Magnesium in PDB 4o4l: Tubulin-Peloruside A-Epothilone A Complex

The structure of Tubulin-Peloruside A-Epothilone A Complex, PDB code: 4o4l was solved by A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.10 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.400, 156.330, 180.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.4

The structure of Tubulin-Peloruside A-Epothilone A Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Peloruside A-Epothilone A Complex (pdb code 4o4l). 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-Peloruside A-Epothilone A Complex, PDB code: 4o4l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Peloruside A-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Peloruside A-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.3 occ:1.00 O A:HOH648 2.1 34.3 1.0 O A:HOH601 2.1 33.1 1.0 O A:HOH605 2.1 31.3 1.0 O2G A:GTP501 2.1 35.2 1.0 O A:HOH613 2.2 32.6 1.0 O1B A:GTP501 2.2 24.9 1.0 PG A:GTP501 3.3 35.2 1.0 PB A:GTP501 3.4 28.6 1.0 O1G A:GTP501 3.7 29.2 1.0 O3B A:GTP501 3.7 49.8 1.0 O3A A:GTP501 3.9 32.9 1.0 NZ B:LYS254 3.9 44.9 1.0 OE1 A:GLU71 3.9 65.4 1.0 OD1 A:ASP69 4.1 39.1 1.0 CB A:GLN11 4.1 35.2 1.0 CG A:GLU71 4.1 48.6 1.0 OD2 A:ASP98 4.2 39.9 1.0 OD2 A:ASP69 4.2 36.6 1.0 CB A:ASP98 4.3 36.2 1.0 N A:GLN11 4.4 34.1 1.0 CD A:GLU71 4.5 55.3 1.0 O3G A:GTP501 4.5 29.2 1.0 CG A:ASP69 4.6 43.2 1.0 CG A:ASP98 4.6 39.7 1.0 O2B A:GTP501 4.7 36.1 1.0 OE1 A:GLN11 4.7 46.1 1.0 O1A A:GTP501 4.7 35.2 1.0 CA A:GLN11 4.8 35.6 1.0 PA A:GTP501 4.9 31.9 1.0 CE B:LYS254 5.0 34.7 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Peloruside A-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Peloruside A-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.2 occ:1.00 O B:HOH630 2.2 37.4 1.0 O1A B:GDP501 2.2 29.3 1.0 OE1 B:GLN11 2.3 40.0 1.0 O C:HOH637 2.4 52.3 1.0 O B:HOH702 2.4 35.8 1.0 O B:HOH632 2.7 46.0 1.0 PA B:GDP501 3.5 26.2 1.0 CD B:GLN11 3.5 47.9 1.0 O3A B:GDP501 3.8 37.2 1.0 OD2 B:ASP179 3.9 51.7 1.0 CB B:GLN11 4.2 28.6 1.0 C5' B:GDP501 4.3 25.6 1.0 CG B:GLN11 4.3 36.8 1.0 O5' B:GDP501 4.4 29.6 1.0 OD1 B:ASN101 4.4 28.0 1.0 NE2 B:GLN11 4.5 48.7 1.0 O2A B:GDP501 4.6 26.2 1.0 O1B B:GDP501 4.6 23.1 1.0 O C:HOH781 4.7 62.2 1.0 OE1 C:GLU254 4.7 51.6 1.0 C8 B:GDP501 4.8 32.0 1.0 PB B:GDP501 4.8 29.2 1.0 CG B:ASP179 4.9 50.8 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Peloruside A-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Peloruside A-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.8 occ:1.00 O C:HOH610 2.1 27.1 1.0 O1G C:GTP501 2.1 27.7 1.0 O C:HOH601 2.1 29.8 1.0 O1B C:GTP501 2.2 22.7 1.0 O C:HOH604 2.2 28.5 1.0 PG C:GTP501 3.3 31.9 1.0 PB C:GTP501 3.3 25.5 1.0 O3G C:GTP501 3.7 35.8 1.0 O3B C:GTP501 3.7 53.3 1.0 O3A C:GTP501 3.8 44.4 1.0 NZ D:LYS254 3.9 40.4 1.0 OE1 C:GLU71 3.9 59.8 1.0 OD1 C:ASP69 4.1 34.8 1.0 CB C:GLN11 4.2 25.9 1.0 CG C:GLU71 4.3 36.5 1.0 OD2 C:ASP98 4.3 46.6 1.0 OD2 C:ASP69 4.3 28.5 1.0 N C:GLN11 4.4 26.4 1.0 CB C:ASP98 4.5 30.9 1.0 O2G C:GTP501 4.5 27.3 1.0 CD C:GLU71 4.6 48.5 1.0 O2B C:GTP501 4.6 34.6 1.0 O1A C:GTP501 4.6 29.4 1.0 CG C:ASP69 4.7 36.6 1.0 CG C:ASP98 4.7 36.1 1.0 NE2 C:GLN11 4.8 40.6 1.0 PA C:GTP501 4.8 27.1 1.0 CA C:GLN11 4.9 30.8 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Peloruside A-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Peloruside A-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:64.2 occ:1.00 O D:HOH609 2.0 60.8 1.0 OE1 D:GLN11 2.1 77.3 1.0 O D:HOH638 2.3 62.5 1.0 O D:HOH608 2.4 53.8 1.0 O D:HOH604 2.5 68.0 1.0 O1A D:GDP501 2.5 75.5 1.0 CD D:GLN11 3.3 75.4 1.0 PA D:GDP501 3.9 72.2 1.0 C5' D:GDP501 4.2 63.3 1.0 NE2 D:GLN11 4.2 72.7 1.0 CG D:GLN11 4.3 69.3 1.0 CB D:GLN11 4.3 67.4 1.0 O3A D:GDP501 4.4 47.9 1.0 O5' D:GDP501 4.5 50.2 1.0 C8 D:GDP501 4.6 45.4 1.0

A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Laulimalide and Peloruside A. Angew.Chem.Int.Ed.Engl. V. 53 1621 2014.
ISSN: ISSN 1433-7851
PubMed: 24470331
DOI: 10.1002/ANIE.201307749