Magnesium in PDB 7z8m: The Pointed End Complex of Dynactin Bound to BICDR1

The structure of The Pointed End Complex of Dynactin Bound to BICDR1 also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium atom in the The Pointed End Complex of Dynactin Bound to BICDR1 (pdb code 7z8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Pointed End Complex of Dynactin Bound to BICDR1, PDB code: 7z8m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Pointed End Complex of Dynactin Bound to BICDR1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Pointed End Complex of Dynactin Bound to BICDR1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg801 b:77.2 occ:1.00 O2G J:ATP800 3.0 40.6 1.0 OD2 J:ASP140 3.0 61.7 1.0 O1B J:ATP800 3.2 35.7 1.0 O1A J:ATP800 3.4 42.1 1.0 CG J:ASP140 3.9 56.6 1.0 OD1 J:ASP140 4.1 58.0 1.0 PB J:ATP800 4.1 35.1 1.0 O3A J:ATP800 4.1 35.2 1.0 PG J:ATP800 4.3 44.6 1.0 PA J:ATP800 4.4 37.0 1.0 NZ J:LYS26 4.4 45.9 1.0 O3B J:ATP800 4.4 36.2 1.0 CA J:GLY307 4.6 47.0 1.0 CA J:GLY142 4.6 50.9 1.0 OD2 J:ASP19 4.8 50.9 1.0

Magnesium binding site 2 out of 4 in the The Pointed End Complex of Dynactin Bound to BICDR1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Pointed End Complex of Dynactin Bound to BICDR1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg801 b:47.1 occ:1.00 O3B G:ADP800 1.9 44.5 1.0 PB G:ADP800 2.9 44.0 1.0 O1B G:ADP800 3.3 45.7 1.0 CG G:GLN142 3.5 47.9 1.0 O2B G:ADP800 3.7 40.4 1.0 NE2 G:GLN142 3.7 49.6 1.0 OD1 G:ASP159 4.0 49.5 1.0 OD1 G:ASP15 4.1 49.0 1.0 CD G:GLN142 4.1 49.3 1.0 OD2 G:ASP159 4.2 50.7 1.0 O3A G:ADP800 4.3 37.9 1.0 OD2 G:ASP15 4.3 47.3 1.0 CG G:ASP159 4.5 48.9 1.0 CG G:ASP15 4.6 47.4 1.0 CA G:GLY17 4.7 40.2 1.0 CB G:GLN142 4.7 48.3 1.0 OG1 G:THR340 4.8 42.1 1.0

Magnesium binding site 3 out of 4 in the The Pointed End Complex of Dynactin Bound to BICDR1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Pointed End Complex of Dynactin Bound to BICDR1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg801 b:45.9 occ:1.00 O1B H:ADP800 2.2 51.0 1.0 PB H:ADP800 2.9 51.0 1.0 O3B H:ADP800 3.0 49.7 1.0 O3A H:ADP800 3.0 46.6 1.0 O1A H:ADP800 3.5 48.1 1.0 PA H:ADP800 3.8 44.5 1.0 CG1 H:VAL339 4.1 44.9 1.0 OE1 H:GLN137 4.1 46.6 1.0 CA H:GLY301 4.2 42.7 1.0 OD1 H:ASP154 4.2 48.1 1.0 OD2 H:ASP154 4.3 45.7 1.0 O2B H:ADP800 4.3 46.9 1.0 NZ H:LYS18 4.3 45.9 1.0 OD2 H:ASP11 4.5 48.3 1.0 CA H:GLY156 4.5 42.5 1.0 CB H:VAL339 4.6 42.0 1.0 O2A H:ADP800 4.7 45.1 1.0 CD H:GLN137 4.7 45.7 1.0 CG H:ASP154 4.7 45.9 1.0 N H:GLY302 4.8 40.5 1.0 CG2 H:VAL339 4.9 42.3 1.0 NE2 H:GLN137 5.0 46.9 1.0 OD1 H:ASP11 5.0 49.8 1.0

Magnesium binding site 4 out of 4 in the The Pointed End Complex of Dynactin Bound to BICDR1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Pointed End Complex of Dynactin Bound to BICDR1 within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg801 b:68.6 occ:1.00 O3B I:ADP800 2.3 59.4 1.0 O2B I:ADP800 2.8 55.7 1.0 PB I:ADP800 3.0 65.7 1.0 OD1 I:ASP15 3.1 58.9 1.0 OD2 I:ASP15 3.2 55.1 1.0 OG1 I:THR340 3.4 51.5 1.0 CG I:ASP15 3.6 56.1 1.0 CG2 I:THR340 3.7 49.2 1.0 CG I:GLN142 3.8 60.3 1.0 CB I:THR340 4.0 47.7 1.0 O3A I:ADP800 4.1 54.2 1.0 O1B I:ADP800 4.2 64.6 1.0 O2A I:ADP800 4.4 53.0 1.0 OD2 I:ASP159 4.5 55.5 1.0 CB I:GLN142 4.6 57.1 1.0 OD1 I:ASP159 4.6 56.8 1.0 NE2 I:GLN142 4.6 62.0 1.0 CD I:GLN142 4.7 60.8 1.0 PA I:ADP800 4.7 47.5 1.0 NZ I:LYS22 4.9 51.2 1.0 CA I:GLY17 4.9 56.5 1.0 CG I:ASP159 5.0 55.2 1.0

S.Chaaban, A.P.Carter. Structure of Dynein-Dynactin on Microtubules Shows Tandem Adaptor Binding. Nature V. 610 212 2022.
ISSN: ESSN 1476-4687
PubMed: 36071160
DOI: 10.1038/S41586-022-05186-Y