Calcium in PDB 8clg: Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex

The structure of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clg 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)	15.26 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.76, 160.76, 180.96, 90, 90, 90
R / Rfree (%)	17.8 / 22.7

The structure of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

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

Calcium binding site 1 out of 4 in the Epothilone A and Colchicine 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 Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:79.9 occ:1.00 O A:THR41 2.4 89.8 1.0 OD2 A:ASP39 2.4 88.8 1.0 OD1 A:ASP39 2.5 89.7 1.0 O A:GLY44 2.5 90.3 1.0 OE1 A:GLU55 2.6 68.5 1.0 OE2 A:GLU55 2.6 71.1 1.0 CG A:ASP39 2.8 88.5 1.0 CD A:GLU55 3.0 69.4 1.0 CB A:THR41 3.2 88.9 1.0 C A:THR41 3.4 90.9 1.0 C A:GLY44 3.5 89.0 1.0 CA A:THR41 3.7 88.7 1.0 CG2 A:THR41 3.9 90.7 1.0 OG1 A:THR41 4.0 88.1 1.0 N A:THR41 4.1 89.2 1.0 N A:GLY45 4.2 93.2 1.0 CA A:GLY45 4.2 93.7 1.0 N A:GLY44 4.3 91.1 1.0 OD2 A:ASP47 4.3 75.8 1.0 CB A:ASP39 4.3 89.2 1.0 CA A:GLY44 4.4 90.6 1.0 CG A:GLU55 4.5 69.6 1.0 N A:ILE42 4.5 97.3 1.0 CZ A:PHE49 4.6 69.7 1.0 CE1 A:HIS61 4.7 66.5 1.0 ND2 A:ASN50 4.9 67.8 1.0 CE1 A:PHE49 4.9 67.4 1.0 OD1 A:ASN50 4.9 66.1 1.0

Calcium binding site 2 out of 4 in the Epothilone A and Colchicine 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 Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:77.6 occ:0.00 OD2 B:ASP120 3.9 70.6 1.0 OD1 B:ASP120 3.9 69.8 1.0 CG B:ASP120 4.3 70.0 1.0 CB B:ASP116 4.4 64.8 1.0 CG B:ASP116 4.8 65.4 1.0 OD2 B:ASP116 4.9 69.1 1.0 O B:ASP116 5.0 64.3 1.0

Calcium binding site 3 out of 4 in the Epothilone A and Colchicine 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 3 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:94.7 occ:0.00 OE2 B:GLU113 2.4 84.2 1.0 CD B:GLU113 3.0 81.5 1.0 OE1 B:GLU113 3.3 81.2 1.0 CG B:GLU113 4.2 77.4 1.0 CB B:GLU113 4.7 74.7 1.0 OE1 B:GLU110 4.9 51.3 1.0

Calcium binding site 4 out of 4 in the Epothilone A and Colchicine 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 4 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:71.5 occ:1.00 OG1 C:THR41 1.8 93.1 1.0 OE2 C:GLU55 2.1 68.5 1.0 OD2 C:ASP39 2.3 70.1 1.0 O C:THR41 2.4 91.3 1.0 OE1 C:GLU55 2.7 69.4 1.0 O C:GLY44 2.7 73.1 1.0 CD C:GLU55 2.7 66.9 1.0 OD1 C:ASP39 2.8 73.6 1.0 CG C:ASP39 2.9 70.8 1.0 CB C:THR41 3.1 91.7 1.0 C C:THR41 3.3 92.8 1.0 C C:GLY44 3.5 71.0 1.0 CA C:THR41 3.6 93.5 1.0 N C:THR41 4.2 92.4 1.0 CG C:GLU55 4.2 63.3 1.0 N C:GLY45 4.2 73.8 1.0 CG2 C:THR41 4.2 91.9 1.0 OD2 C:ASP47 4.3 67.1 1.0 CA C:GLY45 4.3 74.5 1.0 CZ C:PHE49 4.4 51.0 1.0 N C:GLY44 4.4 72.3 1.0 CB C:ASP39 4.4 70.6 1.0 CA C:GLY44 4.4 70.4 1.0 N C:ILE42 4.4 82.9 1.0 OD1 C:ASN50 4.6 52.0 1.0 NE2 C:HIS61 4.6 53.8 1.0 CE1 C:PHE49 4.7 49.1 1.0 ND2 C:ASN50 4.8 49.0 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