Magnesium in PDB 8clh: Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex

The structure of Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clh 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)	15.29 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107, 160.34, 181.92, 90, 90, 90
R / Rfree (%)	18.5 / 23.9

The structure of Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex (pdb code 8clh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, 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 Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.8 occ:1.00 O1B A:GTP501 2.0 49.0 1.0 O A:HOH625 2.0 57.3 1.0 O A:HOH610 2.1 55.9 1.0 O2G A:GTP501 2.1 53.0 1.0 O A:HOH616 2.2 61.3 1.0 O A:HOH601 2.2 55.0 1.0 PB A:GTP501 3.2 55.7 1.0 PG A:GTP501 3.3 61.9 1.0 O3B A:GTP501 3.5 75.4 1.0 O1G A:GTP501 3.9 54.0 1.0 O3A A:GTP501 3.9 68.2 1.0 NZ B:LYS254 4.0 60.7 1.0 OD1 A:ASP69 4.0 57.0 1.0 OD2 A:ASP69 4.2 58.3 1.0 CB A:GLN11 4.2 53.4 1.0 OD2 A:ASP98 4.3 53.0 1.0 CG A:GLU71 4.3 65.0 1.0 OE2 A:GLU71 4.3 66.7 1.0 N A:GLN11 4.4 50.8 1.0 ND2 B:ASN249 4.5 118.2 1.0 O2B A:GTP501 4.5 61.4 1.0 CB A:ASP98 4.5 53.3 1.0 CG A:ASP69 4.5 57.3 1.0 O3G A:GTP501 4.6 51.0 1.0 O1A A:GTP501 4.7 57.2 1.0 OE1 A:GLN11 4.7 58.1 1.0 CG A:ASP98 4.7 52.6 1.0 CD A:GLU71 4.8 66.6 1.0 PA A:GTP501 4.8 60.0 1.0 CA A:GLN11 4.9 51.8 1.0 OG1 A:THR145 5.0 49.6 1.0 CG B:ASN249 5.0 114.8 1.0

Magnesium binding site 2 out of 4 in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, 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 Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:83.2 occ:1.00 NE2 B:GLN11 2.5 67.0 1.0 O B:HOH623 2.7 66.9 1.0 O B:HOH611 2.7 36.1 1.0 O1A B:GDP501 3.0 63.3 1.0 CD B:GLN11 3.9 66.2 1.0 OD1 B:ASN101 4.0 56.5 1.0 PA B:GDP501 4.2 50.9 1.0 O3A B:GDP501 4.2 56.6 1.0 OE2 C:GLU254 4.5 79.2 1.0 OE1 B:GLN11 4.6 67.6 1.0 CB B:GLN11 4.6 63.1 1.0 CG B:GLN11 4.8 64.4 1.0 O1B B:GDP501 4.8 51.2 1.0 CG B:ASN101 4.9 56.0 1.0 ND2 B:ASN101 5.0 56.8 1.0

Magnesium binding site 3 out of 4 in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, 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 3 of Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:52.5 occ:1.00 O C:HOH616 2.0 48.9 1.0 O C:HOH611 2.0 47.7 1.0 O1B C:GTP502 2.0 45.8 1.0 O1G C:GTP502 2.0 42.6 1.0 O C:HOH604 2.1 55.4 1.0 O C:HOH624 2.1 50.1 1.0 PG C:GTP502 3.2 52.9 1.0 PB C:GTP502 3.2 49.5 1.0 O3B C:GTP502 3.5 57.6 1.0 O2G C:GTP502 3.7 47.0 1.0 OE2 C:GLU71 3.7 61.6 1.0 O3A C:GTP502 3.9 60.8 1.0 OD2 C:ASP98 3.9 47.8 1.0 NZ D:LYS254 4.0 53.6 1.0 OD1 C:ASP69 4.0 50.3 1.0 OD2 C:ASP69 4.2 51.9 1.0 CG C:GLU71 4.2 60.2 1.0 CB C:GLN11 4.3 50.4 1.0 CB C:ASP98 4.3 47.8 1.0 CD C:GLU71 4.4 61.3 1.0 O3G C:GTP502 4.5 42.4 1.0 N C:GLN11 4.5 48.2 1.0 O2B C:GTP502 4.5 56.2 1.0 CG C:ASP98 4.5 48.0 1.0 CG C:ASP69 4.6 50.3 1.0 NE2 C:GLN11 4.6 53.8 1.0 O1A C:GTP502 4.8 51.1 1.0 PA C:GTP502 4.9 49.5 1.0 CA C:GLN11 4.9 49.1 1.0

Magnesium binding site 4 out of 4 in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, 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 4 of Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:93.2 occ:1.00 O1A D:GDP501 2.5 114.8 1.0 OE1 D:GLN11 3.0 91.5 1.0 PA D:GDP501 3.8 78.6 1.0 OD1 D:ASN101 3.8 85.8 1.0 O3A D:GDP501 4.0 100.6 1.0 C5' D:GDP501 4.2 81.8 1.0 CD D:GLN11 4.3 89.6 1.0 O5' D:GDP501 4.5 75.1 1.0 CG D:ASN101 4.7 87.2 1.0 ND2 D:ASN101 4.9 90.2 1.0 CB D:GLN11 4.9 83.8 1.0 O2A D:GDP501 4.9 72.4 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