Calcium 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
Magnesium	(Mg)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Drug Cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca503 b:96.1 occ:1.00 OE1 A:GLU55 2.4 99.1 1.0 O A:GLY44 2.4 105.9 1.0 OD1 A:ASP39 2.5 100.0 1.0 OD2 A:ASP39 2.5 99.4 1.0 O A:THR41 2.6 102.8 1.0 CG A:ASP39 2.8 99.6 1.0 OE2 A:GLU55 2.8 96.9 1.0 CD A:GLU55 2.9 97.7 1.0 CB A:THR41 3.3 102.2 1.0 C A:THR41 3.5 104.2 1.0 C A:GLY44 3.6 105.9 1.0 OD2 A:ASP47 3.8 90.1 1.0 CA A:THR41 3.8 104.0 1.0 CG2 A:THR41 3.9 103.0 1.0 CA A:GLY45 4.0 120.0 1.0 N A:THR41 4.1 103.7 1.0 N A:GLY45 4.2 120.6 1.0 CB A:ASP39 4.3 100.0 1.0 CZ A:PHE49 4.4 79.7 1.0 OG1 A:THR41 4.4 102.5 1.0 CG A:GLU55 4.4 97.4 1.0 OD1 A:ASN50 4.4 84.9 1.0 NE2 A:HIS61 4.6 84.5 1.0 CE1 A:PHE49 4.6 76.5 1.0 N A:GLY44 4.7 108.5 1.0 CA A:GLY44 4.7 106.9 1.0 N A:ILE42 4.8 110.4 1.0 ND2 A:ASN50 4.9 84.0 1.0 C A:GLY45 4.9 118.5 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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 C:Ca504 b:89.6 occ:1.00 OG1 C:THR41 2.2 113.6 1.0 O C:GLY44 2.2 88.4 1.0 O C:THR41 2.3 113.4 1.0 OD2 C:ASP39 2.4 85.3 1.0 OE1 C:GLU55 2.5 84.8 1.0 OE2 C:GLU55 2.5 83.3 1.0 OD1 C:ASP39 2.8 87.6 1.0 CD C:GLU55 2.8 83.1 1.0 CG C:ASP39 2.9 86.5 1.0 C C:THR41 3.3 115.2 1.0 C C:GLY44 3.4 88.6 1.0 CB C:THR41 3.4 115.7 1.0 CA C:THR41 3.8 116.4 1.0 CA C:GLY45 4.1 94.5 1.0 N C:THR41 4.1 116.2 1.0 N C:GLY45 4.2 94.2 1.0 CG C:GLU55 4.4 80.9 1.0 N C:ILE42 4.4 118.1 1.0 CB C:ASP39 4.4 86.9 1.0 CG2 C:THR41 4.4 117.0 1.0 CA C:GLY44 4.5 88.3 1.0 N C:GLY44 4.6 89.3 1.0 NE2 C:HIS61 4.7 65.2 1.0 OD1 C:ASN50 4.7 61.4 1.0 CZ C:PHE49 4.7 63.0 1.0 CA C:ILE42 4.9 117.1 1.0 ND2 C:ASN50 4.9 58.9 1.0 CE1 C:PHE49 5.0 61.3 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