Calcium in PDB 8clc: Tubulin (T2R-Ttl) Complex

The structure of Tubulin (T2R-Ttl) Complex, PDB code: 8clc 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)	15.20 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.53, 160.48, 181.24, 90, 90, 90
R / Rfree (%)	18.6 / 23.4

The structure of Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

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

Calcium binding site 1 out of 2 in the 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 Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.9 occ:1.00 OG1 A:THR41 2.4 128.6 1.0 OD2 A:ASP39 2.5 101.1 1.0 O A:THR41 2.5 125.4 1.0 OE2 A:GLU55 2.6 105.6 1.0 O A:GLY44 2.7 126.8 1.0 OE1 A:GLU55 2.8 102.5 1.0 OD1 A:ASP39 2.8 105.2 1.0 CG A:ASP39 3.0 103.4 1.0 CD A:GLU55 3.0 102.6 1.0 CB A:THR41 3.5 127.3 1.0 C A:THR41 3.6 126.7 1.0 C A:GLY44 3.7 125.8 1.0 OD2 A:ASP47 3.9 94.2 1.0 CA A:THR41 3.9 128.1 1.0 N A:THR41 4.2 128.2 1.0 CA A:GLY45 4.3 118.6 1.0 N A:GLY45 4.3 115.7 1.0 CB A:ASP39 4.5 103.7 1.0 N A:GLY44 4.5 129.6 1.0 CZ A:PHE49 4.5 83.9 1.0 OD1 A:ASN50 4.5 95.6 1.0 CG A:GLU55 4.5 102.0 1.0 CE2 A:PHE49 4.6 82.5 1.0 ND2 A:ASN50 4.6 89.1 1.0 NE2 A:HIS61 4.6 76.0 1.0 CA A:GLY44 4.6 129.7 1.0 CG2 A:THR41 4.8 121.5 1.0 N A:ILE42 4.8 103.7 1.0

Calcium binding site 2 out of 2 in the 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 Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:72.1 occ:1.00 OG1 C:THR41 2.3 100.0 1.0 OE2 C:GLU55 2.3 71.5 1.0 O C:GLY44 2.4 75.4 1.0 OD2 C:ASP39 2.4 86.1 1.0 O C:THR41 2.5 100.8 1.0 OD1 C:ASP39 2.6 83.4 1.0 OE1 C:GLU55 2.7 70.8 1.0 CG C:ASP39 2.8 85.2 1.0 CD C:GLU55 2.9 68.8 1.0 CB C:THR41 3.4 99.1 1.0 C C:THR41 3.5 101.8 1.0 C C:GLY44 3.5 77.1 1.0 CA C:THR41 3.8 101.4 1.0 OD2 C:ASP47 3.9 85.6 1.0 N C:THR41 4.1 100.3 1.0 CA C:GLY45 4.2 91.7 1.0 N C:GLY45 4.3 87.6 1.0 CG C:GLU55 4.3 65.0 1.0 CB C:ASP39 4.3 82.4 1.0 OD1 C:ASN50 4.4 64.1 1.0 CZ C:PHE49 4.6 55.2 1.0 N C:GLY44 4.6 74.3 1.0 CA C:GLY44 4.6 74.0 1.0 NE2 C:HIS61 4.6 69.9 1.0 CG2 C:THR41 4.6 97.2 1.0 N C:ILE42 4.7 100.5 1.0 O C:HOH610 4.8 64.1 1.0 ND2 C:ASN50 4.8 55.3 1.0 CE1 C:PHE49 4.8 57.9 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