Calcium in PDB 6y6d: Tubulin-7-Aminonoscapine Complex

The structure of Tubulin-7-Aminonoscapine Complex, PDB code: 6y6d was solved by M.A.Oliva, A.E.Prota, J.Rodriguez-Salarichs, W.Gu, Y.L.Bennani, J.Jimenez-Barbero, A.Canales, M.O.Steinmetz, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.34 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.360, 157.150, 180.370, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.4

The structure of Tubulin-7-Aminonoscapine Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-7-Aminonoscapine Complex (pdb code 6y6d). 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-7-Aminonoscapine Complex, PDB code: 6y6d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:86.6 occ:1.00 O A:GLY44 2.3 97.0 1.0 OD2 A:ASP39 2.4 86.9 1.0 O A:THR41 2.4 0.6 1.0 OE2 A:GLU55 2.4 91.0 1.0 OD1 A:ASP39 2.4 85.5 1.0 OG1 A:THR41 2.4 0.1 1.0 OE1 A:GLU55 2.5 91.8 1.0 CG A:ASP39 2.7 84.7 1.0 CD A:GLU55 2.8 87.9 1.0 CB A:THR41 3.4 0.8 1.0 C A:THR41 3.4 0.9 1.0 C A:GLY44 3.5 0.2 1.0 CA A:THR41 3.8 0.3 1.0 N A:THR41 4.0 1.0 1.0 CB A:ASP39 4.2 87.1 1.0 CZ A:PHE49 4.3 71.2 1.0 CG A:GLU55 4.3 85.2 1.0 CA A:GLY45 4.3 99.4 1.0 N A:GLY45 4.3 99.6 1.0 N A:GLY44 4.4 0.5 1.0 OD2 A:ASP47 4.5 91.6 1.0 NE2 A:HIS61 4.5 89.7 1.0 CA A:GLY44 4.5 0.3 1.0 N A:ILE42 4.6 0.3 1.0 OD1 A:ASN50 4.7 89.0 1.0 CG2 A:THR41 4.7 98.0 1.0 ND2 A:ASN50 4.9 75.4 1.0 CE1 A:PHE49 4.9 72.3 1.0

Calcium binding site 2 out of 2 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:69.3 occ:1.00 OD2 C:ASP39 2.4 60.0 1.0 O C:THR41 2.4 71.8 1.0 O C:HOH602 2.4 69.7 1.0 OE1 C:GLU55 2.4 58.1 1.0 OE2 C:GLU55 2.4 60.1 1.0 OG1 C:THR41 2.5 70.2 1.0 OD1 C:ASP39 2.5 63.0 1.0 O C:GLY44 2.5 75.3 1.0 CG C:ASP39 2.7 60.1 1.0 CD C:GLU55 2.7 61.2 1.0 C C:THR41 3.4 76.9 1.0 CB C:THR41 3.5 71.5 1.0 C C:GLY44 3.6 79.4 1.0 CA C:THR41 3.8 74.0 1.0 N C:THR41 4.2 71.6 1.0 O C:HOH613 4.2 63.9 1.0 CB C:ASP39 4.2 70.3 1.0 CG C:GLU55 4.3 57.9 1.0 CA C:GLY45 4.4 76.9 1.0 N C:GLY45 4.4 74.8 1.0 OD2 C:ASP47 4.4 84.4 1.0 N C:GLY44 4.4 88.8 1.0 CA C:GLY44 4.5 83.9 1.0 N C:ILE42 4.5 82.8 1.0 CZ C:PHE49 4.5 55.2 1.0 OD1 C:ASN50 4.6 51.3 1.0 NE2 C:HIS61 4.7 51.3 1.0 CG2 C:THR41 4.8 63.8 1.0 CE1 C:PHE49 4.9 54.5 1.0 ND2 C:ASN50 4.9 51.1 1.0 CA C:ILE42 5.0 85.2 1.0

M.A.Oliva, A.E.Prota, J.Rodriguez-Salarichs, Y.L.Bennani, J.Jimenez-Barbero, K.Bargsten, A.Canales, M.O.Steinmetz, J.F.Diaz. Structural Basis of Noscapine Activation For Tubulin Binding. J.Med.Chem. V. 63 8495 2020.
ISSN: ISSN 0022-2623
PubMed: 32657585
DOI: 10.1021/ACS.JMEDCHEM.0C00855