Calcium in PDB 6gj4: Tubulin-6J Complex

The structure of Tubulin-6J Complex, PDB code: 6gj4 was solved by M.Brindisi, C.Ulivieri, G.Alfano, S.Gemma, F.D.A.Balaguer, T.Khan, A.Grillo, G.Chemi, G.Menchon, A.E.Prota, N.Olieric, D.L.Agell, I.Barasoain, J.F.Diaz, A.Nebbioso, M.R.Conte, L.Lopresti, S.Magnano, R.Amet, P.Kinsella, D.M.Zisterer, O.Ibrahim, J.O'sullivan, L.Morbidelli, R.Spaccapelo, C.Baldari, S.Butini, E.Novellino, G.Campiani, L.Altucci, M.O.Steinmetz, S.Brogi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.02 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.970, 157.810, 181.220, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.1

The structure of Tubulin-6J Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-6J Complex (pdb code 6gj4). 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-6J Complex, PDB code: 6gj4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.1 occ:1.00 OG1 A:THR41 2.3 0.7 1.0 OE2 A:GLU55 2.4 94.3 1.0 OD1 A:ASP39 2.7 87.0 1.0 OD2 A:ASP39 2.7 81.7 1.0 O A:GLY44 2.7 0.9 1.0 O A:THR41 2.8 0.5 1.0 CG A:ASP39 3.0 87.8 1.0 CD A:GLU55 3.1 90.0 1.0 OE1 A:GLU55 3.2 94.7 1.0 CA A:GLY45 3.6 0.0 1.0 CB A:THR41 3.6 0.7 1.0 C A:GLY44 3.7 0.5 1.0 C A:THR41 3.8 0.5 1.0 CZ A:PHE49 4.0 82.3 1.0 CA A:THR41 4.1 0.8 1.0 OD1 A:ASN50 4.1 84.5 1.0 N A:GLY45 4.2 0.7 1.0 OD2 A:ASP47 4.2 98.6 1.0 N A:THR41 4.3 0.9 1.0 CB A:ASP39 4.4 88.3 1.0 ND2 A:ASN50 4.6 69.3 1.0 CG A:GLU55 4.6 89.7 1.0 CG2 A:THR41 4.7 0.1 1.0 CE1 A:PHE49 4.7 81.9 1.0 CG A:ASP47 4.8 96.6 1.0 CE2 A:PHE49 4.8 81.2 1.0 CG A:ASN50 4.8 78.3 1.0 C A:GLY45 4.9 0.4 1.0 NE2 A:HIS61 5.0 90.9 1.0 N A:ILE42 5.0 0.5 1.0

Calcium binding site 2 out of 2 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:77.2 occ:1.00 O C:THR41 2.4 97.3 1.0 OE2 C:GLU55 2.4 73.8 1.0 OG1 C:THR41 2.4 86.0 1.0 OD2 C:ASP39 2.4 65.5 1.0 O C:GLY44 2.5 92.8 1.0 OE1 C:GLU55 2.6 80.0 1.0 OD1 C:ASP39 2.7 72.9 1.0 CD C:GLU55 2.8 69.7 1.0 CG C:ASP39 2.9 70.9 1.0 C C:THR41 3.3 91.9 1.0 CB C:THR41 3.3 77.9 1.0 C C:GLY44 3.6 96.3 1.0 CA C:THR41 3.8 84.4 1.0 OD2 C:ASP47 3.9 0.1 1.0 N C:THR41 4.1 79.7 1.0 CA C:GLY45 4.1 87.1 1.0 N C:GLY45 4.3 85.8 1.0 CG C:GLU55 4.4 60.2 1.0 N C:ILE42 4.4 95.0 1.0 CB C:ASP39 4.4 76.1 1.0 OD1 C:ASN50 4.5 54.5 1.0 CZ C:PHE49 4.6 61.0 1.0 CA C:GLY44 4.6 0.1 1.0 N C:GLY44 4.6 0.0 1.0 CG2 C:THR41 4.7 70.0 1.0 NE2 C:HIS61 4.8 55.4 1.0 CA C:ILE42 4.9 92.2 1.0 O C:HOH676 4.9 59.2 1.0

M.Brindisi, C.Ulivieri, G.Alfano, S.Gemma, F.De Asis Balaguer, T.Khan, A.Grillo, G.Chemi, G.Menchon, A.E.Prota, N.Olieric, D.Lucena-Agell, I.Barasoain, J.F.Diaz, A.Nebbioso, M.Conte, L.Lopresti, S.Magnano, R.Amet, P.Kinsella, D.M.Zisterer, O.Ibrahim, J.O'sullivan, L.Morbidelli, R.Spaccapelo, C.Baldari, S.Butini, E.Novellino, G.Campiani, L.Altucci, M.O.Steinmetz, S.Brogi. Structure-Activity Relationships, Biological Evaluation and Structural Studies of Novel Pyrrolonaphthoxazepines As Antitumor Agents. Eur J Med Chem V. 162 290 2018.
ISSN: ISSN 1768-3254
PubMed: 30448418
DOI: 10.1016/J.EJMECH.2018.11.004