Calcium in PDB 8diq: Tubulin-RB3_SLD-Ttl in Complex with SB226

The structure of Tubulin-RB3_SLD-Ttl in Complex with SB226, PDB code: 8diq was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.491, 158.414, 181.226, 90, 90, 90
R / Rfree (%)	18.2 / 21

The structure of Tubulin-RB3_SLD-Ttl in Complex with SB226 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with SB226 (pdb code 8diq). 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-RB3_SLD-Ttl in Complex with SB226, PDB code: 8diq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:72.3 occ:1.00 O A:GLY44 2.3 75.0 1.0 OD2 A:ASP39 2.3 73.9 1.0 O A:HOH607 2.4 81.5 1.0 OD1 A:ASP39 2.4 74.5 1.0 O A:THR41 2.5 82.7 1.0 OE2 A:GLU55 2.6 74.3 1.0 OE1 A:GLU55 2.6 61.5 1.0 OG1 A:THR41 2.6 81.3 1.0 CG A:ASP39 2.7 74.9 1.0 CD A:GLU55 2.9 73.6 1.0 C A:GLY44 3.4 80.9 1.0 CB A:THR41 3.5 80.2 1.0 C A:THR41 3.5 83.5 1.0 CA A:THR41 4.0 79.9 1.0 CB A:ASP39 4.2 75.2 1.0 N A:THR41 4.2 82.0 1.0 N A:GLY44 4.3 78.4 1.0 N A:GLY45 4.3 82.6 1.0 CA A:GLY45 4.3 84.3 1.0 CA A:GLY44 4.4 78.7 1.0 O A:HOH631 4.4 60.0 1.0 CG A:GLU55 4.4 70.8 1.0 OD2 A:ASP47 4.4 78.4 1.0 CZ A:PHE49 4.5 65.7 1.0 OD1 A:ASN50 4.6 72.3 1.0 N A:ILE42 4.7 83.8 1.0 NE2 A:HIS61 4.7 73.0 1.0 ND2 A:ASN50 4.8 61.6 1.0 CG2 A:THR41 4.9 71.7 1.0 CE1 A:PHE49 4.9 70.6 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:53.5 occ:1.00 OE1 C:GLU55 2.3 52.4 1.0 O C:THR41 2.3 60.5 1.0 O C:GLY44 2.4 59.2 1.0 OD2 C:ASP39 2.4 61.2 1.0 O C:HOH606 2.5 47.5 1.0 OE2 C:GLU55 2.5 55.6 1.0 OD1 C:ASP39 2.5 63.3 1.0 OG1 C:THR41 2.5 49.6 1.0 CD C:GLU55 2.7 50.8 1.0 CG C:ASP39 2.8 62.5 1.0 C C:THR41 3.4 58.3 1.0 C C:GLY44 3.4 65.7 1.0 CB C:THR41 3.5 53.5 1.0 CA C:THR41 3.9 56.9 1.0 CA C:GLY45 4.1 65.8 1.0 N C:GLY45 4.2 69.8 1.0 O C:HOH608 4.2 53.6 1.0 N C:THR41 4.2 57.6 1.0 CG C:GLU55 4.3 48.6 1.0 CB C:ASP39 4.3 63.1 1.0 N C:GLY44 4.3 69.9 1.0 CA C:GLY44 4.4 66.7 1.0 OD2 C:ASP47 4.5 67.0 1.0 N C:ILE42 4.6 61.5 1.0 OD1 C:ASN50 4.6 51.7 1.0 NE2 C:HIS61 4.7 43.4 1.0 CZ C:PHE49 4.7 45.4 1.0 CE1 C:PHE49 4.8 46.4 1.0 ND2 C:ASN50 4.9 45.6 1.0 CG2 C:THR41 4.9 47.5 1.0 O C:HOH692 4.9 52.0 1.0

S.Deng, S.Banerjee, H.Chen, S.Pochampally, Y.Wang, M.K.Yun, S.W.White, K.Parmar, B.Meibohm, K.L.Hartman, Z.Wu, D.D.Miller, W.Li. SB226, An Inhibitor of Tubulin Polymerization, Inhibits Paclitaxel-Resistant Melanoma Growth and Spontaneous Metastasis. Cancer Lett. 16046 2022.
ISSN: ESSN 1872-7980
PubMed: 36596380
DOI: 10.1016/J.CANLET.2022.216046