Magnesium 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:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Dictyostatin Complex (pdb code 5mf4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-Dictyostatin Complex, PDB code: 5mf4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:61.6 occ:1.00 O2G A:GTP501 2.2 61.8 1.0 O A:HOH618 2.2 51.2 1.0 O A:HOH619 2.2 66.5 1.0 O1B A:GTP501 2.3 49.8 1.0 O A:HOH604 2.3 51.9 1.0 PG A:GTP501 3.3 75.2 1.0 PB A:GTP501 3.4 57.5 1.0 OE1 A:GLU71 3.6 92.8 1.0 O3B A:GTP501 3.7 75.4 1.0 O1G A:GTP501 3.8 50.8 1.0 NZ B:LYS254 3.9 62.6 1.0 CB A:GLN11 3.9 54.8 1.0 O3A A:GTP501 3.9 55.5 1.0 OD1 A:ASP69 4.1 60.2 1.0 OD2 A:ASP98 4.2 80.7 1.0 OD2 A:ASP69 4.2 62.3 1.0 N A:GLN11 4.2 54.0 1.0 OE1 A:GLN11 4.4 66.7 1.0 O1A A:GTP501 4.4 50.7 1.0 CB A:ASP98 4.5 56.8 1.0 O3G A:GTP501 4.6 45.7 1.0 CA A:GLN11 4.6 57.0 1.0 CG A:ASP69 4.6 60.7 1.0 CG A:ASP98 4.7 67.8 1.0 O2B A:GTP501 4.7 66.8 1.0 PA A:GTP501 4.7 51.3 1.0 CD A:GLU71 4.8 93.3 1.0 O B:HOH618 5.0 67.5 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:55.5 occ:1.00 O B:HOH612 1.9 65.8 1.0 OE1 B:GLN11 2.1 62.1 1.0 O1A B:GDP501 2.3 52.3 1.0 O B:HOH622 2.6 60.9 1.0 O B:HOH601 2.9 67.5 1.0 CD B:GLN11 3.3 63.1 1.0 OD2 B:ASP179 3.6 81.4 1.0 PA B:GDP501 3.6 49.9 1.0 OE1 C:GLU254 3.8 87.4 1.0 O3A B:GDP501 4.0 55.5 1.0 CB B:GLN11 4.1 57.8 1.0 CG B:GLN11 4.2 51.4 1.0 NE2 B:GLN11 4.3 70.9 1.0 ND2 B:ASN101 4.4 48.5 1.0 C5' B:GDP501 4.5 48.5 1.0 O5' B:GDP501 4.5 47.2 1.0 O2A B:GDP501 4.6 50.7 1.0 O1B B:GDP501 4.7 46.2 1.0 C8 B:GDP501 4.7 55.1 1.0 CG B:ASP179 4.7 80.9 1.0 CD C:GLU254 4.9 80.3 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:55.7 occ:1.00 O C:HOH637 1.9 51.9 1.0 O C:HOH632 2.0 49.5 1.0 O1G C:GTP501 2.0 52.3 1.0 O C:HOH616 2.1 49.3 1.0 O1B C:GTP501 2.2 40.8 1.0 O C:HOH613 2.3 49.0 1.0 PG C:GTP501 3.2 55.4 1.0 PB C:GTP501 3.3 53.2 1.0 O3B C:GTP501 3.6 61.2 1.0 O2G C:GTP501 3.7 59.8 1.0 NZ D:LYS254 3.7 65.9 1.0 O3A C:GTP501 3.9 55.5 1.0 OE1 C:GLU71 4.0 78.3 1.0 CB C:GLN11 4.2 48.3 1.0 OD1 C:ASP69 4.2 61.7 1.0 OD2 C:ASP98 4.3 68.0 1.0 OD2 C:ASP69 4.4 64.7 1.0 O1A C:GTP501 4.4 56.3 1.0 O3G C:GTP501 4.4 44.7 1.0 N C:GLN11 4.5 44.9 1.0 CB C:ASP98 4.5 60.9 1.0 OE1 C:GLN11 4.6 70.4 1.0 O2B C:GTP501 4.6 60.2 1.0 PA C:GTP501 4.7 52.0 1.0 CG C:ASP69 4.8 63.9 1.0 CG C:ASP98 4.8 65.0 1.0 CE D:LYS254 4.8 61.5 1.0 CA C:GLN11 4.9 46.4 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Dictyostatin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Dictyostatin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.7 occ:1.00 OE1 D:GLN11 1.9 0.1 1.0 O D:HOH603 2.1 59.7 1.0 O1A D:GDP501 2.4 87.5 1.0 O D:HOH611 2.6 69.8 1.0 OD2 D:ASP179 2.9 96.0 1.0 CD D:GLN11 3.2 0.4 1.0 PA D:GDP501 3.7 80.9 1.0 CB D:GLN11 3.9 91.0 1.0 NE2 D:GLN11 4.1 0.8 1.0 CG D:ASP179 4.1 0.8 1.0 CG D:GLN11 4.1 85.9 1.0 O3A D:GDP501 4.2 78.9 1.0 C5' D:GDP501 4.4 82.0 1.0 O5' D:GDP501 4.6 88.6 1.0 OD1 D:ASN101 4.6 0.7 1.0 O2A D:GDP501 4.7 82.3 1.0 C8 D:GDP501 4.7 75.9 1.0 O1B D:GDP501 4.7 85.6 1.0 OD1 D:ASP179 4.8 0.9 1.0 ND2 D:ASN101 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