Calcium in PDB 5ng1: Tubulin-Mtc-Zampanolide Complex

The structure of Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1 was solved by J.J.Field, B.Pera, J.Estevez Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, A.E.Prota, G.Menchon, J.H.Miller, K.-H.Altmann, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.69 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.237, 157.418, 178.858, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22

The structure of Tubulin-Mtc-Zampanolide Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Mtc-Zampanolide Complex (pdb code 5ng1). 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-Mtc-Zampanolide Complex, PDB code: 5ng1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.0 occ:1.00 O A:GLY44 2.9 66.4 1.0 OD1 A:ASP39 2.9 71.1 1.0 O A:THR41 2.9 76.0 1.0 OD2 A:ASP39 2.9 63.3 1.0 OE1 A:GLU55 2.9 84.7 1.0 OG1 A:THR41 2.9 72.3 1.0 OE2 A:GLU55 2.9 72.6 1.0 CG A:ASP39 3.2 68.5 1.0 CD A:GLU55 3.3 77.8 1.0 C A:GLY44 3.5 73.3 1.0 CA A:GLY45 3.7 80.1 1.0 CB A:THR41 3.7 71.4 1.0 OD2 A:ASP47 3.8 71.3 1.0 N A:GLY45 3.8 74.2 1.0 C A:THR41 3.9 69.8 1.0 CZ A:PHE49 3.9 61.8 1.0 OD1 A:ASN50 4.0 66.6 1.0 CA A:THR41 4.2 73.9 1.0 N A:THR41 4.4 80.0 1.0 CA A:GLY44 4.5 75.9 1.0 ND2 A:ASN50 4.5 60.2 1.0 CE1 A:PHE49 4.5 56.5 1.0 C A:GLY45 4.6 73.5 1.0 N A:GLY44 4.6 78.0 1.0 CB A:ASP39 4.6 63.9 1.0 CG A:ASN50 4.7 59.0 1.0 CG A:GLU55 4.8 71.0 1.0 CE2 A:PHE49 4.9 60.9 1.0 CG A:ASP47 4.9 66.1 1.0

Calcium binding site 2 out of 2 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:63.0 occ:1.00 OG1 C:THR41 2.2 79.4 1.0 O C:THR41 2.4 74.3 1.0 O C:GLY44 2.4 62.5 1.0 OE2 C:GLU55 2.5 56.3 1.0 OD2 C:ASP39 2.5 55.8 1.0 OD1 C:ASP39 2.6 53.9 1.0 OE1 C:GLU55 2.6 50.1 1.0 CD C:GLU55 2.8 55.8 1.0 CG C:ASP39 2.9 55.6 1.0 C C:THR41 3.4 68.7 1.0 CB C:THR41 3.4 76.8 1.0 C C:GLY44 3.4 64.6 1.0 CA C:THR41 3.8 68.1 1.0 OD2 C:ASP47 4.0 64.4 1.0 N C:GLY45 4.1 65.9 1.0 CA C:GLY45 4.2 67.5 1.0 N C:THR41 4.2 65.8 1.0 CG C:GLU55 4.3 52.0 1.0 N C:GLY44 4.3 61.9 1.0 O C:HOH619 4.3 56.7 1.0 CB C:ASP39 4.4 60.9 1.0 CA C:GLY44 4.5 61.2 1.0 CZ C:PHE49 4.5 53.6 1.0 OD1 C:ASN50 4.5 50.2 1.0 N C:ILE42 4.6 66.8 1.0 CG2 C:THR41 4.6 85.5 1.0 NE2 C:HIS61 4.6 43.8 1.0 ND2 C:ASN50 4.8 42.2 1.0 CE1 C:PHE49 4.9 55.9 1.0

J.J.Field, B.Pera, J.E.Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, J.M.Andreu, A.E.Prota, G.Menchon, J.H.Miller, K.H.Altmann, J.F.Diaz. Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704