Magnesium in PDB 6pdy: MSP1-Substrate Complex in Open Conformation

The structure of MSP1-Substrate Complex in Open Conformation also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the MSP1-Substrate Complex in Open Conformation (pdb code 6pdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the MSP1-Substrate Complex in Open Conformation, PDB code: 6pdy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the MSP1-Substrate Complex in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MSP1-Substrate Complex in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:0.1 occ:1.00 F3 A:BEF502 2.1 0.7 1.0 F1 A:BEF502 2.1 0.7 1.0 CG2 A:THR161 2.3 1.0 1.0 BE A:BEF502 2.4 0.7 1.0 OD2 A:ASP213 2.4 0.3 1.0 OD1 A:ASP213 2.8 0.3 1.0 CG A:ASP213 2.9 0.3 1.0 O1B A:ADP501 3.7 0.4 1.0 CB A:THR161 3.8 1.0 1.0 F2 A:BEF502 3.9 0.7 1.0 OE2 A:GLU214 3.9 30.0 1.0 N A:THR161 4.2 1.0 1.0 NH1 B:ARG275 4.2 0.1 1.0 O A:ALA261 4.3 0.5 1.0 CA A:THR161 4.4 1.0 1.0 CB A:ASP213 4.4 0.3 1.0 PB A:ADP501 4.5 0.4 1.0 OG1 A:THR161 4.5 1.0 1.0 CE A:LYS160 4.5 1.0 1.0 O2B A:ADP501 4.6 0.4 1.0 CB A:LYS160 4.6 1.0 1.0 CD A:GLU214 4.9 30.0 1.0 O3B A:ADP501 4.9 0.4 1.0 CB A:ALA261 4.9 0.5 1.0

Magnesium binding site 2 out of 4 in the MSP1-Substrate Complex in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MSP1-Substrate Complex in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:55.1 occ:1.00 BE B:BEF502 1.8 54.8 1.0 OG1 B:THR161 2.0 54.6 1.0 F3 B:BEF502 2.1 54.8 1.0 O2B B:ADP501 2.2 60.8 1.0 O2A B:ADP501 2.3 60.8 1.0 CB B:THR161 2.5 54.6 1.0 F1 B:BEF502 2.6 54.8 1.0 O1B B:ADP501 2.9 60.8 1.0 PB B:ADP501 3.0 60.8 1.0 PA B:ADP501 3.1 60.8 1.0 F2 B:BEF502 3.1 54.8 1.0 N B:THR161 3.4 54.6 1.0 O3A B:ADP501 3.4 60.8 1.0 O1A B:ADP501 3.5 60.8 1.0 CA B:THR161 3.6 54.6 1.0 CG2 B:THR161 3.7 54.6 1.0 NH1 C:ARG274 3.9 52.2 1.0 CG B:LYS160 4.2 54.8 1.0 O C:ASP242 4.3 49.4 1.0 O3B B:ADP501 4.4 60.8 1.0 C B:LYS160 4.5 54.8 1.0 O5' B:ADP501 4.6 60.8 1.0 C B:THR161 4.7 54.6 1.0 OD2 C:ASP242 4.8 49.4 1.0 N B:LYS160 4.8 54.8 1.0 N B:MET162 4.8 60.1 1.0 CZ C:ARG274 4.9 52.2 1.0

Magnesium binding site 3 out of 4 in the MSP1-Substrate Complex in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of MSP1-Substrate Complex in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:50.5 occ:1.00 OD2 C:ASP213 1.4 48.4 1.0 F1 C:BEF502 2.1 48.1 1.0 OG1 C:THR161 2.1 46.1 1.0 CG C:ASP213 2.2 48.4 1.0 OD1 C:ASP213 2.4 48.4 1.0 BE C:BEF502 3.2 48.1 1.0 F3 C:BEF502 3.3 48.1 1.0 CB C:THR161 3.5 46.1 1.0 CB C:ASP213 3.7 48.4 1.0 CB C:ALA261 3.9 44.5 1.0 CG2 C:THR161 3.9 46.1 1.0 O D:MET238 4.0 49.5 1.0 O2B C:ADP501 4.2 42.3 1.0 CA C:THR161 4.3 46.1 1.0 F2 C:BEF502 4.5 48.1 1.0 CA C:ASP213 4.7 48.4 1.0 N C:THR161 4.7 46.1 1.0 N C:GLU214 4.7 50.0 1.0 CZ C:PHE211 5.0 42.2 1.0

Magnesium binding site 4 out of 4 in the MSP1-Substrate Complex in Open Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of MSP1-Substrate Complex in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.8 occ:1.00 OD2 D:ASP213 2.0 54.5 1.0 OD1 D:ASP213 2.1 54.5 1.0 F3 E:BEF501 2.1 51.9 1.0 CG D:ASP213 2.3 54.5 1.0 OG1 D:THR161 2.3 46.4 1.0 BE E:BEF501 3.3 51.9 1.0 F2 E:BEF501 3.5 51.9 1.0 O2B D:ADP501 3.6 46.9 1.0 CB D:THR161 3.8 46.4 1.0 CB D:ASP213 3.8 54.5 1.0 F1 E:BEF501 4.1 51.9 1.0 CG D:GLU214 4.3 30.0 1.0 CG2 D:THR161 4.4 46.4 1.0 CA D:THR161 4.5 46.4 1.0 O D:ALA261 4.6 45.0 1.0 N D:GLU214 4.6 58.4 1.0 N D:THR161 4.6 46.4 1.0 O E:ASP242 4.6 59.9 1.0 CA D:ASP213 4.7 54.5 1.0 NH1 E:ARG275 4.7 56.5 1.0 OE2 D:GLU214 4.7 30.0 1.0 CB D:ALA261 4.8 45.0 1.0 CD D:GLU214 4.9 30.0 1.0 C D:ASP213 4.9 54.5 1.0 PB D:ADP501 4.9 46.9 1.0 OG1 E:THR239 4.9 57.0 1.0

L.Wang, A.Myasnikov, X.Pan, P.Walter. Structure of the Aaa Protein MSP1 Reveals Mechanism of Mislocalized Membrane Protein Extraction. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 31999255
DOI: 10.7554/ELIFE.54031