Calcium in PDB 8clb: Colchicine Bound to Tubulin (T2R-Ttl) Complex

The structure of Colchicine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clb was solved by M.Wranik, M.W.Kepa, Q.Bertrand, 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)	15.18 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.71, 160.61, 180.73, 90, 90, 90
R / Rfree (%)	16.3 / 21.4

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

Calcium binding site 1 out of 2 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:98.1 occ:1.00 O A:GLY44 2.2 107.1 1.0 OD2 A:ASP39 2.3 99.3 1.0 OE2 A:GLU55 2.4 100.9 1.0 OD1 A:ASP39 2.5 102.9 1.0 OG1 A:THR41 2.5 114.8 1.0 CG A:ASP39 2.7 100.9 1.0 O A:THR41 2.7 112.5 1.0 OE1 A:GLU55 2.8 103.2 1.0 CD A:GLU55 2.9 102.2 1.0 HA3 A:GLY45 3.3 104.9 1.0 HZ A:PHE49 3.4 68.1 1.0 C A:GLY44 3.4 108.9 1.0 HE1 A:HIS61 3.6 88.8 1.0 HD21 A:ASN50 3.7 78.3 1.0 H A:GLY44 3.8 113.6 1.0 C A:THR41 3.8 113.6 1.0 CB A:THR41 3.8 111.5 1.0 H A:THR41 4.0 111.9 1.0 OD1 A:ASP47 4.1 91.5 1.0 CA A:GLY45 4.1 104.9 1.0 HB A:THR41 4.1 111.5 1.0 CZ A:PHE49 4.1 68.1 1.0 CB A:ASP39 4.2 100.8 1.0 CA A:THR41 4.2 111.9 1.0 N A:GLY45 4.2 107.6 1.0 CG A:GLU55 4.4 96.4 1.0 N A:GLY44 4.4 113.6 1.0 N A:THR41 4.4 111.9 1.0 HE1 A:PHE49 4.5 67.6 1.0 OD1 A:ASN50 4.5 87.2 1.0 CA A:GLY44 4.5 111.6 1.0 ND2 A:ASN50 4.5 78.3 1.0 HB2 A:ASP39 4.5 100.8 1.0 CE1 A:HIS61 4.5 88.8 1.0 HB3 A:ASP39 4.6 100.8 1.0 CE1 A:PHE49 4.7 67.6 1.0 HG3 A:GLU55 4.7 96.4 1.0 HG2 A:GLU55 4.8 96.4 1.0 HA2 A:GLY45 4.8 104.9 1.0 HA2 A:GLY44 4.8 111.6 1.0 C A:GLY45 4.9 104.8 1.0 HA A:ILE42 4.9 103.1 1.0 CG2 A:THR41 4.9 109.4 1.0 N A:ILE42 4.9 105.3 1.0 CG A:ASN50 4.9 82.8 1.0 HA A:ASP39 5.0 101.6 1.0 HG23 A:THR41 5.0 109.4 1.0

Calcium binding site 2 out of 2 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:91.7 occ:1.00 OG1 C:THR41 1.9 81.1 1.0 OE2 C:GLU55 2.3 76.5 1.0 OD2 C:ASP39 2.3 74.1 1.0 O C:GLY44 2.3 89.5 1.0 OD1 C:ASP39 2.5 77.4 1.0 O C:THR41 2.6 84.9 1.0 OE1 C:GLU55 2.7 71.5 1.0 CG C:ASP39 2.7 74.2 1.0 CD C:GLU55 2.8 72.5 1.0 CB C:THR41 3.3 87.9 1.0 HA3 C:GLY45 3.3 69.9 1.0 C C:GLY44 3.5 88.7 1.0 HZ C:PHE49 3.5 55.7 1.0 C C:THR41 3.6 87.2 1.0 H C:THR41 3.7 86.9 1.0 HB C:THR41 3.7 87.9 1.0 CA C:THR41 3.8 87.8 1.0 HE2 C:HIS61 3.8 58.8 1.0 H C:GLY44 4.0 84.5 1.0 HD21 C:ASN50 4.1 58.5 1.0 N C:THR41 4.1 86.9 1.0 OD2 C:ASP47 4.1 73.3 1.0 CA C:GLY45 4.2 69.9 1.0 HE1 C:PHE49 4.2 57.6 1.0 HG23 C:THR41 4.2 84.7 1.0 CG2 C:THR41 4.2 84.7 1.0 CB C:ASP39 4.3 74.0 1.0 N C:GLY45 4.3 68.6 1.0 OD1 C:ASN50 4.3 61.6 1.0 CZ C:PHE49 4.3 55.7 1.0 CG C:GLU55 4.3 66.9 1.0 HG21 C:THR41 4.3 84.7 1.0 NE2 C:HIS61 4.5 58.8 1.0 N C:GLY44 4.6 84.5 1.0 CA C:GLY44 4.6 89.6 1.0 CE1 C:PHE49 4.6 57.6 1.0 HB3 C:ASP39 4.6 74.0 1.0 HG3 C:GLU55 4.6 66.9 1.0 HB2 C:ASP39 4.6 74.0 1.0 HA2 C:GLY45 4.6 69.9 1.0 HG2 C:GLU55 4.7 66.9 1.0 HA C:THR41 4.7 87.8 1.0 ND2 C:ASN50 4.8 58.5 1.0 N C:ILE42 4.8 81.2 1.0 HA2 C:GLY44 4.9 89.6 1.0 CG C:ASN50 5.0 58.0 1.0 HA C:ILE42 5.0 82.1 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