Calcium in PDB 6k9v: Crystal Structure of Tubulin in Complex with Inhibitor D64

The structure of Crystal Structure of Tubulin in Complex with Inhibitor D64, PDB code: 6k9v was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.73 / 2.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.219, 157.435, 180.045, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.8

The structure of Crystal Structure of Tubulin in Complex with Inhibitor D64 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin in Complex with Inhibitor D64 (pdb code 6k9v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Tubulin in Complex with Inhibitor D64, PDB code: 6k9v:

Calcium binding site 1 out of 1 in the Crystal Structure of Tubulin in Complex with Inhibitor D64


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tubulin in Complex with Inhibitor D64 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:41.6 occ:1.00 OE2 C:GLU55 2.4 39.4 1.0 O C:THR41 2.4 45.7 1.0 OG1 C:THR41 2.4 52.8 1.0 OD2 C:ASP39 2.5 36.0 1.0 O C:GLY44 2.5 44.3 1.0 OE1 C:GLU55 2.5 35.5 1.0 O C:HOH605 2.6 34.7 1.0 OD1 C:ASP39 2.6 43.4 1.0 CD C:GLU55 2.8 35.5 1.0 CG C:ASP39 2.9 41.3 1.0 HA3 C:GLY45 3.1 55.4 1.0 C C:GLY44 3.4 47.6 1.0 C C:THR41 3.5 41.9 1.0 CB C:THR41 3.5 40.6 1.0 HB C:THR41 3.7 48.7 1.0 HZ C:PHE49 3.8 39.4 1.0 HD21 C:ASN50 3.9 34.8 1.0 CA C:GLY45 4.0 46.2 1.0 H C:THR41 4.0 56.0 1.0 CA C:THR41 4.0 42.2 1.0 HE1 C:PHE49 4.1 42.5 1.0 N C:GLY45 4.1 47.6 1.0 H C:GLY44 4.1 54.8 1.0 OD2 C:ASP47 4.3 51.8 1.0 CG C:GLU55 4.3 37.4 1.0 HA2 C:GLY45 4.3 55.4 1.0 O C:HOH637 4.3 41.5 1.0 N C:THR41 4.3 46.6 1.0 CB C:ASP39 4.4 46.9 1.0 OD1 C:ASN50 4.4 40.9 1.0 CA C:GLY44 4.5 47.5 1.0 CZ C:PHE49 4.5 32.8 1.0 NE2 C:HIS61 4.5 34.0 1.0 HA C:ILE42 4.6 56.5 1.0 N C:GLY44 4.6 45.6 1.0 N C:ILE42 4.6 45.2 1.0 CE1 C:PHE49 4.6 35.5 1.0 ND2 C:ASN50 4.7 29.0 1.0 HA2 C:GLY44 4.7 57.0 1.0 HG2 C:GLU55 4.7 44.8 1.0 HG3 C:GLU55 4.7 44.8 1.0 HB2 C:ASP39 4.8 56.2 1.0 HB3 C:ASP39 4.8 56.2 1.0 CG2 C:THR41 4.8 43.4 1.0 H C:GLY45 4.9 57.1 1.0 O C:HOH682 4.9 36.5 1.0 HA C:THR41 4.9 50.7 1.0 HG21 C:THR41 5.0 52.1 1.0 CG C:ASN50 5.0 32.0 1.0

Y.Li, J.Yang, L.Niu, D.Hu, H.Li, L.Chen, Y.Yu, Q.Chen. Structural Insights Into the Design of Indole Derivatives As Tubulin Polymerization Inhibitors. Febs Lett. 2019.
ISSN: ISSN 0014-5793
PubMed: 31369682
DOI: 10.1002/1873-3468.13566