Magnesium in PDB 8cl9: Tubulin-Darpin D1 Complex

The structure of Tubulin-Darpin D1 Complex, PDB code: 8cl9 was solved by M.Wranik, Q.Bertrand, T.Weinert, M.W.Kepa, M.Steinmetz, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.47, 91.19, 82.7, 90, 96.43, 90
R / Rfree (%)	18.5 / 24.1

The binding sites of Magnesium atom in the Tubulin-Darpin D1 Complex (pdb code 8cl9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Tubulin-Darpin D1 Complex, PDB code: 8cl9:

Magnesium binding site 1 out of 1 in the 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 Tubulin-Darpin D1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.4 occ:1.00 O1G A:GTP501 2.0 13.9 1.0 O A:HOH607 2.0 18.8 1.0 O A:HOH608 2.0 20.1 1.0 O A:HOH652 2.1 15.8 1.0 O2B A:GTP501 2.3 16.4 1.0 O A:HOH603 2.4 21.9 1.0 PG A:GTP501 3.3 18.5 1.0 PB A:GTP501 3.4 14.4 1.0 OE2 A:GLU71 3.4 41.8 1.0 O3B A:GTP501 3.6 29.5 1.0 OD1 A:ASP69 3.8 10.9 1.0 CG A:GLU71 3.9 27.4 1.0 O3A A:GTP501 3.9 20.8 1.0 O2G A:GTP501 3.9 17.3 1.0 OD2 A:ASP69 3.9 18.3 1.0 CD A:GLU71 4.1 33.7 1.0 CB A:ASP98 4.2 17.6 1.0 CB A:GLN11 4.3 16.4 1.0 NZ B:LYS254 4.3 24.1 1.0 CG A:ASP69 4.3 16.4 1.0 N A:GLN11 4.4 15.4 1.0 OD2 A:ASP98 4.4 20.6 1.0 O3G A:GTP501 4.4 19.8 1.0 CG A:ASP98 4.7 19.9 1.0 O1B A:GTP501 4.8 20.5 1.0 O2A A:GTP501 4.8 32.5 1.0 OG1 A:THR145 4.8 15.3 1.0 CA A:GLN11 4.9 17.9 1.0 PA A:GTP501 4.9 14.7 1.0 NE2 A:GLN11 4.9 15.8 1.0

M.Wranik, M.W.Kepa, E.V.Beale, D.James, Q.Bertrand, T.Weinert, A.Furrer, H.Glover, D.Gashi, M.Carrillo, Y.Kondo, R.T.Stipp, G.Khusainov, K.Nass, D.Ozerov, C.Cirelli, P.J.M.Johnson, F.Dworkowski, J.H.Beale, S.Stubbs, T.Zamofing, M.Schneider, K.Krauskopf, L.Gao, O.Thorn-Seshold, C.Bostedt, C.Bacellar, M.O.Steinmetz, C.Milne, J.Standfuss. A Multi-Reservoir Extruder For Time-Resolved Serial Protein Crystallography and Compound Screening at X-Ray Free-Electron Lasers. Nat Commun V. 14 7956 2023.
ISSN: ESSN 2041-1723
PubMed: 38042952
DOI: 10.1038/S41467-023-43523-5