Magnesium in PDB 7yyq: Molecular Snapshots of Drug Release From Tubulin: Dark State

The structure of Molecular Snapshots of Drug Release From Tubulin: Dark State, PDB code: 7yyq 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)	9.49 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.53, 92.58, 83.99, 90, 96.71, 90
R / Rfree (%)	12.1 / 15.4

The structure of Molecular Snapshots of Drug Release From Tubulin: Dark 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 State (pdb code 7yyq). 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 State, PDB code: 7yyq:
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 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 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.1 occ:1.00 O1G A:GTP501 2.1 28.4 1.0 O2B A:GTP501 2.1 26.2 1.0 O A:HOH713 2.1 28.8 1.0 O A:HOH642 2.1 26.4 1.0 O A:HOH673 2.1 24.2 1.0 O A:HOH829 2.2 26.2 1.0 PG A:GTP501 3.2 26.0 1.0 PB A:GTP501 3.2 24.2 1.0 HB2 A:GLN11 3.4 29.0 1.0 HZ1 B:LYS252 3.4 41.7 0.6 O3B A:GTP501 3.5 22.9 1.0 H A:GLN11 3.6 26.9 1.0 O2G A:GTP501 3.7 27.8 1.0 O3A A:GTP501 3.8 24.4 1.0 HB2 A:ASP98 3.9 37.1 1.0 HG2 A:GLU71 4.0 41.4 1.0 O A:HOH755 4.0 36.8 0.6 OD1 A:ASP69 4.1 25.0 1.0 HB3 A:GLN11 4.1 29.0 1.0 HZ2 B:LYS252 4.1 41.7 0.6 HG3 A:GLU71 4.1 41.4 1.0 OE2 A:GLU71 4.1 36.1 1.0 NZ B:LYS252 4.2 34.8 0.6 CB A:GLN11 4.2 24.2 1.0 OD2 A:ASP69 4.3 27.2 1.0 OD2 A:ASP98 4.3 32.1 1.0 N A:GLN11 4.4 22.5 1.0 CG A:GLU71 4.4 34.5 1.0 HB3 A:ASP98 4.5 37.1 1.0 HG1 A:THR145 4.5 30.6 1.0 HZ3 B:LYS252 4.5 41.7 0.6 O3G A:GTP501 4.5 27.2 1.0 O1B A:GTP501 4.5 25.8 1.0 CB A:ASP98 4.6 31.0 1.0 CG A:ASP69 4.6 25.8 1.0 O2A A:GTP501 4.6 26.0 1.0 HB A:THR145 4.7 30.2 1.0 OE1 A:GLN11 4.7 32.6 1.0 CG A:ASP98 4.8 31.0 1.0 HZ1 B:LYS252 4.8 45.2 0.4 PA A:GTP501 4.8 25.0 1.0 HA2 A:GLY10 4.8 28.3 1.0 CD A:GLU71 4.8 34.7 1.0 CA A:GLN11 4.9 22.3 1.0

Magnesium binding site 2 out of 2 in the Molecular Snapshots of Drug Release From Tubulin: Dark 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 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:49.6 occ:0.37 OE1 B:GLN11 0.9 42.6 0.4 CD B:GLN11 1.7 45.4 0.4 O B:HOH762 1.9 36.8 0.4 O1G B:GTP602 1.9 41.7 0.4 HE22 B:GLN11 2.1 54.5 0.4 O B:HOH706 2.2 35.1 0.4 NE2 B:GLN11 2.2 45.4 0.4 O B:HOH740 2.7 58.2 0.4 O2B B:GTP602 2.7 40.8 1.0 HE21 B:GLN11 3.1 54.5 0.4 O B:HOH706 3.1 39.2 0.6 CG B:GLN11 3.2 46.3 0.4 PG B:GTP602 3.3 44.9 0.4 O B:HOH701 3.3 29.5 0.4 HB2 B:GLN11 3.3 55.1 0.6 HG2 B:GLN11 3.4 55.6 0.4 HB2 B:GLN11 3.5 53.2 0.4 O B:HOH753 3.6 44.2 0.6 HB3 B:GLN11 3.7 55.1 0.6 PB B:GTP602 3.7 38.8 1.0 O2G B:GTP602 3.8 46.8 0.4 HG3 B:GLN11 3.8 55.6 0.4 HB2 B:GLU69 3.9 91.5 1.0 H B:GLN11 3.9 50.1 1.0 CB B:GLN11 3.9 44.3 0.4 O3B B:GTP602 4.0 40.1 1.0 CB B:GLN11 4.0 45.9 0.6 O3A B:GTP602 4.0 38.1 1.0 HG2 B:GLU69 4.3 96.3 1.0 HB3 B:GLU69 4.3 91.5 1.0 O3G B:GTP602 4.4 45.4 0.4 O2A B:GTP602 4.4 36.8 1.0 CB B:GLU69 4.5 76.3 1.0 O B:HOH800 4.6 59.8 1.0 N B:GLN11 4.6 41.7 1.0 HB3 B:GLN11 4.6 53.2 0.4 OD2 B:ASP67 4.8 50.0 1.0 PA B:GTP602 4.8 37.9 1.0 OE1 B:GLN11 4.8 56.2 0.6 HG1 B:THR72 4.8 85.2 1.0 CG B:GLU69 4.8 80.3 1.0 OD1 B:ASP67 4.9 47.0 1.0 CA B:GLN11 4.9 43.5 0.6 CA B:GLN11 4.9 43.0 0.4 HG1 B:THR143 4.9 49.4 1.0 CD B:GLN11 4.9 53.7 0.6 OE1 B:GLU69 4.9 83.6 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