Magnesium in PDB 7yz6: Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State)

The structure of Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State), PDB code: 7yz6 was solved by M.Wranik, T.Weinert, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.75 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.28, 91.87, 83.69, 90, 96.82, 90
R / Rfree (%)	16.9 / 22

The structure of Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State) (pdb code 7yz6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State), PDB code: 7yz6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.2 occ:1.00 O A:HOH639 1.9 18.9 1.0 O1G A:GTP501 2.0 21.3 1.0 O A:HOH676 2.0 21.9 1.0 O A:HOH623 2.1 16.5 1.0 O2B A:GTP501 2.1 25.0 1.0 O A:HOH651 2.2 21.9 1.0 PB A:GTP501 3.1 19.6 1.0 PG A:GTP501 3.2 27.2 1.0 O3B A:GTP501 3.5 29.8 1.0 O3A A:GTP501 3.6 24.1 1.0 O2G A:GTP501 3.7 22.0 1.0 OE2 A:GLU71 3.9 35.2 1.0 CB A:GLN11 4.1 18.0 1.0 OD1 A:ASP69 4.3 20.7 1.0 NZ B:LYS252 4.3 34.0 0.6 OD2 A:ASP69 4.3 26.4 1.0 OD2 A:ASP98 4.4 25.9 1.0 O3G A:GTP501 4.4 21.3 1.0 N A:GLN11 4.4 22.6 1.0 CG A:GLU71 4.4 28.4 1.0 O1B A:GTP501 4.5 22.9 1.0 OE1 A:GLN11 4.5 30.5 1.0 O2A A:GTP501 4.5 23.8 1.0 CD A:GLU71 4.6 33.9 1.0 PA A:GTP501 4.6 26.2 1.0 CB A:ASP98 4.7 21.4 1.0 CG A:ASP69 4.8 22.5 1.0 CA A:GLN11 4.9 19.3 1.0 CG A:ASP98 4.9 29.3 1.0

Magnesium binding site 2 out of 2 in the Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Molecular Snapshots of Drug Release From Tubulin: Dark (Steady State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:46.5 occ:0.37 OE1 B:GLN11 0.5 46.0 0.4 CD B:GLN11 1.6 43.7 0.4 O1G B:GTP602 2.2 42.5 0.4 NE2 B:GLN11 2.4 46.8 0.4 CG B:GLN11 2.9 42.7 0.4 O2B B:GTP602 2.9 45.7 1.0 O B:HOH708 3.2 43.4 1.0 PG B:GTP602 3.6 46.5 0.4 CB B:GLN11 3.6 42.0 0.4 CB B:GLN11 3.6 42.0 0.6 O3A B:GTP602 3.7 36.6 1.0 PB B:GTP602 3.8 37.8 1.0 OE1 B:GLN11 3.9 43.4 0.6 O B:HOH703 4.0 47.0 1.0 O3G B:GTP602 4.1 45.7 0.4 O3B B:GTP602 4.1 32.9 1.0 N B:GLN11 4.3 36.7 1.0 O2A B:GTP602 4.5 39.0 1.0 CA B:GLN11 4.5 41.3 0.4 CA B:GLN11 4.5 41.3 0.6 CB B:GLU69 4.6 70.1 1.0 PA B:GTP602 4.7 36.6 1.0 O2G B:GTP602 4.7 36.5 0.4 CG B:GLN11 4.7 39.2 0.6 CD B:GLN11 4.7 41.8 0.6 OD2 B:ASP67 4.8 50.4 1.0 CG B:GLU69 4.9 74.6 1.0 OE1 B:GLU69 5.0 77.4 1.0

M.Wranik, T.Weinert, C.Slavov, T.Masini, A.Furrer, N.Gaillard, D.Gioia, M.Ferrarotti, D.James, H.Glover, M.Carrillo, D.Kekilli, R.Stipp, P.Skopintsev, S.Brunle, T.Muhlethaler, J.Beale, D.Gashi, K.Nass, D.Ozerov, P.Johnson, C.Cirelli, C.Bacellar, M.Braun, M.Wang, F.Dworkowski, C.Milne, A.Cavalli, J.Wachtveitl, M.Steinmetz, J.Standfuss. Watching the Release of A Photopharmacological Drug From Tubulin Using Time-Resolved Serial Crystallography Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-36481-5