Calcium in PDB 4tv9: Tubulin-PM060184 Complex

The structure of Tubulin-PM060184 Complex, PDB code: 4tv9 was solved by A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.04 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.200, 157.290, 180.220, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.8

The structure of Tubulin-PM060184 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-PM060184 Complex (pdb code 4tv9). 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-PM060184 Complex, PDB code: 4tv9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:72.6 occ:1.00 O A:GLY44 2.4 86.6 1.0 OD2 A:ASP39 2.4 75.7 1.0 O A:THR41 2.4 84.1 1.0 OG1 A:THR41 2.5 68.0 1.0 OE2 A:GLU55 2.5 64.0 1.0 OD1 A:ASP39 2.6 76.9 1.0 O A:HOH742 2.6 71.0 1.0 OE1 A:GLU55 2.7 67.5 1.0 CG A:ASP39 2.9 76.2 1.0 CD A:GLU55 3.0 67.3 1.0 CB A:THR41 3.3 76.0 1.0 C A:GLY44 3.4 83.4 1.0 C A:THR41 3.4 85.3 1.0 CA A:THR41 3.8 84.8 1.0 CA A:GLY45 4.0 81.8 1.0 N A:GLY45 4.1 83.5 1.0 N A:THR41 4.2 85.5 1.0 CB A:ASP39 4.4 74.0 1.0 CZ A:PHE49 4.4 74.5 1.0 CA A:GLY44 4.4 85.9 1.0 N A:GLY44 4.5 87.4 1.0 CG A:GLU55 4.5 69.4 1.0 OD1 A:ASN50 4.5 74.0 1.0 OD2 A:ASP47 4.6 71.5 1.0 N A:ILE42 4.6 88.0 1.0 CG2 A:THR41 4.7 72.9 1.0 ND2 A:ASN50 4.8 64.4 1.0 NE2 A:HIS61 4.9 79.7 1.0 CE1 A:PHE49 5.0 69.8 1.0

Calcium binding site 2 out of 2 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:56.7 occ:1.00 O C:THR41 2.4 54.4 1.0 OD2 C:ASP39 2.4 63.8 1.0 OE1 C:GLU55 2.4 51.4 1.0 O C:GLY44 2.5 63.3 1.0 OE2 C:GLU55 2.5 53.1 1.0 O C:HOH732 2.5 53.4 1.0 OG1 C:THR41 2.5 54.4 1.0 OD1 C:ASP39 2.7 58.1 1.0 CD C:GLU55 2.8 49.9 1.0 CG C:ASP39 2.9 63.2 1.0 C C:THR41 3.4 61.4 1.0 CB C:THR41 3.5 58.6 1.0 C C:GLY44 3.5 72.7 1.0 CA C:THR41 3.9 65.0 1.0 N C:THR41 4.3 69.3 1.0 N C:GLY45 4.3 69.8 1.0 CG C:GLU55 4.3 48.8 1.0 CA C:GLY45 4.3 69.3 1.0 O C:HOH648 4.4 52.1 1.0 CB C:ASP39 4.4 61.9 1.0 N C:GLY44 4.4 70.3 1.0 CA C:GLY44 4.5 73.6 1.0 OD2 C:ASP47 4.5 56.0 1.0 N C:ILE42 4.5 64.4 1.0 NE2 C:HIS61 4.6 45.7 1.0 OD1 C:ASN50 4.6 47.8 1.0 CZ C:PHE49 4.6 51.1 1.0 CG2 C:THR41 4.9 53.8 1.0 ND2 C:ASN50 4.9 46.6 1.0 CA C:ILE42 4.9 66.3 1.0 CE1 C:PHE49 5.0 50.4 1.0

A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz. A New Tubulin-Binding Site and Pharmacophore For Microtubule-Destabilizing Anticancer Drugs. Proc.Natl.Acad.Sci.Usa V. 111 13817 2014.
ISSN: ESSN 1091-6490
PubMed: 25114240
DOI: 10.1073/PNAS.1408124111