Calcium 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:

Magnesium

(Mg)

2 atoms

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

Calcium 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 Calcium with other atoms in the Ca binding site number 1 of Vinblastine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:91.4 occ:1.00 OD2 A:ASP39 2.2 105.5 1.0 OE2 A:GLU55 2.3 99.1 1.0 OG1 A:THR41 2.6 101.4 1.0 OD1 A:ASP39 2.7 109.0 1.0 O A:GLY44 2.7 113.6 1.0 CG A:ASP39 2.7 107.0 1.0 CD A:GLU55 3.0 100.9 1.0 OE1 A:GLU55 3.0 104.4 1.0 O A:THR41 3.1 102.9 1.0 C A:GLY44 3.6 112.8 1.0 CZ A:PHE49 3.7 79.6 1.0 CB A:THR41 3.8 103.3 1.0 CA A:GLY45 3.9 141.0 1.0 C A:THR41 4.1 106.0 1.0 N A:GLY45 4.1 141.5 1.0 OD1 A:ASN50 4.2 84.9 1.0 CB A:ASP39 4.2 107.1 1.0 CA A:THR41 4.4 106.5 1.0 OD2 A:ASP47 4.4 96.8 1.0 CE1 A:PHE49 4.4 77.1 1.0 CG A:GLU55 4.4 97.3 1.0 N A:THR41 4.5 102.7 1.0 ND2 A:ASN50 4.6 79.4 1.0 CE2 A:PHE49 4.6 77.7 1.0 NE2 A:HIS61 4.7 85.2 1.0 CA A:GLY44 4.7 114.5 1.0 N A:GLY44 4.8 116.6 1.0 CG A:ASN50 4.8 81.7 1.0 CG A:ASP47 4.9 95.3 1.0 CG2 A:THR41 5.0 104.1 1.0 CA A:ASP39 5.0 108.0 1.0

Calcium 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 Calcium with other atoms in the Ca binding site number 2 of Vinblastine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:30.1 occ:1.00 OE2 C:GLU55 1.9 76.9 1.0 OG1 C:THR41 2.2 81.5 1.0 OD2 C:ASP39 2.3 79.2 1.0 O C:THR41 2.4 81.9 1.0 CD C:GLU55 2.7 80.0 1.0 OD1 C:ASP39 2.7 83.4 1.0 OE1 C:GLU55 2.9 82.4 1.0 CG C:ASP39 2.9 80.5 1.0 O C:GLY44 3.3 84.8 1.0 CB C:THR41 3.5 84.7 1.0 C C:THR41 3.5 84.4 1.0 C C:GLY44 3.9 83.3 1.0 OD2 C:ASP47 4.0 69.0 1.0 CA C:THR41 4.0 84.2 1.0 CG C:GLU55 4.1 76.6 1.0 CA C:GLY45 4.1 87.5 1.0 CZ C:PHE49 4.2 54.4 1.0 OD1 C:ASN50 4.3 62.8 1.0 ND2 C:ASN50 4.3 58.5 1.0 CE1 C:PHE49 4.3 52.8 1.0 N C:GLY45 4.3 86.9 1.0 NE2 C:HIS61 4.3 69.5 1.0 CB C:ASP39 4.3 78.3 1.0 N C:THR41 4.5 84.1 1.0 CG2 C:THR41 4.6 86.0 1.0 N C:ILE42 4.7 97.0 1.0 CG C:ASN50 4.7 59.9 1.0 CA C:GLY44 4.9 82.5 1.0 N C:GLY44 5.0 84.5 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