Magnesium in PDB 7z02: Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex

The structure of Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex, PDB code: 7z02 was solved by M.Wranik, T.Weinert, J.Standfuss, M.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.683, 91.615, 83.11, 90, 97.39, 90
R / Rfree (%)	20.5 / 25.8

The binding sites of Magnesium atom in the Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex (pdb code 7z02). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex, PDB code: 7z02:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:40.9 occ:1.00 MG A:MG503 2.1 28.8 1.0 O1G A:GTP501 2.4 32.0 1.0 O2B A:GTP501 2.6 33.9 1.0 HB2 A:GLN11 3.2 67.1 1.0 HZ1 B:LYS254 3.2 61.9 1.0 O B:HOH603 3.3 39.9 1.0 OE2 A:GLU71 3.3 55.9 1.0 O3A A:GTP501 3.5 33.6 1.0 PB A:GTP501 3.5 33.1 1.0 PG A:GTP501 3.6 35.5 1.0 HB3 A:GLN11 3.6 58.6 1.0 OE1 A:GLN11 3.7 31.4 1.0 CB A:GLN11 3.8 32.2 1.0 O3G A:GTP501 4.0 34.1 1.0 H A:GLN11 4.0 71.3 1.0 NZ B:LYS254 4.1 42.4 1.0 O3B A:GTP501 4.1 32.3 1.0 HZ2 B:LYS254 4.1 60.6 1.0 O2A A:GTP501 4.2 32.2 1.0 HG2 A:GLU71 4.3 69.9 1.0 CD A:GLU71 4.3 53.1 1.0 CD A:GLN11 4.3 33.8 1.0 PA A:GTP501 4.4 34.7 1.0 HZ3 B:LYS254 4.5 74.0 1.0 CG A:GLN11 4.7 31.0 1.0 N A:GLN11 4.8 30.6 1.0 HE3 B:LYS254 4.8 67.9 1.0 HG21 A:VAL74 4.8 72.0 1.0 O1B A:GTP501 4.8 31.1 1.0 O2G A:GTP501 4.8 33.7 1.0 CG A:GLU71 4.9 51.2 1.0 CA A:GLN11 4.9 33.4 1.0 CE B:LYS254 4.9 46.5 1.0 HB2 A:ASP98 4.9 77.0 1.0 HE2 B:LYS254 5.0 64.0 1.0

Magnesium binding site 2 out of 2 in the Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Z-SBTUB2M Photoswitch Bound to Tubulin-Darpin D1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.8 occ:1.00 MG A:MG502 2.1 40.9 1.0 O2B A:GTP501 2.3 33.9 1.0 O1G A:GTP501 2.3 32.0 1.0 HG2 A:GLU71 2.6 69.9 1.0 OE2 A:GLU71 3.0 55.9 1.0 OD1 A:ASP69 3.2 47.2 1.0 OD2 A:ASP69 3.4 50.7 1.0 HB2 A:GLN11 3.4 67.1 1.0 CG A:GLU71 3.5 51.2 1.0 CD A:GLU71 3.6 53.1 1.0 H A:GLN11 3.6 71.3 1.0 PB A:GTP501 3.6 33.1 1.0 PG A:GTP501 3.7 35.5 1.0 CG A:ASP69 3.7 47.7 1.0 HG3 A:GLU71 4.0 71.0 1.0 HB2 A:ASP98 4.0 77.0 1.0 O3B A:GTP501 4.0 32.3 1.0 HB3 A:ASP98 4.1 70.5 1.0 CB A:GLN11 4.2 32.2 1.0 N A:GLN11 4.2 30.6 1.0 HB3 A:GLN11 4.3 58.6 1.0 H A:GLU71 4.3 63.4 1.0 HB3 A:GLU71 4.4 59.6 1.0 HA2 A:GLY10 4.4 62.0 1.0 O3A A:GTP501 4.4 33.6 1.0 HG1 A:THR145 4.5 61.7 1.0 O2G A:GTP501 4.5 33.7 1.0 CB A:ASP98 4.5 44.4 1.0 CB A:GLU71 4.5 54.4 1.0 HG21 A:VAL74 4.6 72.0 1.0 OE1 A:GLU71 4.7 50.5 1.0 O3G A:GTP501 4.7 34.1 1.0 O1B A:GTP501 4.7 31.1 1.0 O B:HOH603 4.7 39.9 1.0 OG1 A:THR145 4.7 33.6 1.0 CA A:GLN11 4.8 33.4 1.0 HG23 A:VAL74 4.8 68.0 1.0 H A:LEU70 4.8 64.9 1.0 HB A:THR145 4.8 69.9 1.0 HZ1 B:LYS254 4.8 61.9 1.0 HA A:GLN11 4.9 65.9 1.0 OE1 A:GLN11 4.9 31.4 1.0 N A:GLU71 5.0 55.1 1.0

L.Gao, J.C.M.Meiring, A.Varady, I.E.Ruider, C.Heise, M.Wranik, C.D.Velasco, J.A.Taylor, B.Terni, T.Weinert, J.Standfuss, C.C.Cabernard, A.Llobet, M.O.Steinmetz, A.R.Bausch, M.Distel, J.Thorn-Seshold, A.Akhmanova, O.Thorn-Seshold. In Vivo Photocontrol of Microtubule Dynamics and Integrity, Migration and Mitosis, By the Potent Gfp-Imaging-Compatible Photoswitchable Reagents SBTUBA4P and SBTUB2M. J.Am.Chem.Soc. V. 144 5614 2022.
ISSN: ESSN 1520-5126
PubMed: 35290733
DOI: 10.1021/JACS.2C01020