Magnesium in PDB 8cle: Vinblastine Bound to Tubulin (T2R-Ttl) Complex

The structure of Vinblastine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8cle was solved by M.Wranik, Q.Bertrand, M.W.Kepa, T.Weinert, M.Steinmetz, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.13 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.39, 159.74, 182.24, 90, 90, 90
R / Rfree (%)	20 / 24.8

The structure of Vinblastine Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Vinblastine Bound to Tubulin (T2R-Ttl) Complex (pdb code 8cle). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Vinblastine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8cle:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Vinblastine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vinblastine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.2 occ:1.00 O2G A:GTP501 2.3 50.0 1.0 O1B A:GTP501 2.4 55.0 1.0 PG A:GTP501 3.7 51.2 1.0 PB A:GTP501 3.7 55.1 1.0 CG A:GLU71 3.8 70.5 1.0 OD2 A:ASP98 4.0 54.9 1.0 O3B A:GTP501 4.0 53.2 1.0 OD2 A:ASP69 4.1 70.0 1.0 OD1 A:ASP69 4.1 69.6 1.0 NZ B:LYS254 4.1 47.9 1.0 CB A:GLN11 4.2 60.0 1.0 OE2 A:GLU71 4.2 72.0 1.0 CD A:GLU71 4.4 74.0 1.0 O1G A:GTP501 4.5 54.8 1.0 O3A A:GTP501 4.5 54.3 1.0 CG A:ASP69 4.5 69.9 1.0 CB A:ASP98 4.6 58.0 1.0 N A:GLN11 4.7 55.6 1.0 O3G A:GTP501 4.7 49.5 1.0 O1A A:GTP501 4.7 50.3 1.0 CG A:ASP98 4.7 56.1 1.0 O2B A:GTP501 4.8 55.0 1.0 NE2 A:GLN11 4.9 64.0 1.0

Magnesium binding site 2 out of 2 in the Vinblastine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vinblastine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:41.7 occ:1.00 O1B C:GTP502 2.7 47.3 1.0 O1G C:GTP502 2.8 48.2 1.0 O3G C:GTP502 3.1 47.5 1.0 PG C:GTP502 3.4 46.5 1.0 PB C:GTP502 3.7 48.4 1.0 OE2 C:GLU71 3.8 57.6 1.0 OD2 C:ASP69 3.8 60.8 1.0 OD1 C:ASP69 3.9 58.3 1.0 O3B C:GTP502 3.9 46.8 1.0 O3A C:GTP502 4.0 48.8 1.0 CG C:GLU71 4.0 55.4 1.0 OD2 C:ASP98 4.2 53.1 1.0 NZ D:LYS254 4.2 55.9 1.0 CB C:GLN11 4.3 48.6 1.0 NE2 C:GLN11 4.3 57.8 1.0 CG C:ASP69 4.3 59.2 1.0 CD C:GLU71 4.4 58.2 1.0 N C:GLN11 4.5 43.6 1.0 CB C:ASP98 4.5 53.4 1.0 CG C:ASP98 4.8 54.5 1.0 O2G C:GTP502 4.9 44.5 1.0 CA C:GLN11 5.0 45.4 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