Calcium in PDB 5mf4: Tubulin-Dictyostatin Complex

The structure of Tubulin-Dictyostatin Complex, PDB code: 5mf4 was solved by C.Trigili, I.Barasoain, P.A.Sanchez-Murcia, K.Bargsten, M.Redondo-Horcajo, A.Nogales, N.M.Gardner, A.Meyer, G.J.Naylor, E.Gomez-Rubio, F.Gago, M.O.Steinmetz, I.Paterson, A.E.Prota, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.85 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.010, 156.510, 179.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.3

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

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-Dictyostatin Complex (pdb code 5mf4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tubulin-Dictyostatin Complex, PDB code: 5mf4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:99.7 occ:1.00 OD1 A:ASP39 2.2 0.3 1.0 O A:GLY44 2.3 0.7 1.0 O A:THR41 2.3 0.4 1.0 OE2 A:GLU55 2.3 0.9 1.0 OD2 A:ASP39 2.4 0.9 1.0 O A:HOH614 2.5 98.2 1.0 CG A:ASP39 2.6 0.7 1.0 OG1 A:THR41 2.8 0.7 1.0 OE1 A:GLU55 2.8 97.1 1.0 CD A:GLU55 2.9 98.8 1.0 C A:THR41 3.4 0.1 1.0 C A:GLY44 3.5 0.7 1.0 CB A:THR41 3.8 0.9 1.0 CA A:THR41 4.0 0.3 1.0 CB A:ASP39 4.1 0.8 1.0 N A:GLY44 4.2 0.9 1.0 N A:THR41 4.3 0.3 1.0 N A:GLY45 4.4 0.8 1.0 CG A:GLU55 4.4 91.6 1.0 CA A:GLY44 4.4 0.1 1.0 CA A:GLY45 4.4 0.7 1.0 N A:ILE42 4.6 0.6 1.0 CZ A:PHE49 4.6 86.9 1.0 OD1 A:ASN50 4.7 87.5 1.0 NE2 A:HIS61 4.7 84.3 1.0 OD2 A:ASP47 4.7 96.3 1.0 CA A:ASP39 4.9 0.9 1.0 CA A:ILE42 4.9 0.6 1.0 O A:ASP39 4.9 0.7 1.0 C A:ASP39 4.9 0.6 1.0 ND2 A:ASN50 5.0 84.1 1.0

Calcium binding site 2 out of 3 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:79.6 occ:1.00 OD2 C:ASP39 2.3 71.4 1.0 O C:GLY44 2.4 0.1 1.0 O C:THR41 2.4 87.7 1.0 OE2 C:GLU55 2.5 68.2 1.0 OG1 C:THR41 2.6 77.7 1.0 OE1 C:GLU55 2.7 71.4 1.0 O C:HOH603 2.7 74.6 1.0 OD1 C:ASP39 2.7 76.8 1.0 CG C:ASP39 2.8 80.0 1.0 CD C:GLU55 2.9 63.0 1.0 C C:THR41 3.4 89.8 1.0 C C:GLY44 3.5 0.1 1.0 CB C:THR41 3.5 86.7 1.0 CA C:THR41 3.9 88.4 1.0 N C:THR41 4.2 89.2 1.0 CB C:ASP39 4.3 85.5 1.0 N C:GLY45 4.3 93.0 1.0 CA C:GLY45 4.3 92.0 1.0 N C:GLY44 4.3 0.6 1.0 CG C:GLU55 4.4 67.2 1.0 CA C:GLY44 4.5 0.1 1.0 N C:ILE42 4.5 93.6 1.0 CZ C:PHE49 4.6 67.9 1.0 OD2 C:ASP47 4.6 93.4 1.0 OD1 C:ASN50 4.7 65.4 1.0 NE2 C:HIS61 4.7 70.4 1.0 CE1 C:PHE49 4.9 71.4 1.0 ND2 C:ASN50 4.9 63.2 1.0 CG2 C:THR41 4.9 82.6 1.0 CA C:ILE42 5.0 87.6 1.0

Calcium binding site 3 out of 3 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:0.9 occ:1.00 O1B F:ACP402 2.4 0.9 1.0 OE2 F:GLU331 2.5 0.1 1.0 O1G F:ACP402 2.7 0.3 1.0 ND2 F:ASN333 2.9 1.0 1.0 OE1 F:GLU331 2.9 0.2 1.0 CD F:GLU331 3.1 0.0 1.0 CE F:LYS74 3.8 0.3 1.0 PB F:ACP402 3.9 0.2 1.0 CG F:ASN333 4.1 0.1 1.0 NZ F:LYS74 4.1 0.6 1.0 PG F:ACP402 4.1 0.5 1.0 O2B F:ACP402 4.3 0.8 1.0 OD1 F:ASN333 4.5 0.5 1.0 C3B F:ACP402 4.6 0.1 1.0 CG F:GLU331 4.6 0.3 1.0 O F:HOH506 4.8 89.6 1.0 O2G F:ACP402 4.8 0.9 1.0 O1A F:ACP402 5.0 0.4 1.0

C.Trigili, I.Barasoain, P.A.Sanchez-Murcia, K.Bargsten, M.Redondo-Horcajo, A.Nogales, N.M.Gardner, A.Meyer, G.J.Naylor, E.Gomez-Rubio, F.Gago, M.O.Steinmetz, I.Paterson, A.E.Prota, J.F.Diaz. Structural Determinants of the Dictyostatin Chemotype For Tubulin Binding Affinity and Antitumor Activity Against Taxane- and Epothilone-Resistant Cancer Cells. Acs Omega V. 1 1192 2016.
ISSN: ESSN 2470-1343
PubMed: 30023505
DOI: 10.1021/ACSOMEGA.6B00317