155.0 1.0 N3B D:GNP302 2.4 155.0 1.0 PA D:GNP302 2.4 155.0 1.0 O2A D:GNP302 2.5 155.0 1.0 CB D:THR56 2.5 185.9 1.0 PG D:GNP302 2.6 155.0 1.0 O3A D:GNP302 2.8 155.0 1.0 N D:THR56 3.0 185.9 1.0 O3G D:GNP302 3.1 155.0 1.0 CA D:THR56 3.3 185.9 1.0 CG2 D:THR56 3.8 185.9 1.0 O1B D:GNP302 3.8 155.0 1.0 O5' D:GNP302 4.0 155.0 1.0 O1G D:GNP302 4.0 155.0 1.0 N D:SER57 4.2 188.8 1.0 C D:THR56 4.2 185.9 1.0 N D:LYS55 4.2 181.2 1.0 C D:LYS55 4.2 181.2 1.0 NZ D:LYS55 4.3 181.2 1.0 OG1 D:THR74 4.5 159.0 1.0 N D:THR74 4.5 159.0 1.0 CA D:SER73 4.6 166.4 1.0 CA D:LYS55 4.6 181.2 1.0 C D:GLY54 4.7 193.1 1.0 OD1 D:ASP97 4.7 156.3 1.0 OD2 D:ASP97 4.7 156.3 1.0 N D:GLY54 4.8 193.1 1.0 O D:LYS72 4.8 189.9 1.0 CA D:GLY54 4.8 193.1 1.0 CB D:LYS55 4.8 181.2 1.0 SG D:CYS71 4.9 207.3 1.0 C5' D:GNP302 4.9 155.0 1.0 CG2 D:THR74 5.0 159.0 1.0

X.Li, H.Zhu, B.T.Huang, X.Li, H.Kim, H.Tan, Y.Zhang, I.Choi, J.Peng, P.Xu, J.Sun, Z.Yue. RAB12-LRRK2 Complex Suppresses Primary Ciliogenesis and Regulates Centrosome Homeostasis in Astrocytes. Nat Commun V. 15 8434 2024.
ISSN: ESSN 2041-1723
PubMed: 39343966
DOI: 10.1038/S41467-024-52723-6