Magnesium in PDB 4o4i: Tubulin-Laulimalide-Epothilone A Complex

The structure of Tubulin-Laulimalide-Epothilone A Complex, PDB code: 4o4i 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)	52.21 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.200, 158.030, 180.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.4

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

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Laulimalide-Epothilone A Complex (pdb code 4o4i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Tubulin-Laulimalide-Epothilone A Complex, PDB code: 4o4i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Tubulin-Laulimalide-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-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.9 occ:1.00 O A:HOH603 2.5 20.6 1.0 O1B A:GTP501 2.6 25.9 1.0 O A:HOH706 2.6 20.6 1.0 O2G A:GTP501 2.6 34.1 1.0 O A:HOH704 2.6 32.0 1.0 OE1 A:GLU71 3.3 67.2 1.0 O1G A:GTP501 3.4 22.2 1.0 PG A:GTP501 3.4 28.2 1.0 PB A:GTP501 3.6 22.7 1.0 NZ B:LYS254 3.8 40.7 1.0 O3B A:GTP501 3.9 42.6 1.0 O3A A:GTP501 3.9 29.4 1.0 OD2 A:ASP98 4.0 38.2 1.0 OD1 A:ASP69 4.2 28.0 1.0 OD2 A:ASP69 4.3 31.0 1.0 CB A:GLN11 4.3 31.4 1.0 CD A:GLU71 4.4 64.2 1.0 CB A:ASP98 4.5 25.3 1.0 N A:GLN11 4.5 29.7 1.0 CG A:ASP98 4.6 32.4 1.0 O1A A:GTP501 4.6 23.4 1.0 CG A:ASP69 4.7 28.9 1.0 O3G A:GTP501 4.8 26.9 1.0 PA A:GTP501 4.9 27.1 1.0 O2B A:GTP501 4.9 30.5 1.0 CA A:GLN11 4.9 30.1 1.0 OE2 A:GLU71 5.0 70.2 1.0

Magnesium binding site 2 out of 6 in the Tubulin-Laulimalide-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-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:54.9 occ:1.00 O B:HOH685 2.7 77.4 1.0 MG B:MG504 2.9 28.4 1.0 O1B B:GDP501 3.2 25.5 1.0 O B:HOH615 3.6 33.1 1.0 O3A B:GDP501 3.6 28.3 1.0 O B:HOH655 3.6 33.0 1.0 OE2 B:GLU71 3.7 68.8 1.0 PB B:GDP501 3.8 24.7 1.0 O C:HOH618 3.8 42.0 1.0 O B:HOH605 3.9 22.7 1.0 O1A B:GDP501 3.9 28.8 1.0 OE1 B:GLN11 3.9 37.4 1.0 O3B B:GDP501 4.0 27.6 1.0 CB B:GLN11 4.0 30.5 1.0 PA B:GDP501 4.4 29.0 1.0 OD1 B:ASN101 4.4 33.5 1.0 CD B:GLN11 4.5 40.8 1.0 O B:HOH678 4.6 46.8 1.0 O B:HOH684 4.6 65.5 1.0 CD B:GLU71 4.7 62.9 1.0 O C:HOH655 4.8 38.1 1.0 CG B:GLN11 4.9 31.0 1.0

Magnesium binding site 3 out of 6 in the Tubulin-Laulimalide-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-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:28.4 occ:1.00 OE1 B:GLN11 2.5 37.4 1.0 O1A B:GDP501 2.6 28.8 1.0 O B:HOH684 2.6 65.5 1.0 O C:HOH618 2.7 42.0 1.0 MG B:MG502 2.9 54.9 1.0 OD2 B:ASP179 3.5 52.8 1.0 CD B:GLN11 3.6 40.8 1.0 PA B:GDP501 3.7 29.0 1.0 O3A B:GDP501 3.9 28.3 1.0 OD1 B:ASN101 4.0 33.5 1.0 C5' B:GDP501 4.2 26.1 1.0 CB B:GLN11 4.3 30.5 1.0 CG B:GLN11 4.3 31.0 1.0 O5' B:GDP501 4.3 23.0 1.0 OE1 C:GLU254 4.4 51.7 1.0 O B:HOH685 4.5 77.4 1.0 CG B:ASP179 4.5 48.7 1.0 NE2 B:GLN11 4.6 43.9 1.0 C8 B:GDP501 4.8 24.0 1.0 O1B B:GDP501 4.9 25.5 1.0 CG B:ASN101 4.9 33.1 1.0 O2A B:GDP501 5.0 35.3 1.0

Magnesium binding site 4 out of 6 in the Tubulin-Laulimalide-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-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:29.8 occ:1.00 O1G C:GTP501 2.4 19.6 1.0 O1B C:GTP501 2.5 23.9 1.0 O C:HOH606 2.5 28.1 1.0 O C:HOH604 2.6 20.6 1.0 O C:HOH602 2.6 36.8 1.0 PG C:GTP501 3.4 23.4 1.0 O2G C:GTP501 3.4 23.0 1.0 PB C:GTP501 3.7 21.4 1.0 OD2 C:ASP98 3.8 40.7 1.0 OE1 C:GLU71 3.9 47.8 1.0 NZ D:LYS254 3.9 32.7 1.0 O3B C:GTP501 3.9 43.0 1.0 OD2 C:ASP69 4.1 22.5 1.0 O C:HOH616 4.2 66.9 1.0 OD1 C:ASP69 4.3 30.1 1.0 O3A C:GTP501 4.3 42.1 1.0 CB C:GLN11 4.3 22.4 1.0 CB C:ASP98 4.4 34.0 1.0 CG C:ASP98 4.5 39.3 1.0 CB C:GLU71 4.6 34.8 1.0 N C:GLN11 4.6 20.5 1.0 CG C:ASP69 4.6 25.1 1.0 O1A C:GTP501 4.7 18.4 1.0 O3G C:GTP501 4.8 19.4 1.0 CD C:GLU71 4.8 49.2 1.0 OE1 C:GLN11 4.9 43.2 1.0 O D:HOH639 4.9 29.4 1.0 O2B C:GTP501 4.9 27.3 1.0 CG C:GLU71 5.0 45.8 1.0

Magnesium binding site 5 out of 6 in the Tubulin-Laulimalide-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:62.8 occ:1.00 O1B D:GDP501 2.9 34.5 1.0 OE1 D:GLN11 3.0 51.5 1.0 O D:HOH604 3.2 45.5 1.0 CB D:GLN11 3.4 48.1 1.0 CD D:GLN11 3.6 52.2 1.0 O3A D:GDP501 3.7 46.0 1.0 OE2 D:GLU71 3.8 88.8 1.0 O1A D:GDP501 3.8 47.9 1.0 PB D:GDP501 3.9 37.6 1.0 O D:HOH660 3.9 42.4 1.0 CG D:GLN11 4.1 47.2 1.0 PA D:GDP501 4.3 42.0 1.0 NE2 D:GLN11 4.4 55.1 1.0 O3B D:GDP501 4.5 36.1 1.0 CD D:GLU71 4.6 90.1 1.0 CA D:GLN11 4.6 45.7 1.0 N D:GLN11 4.6 40.7 1.0 OE1 D:GLU71 4.7 93.6 1.0 O2A D:GDP501 4.8 41.4 1.0

Magnesium binding site 6 out of 6 in the Tubulin-Laulimalide-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tubulin-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:77.2 occ:1.00 O2G F:ACP500 2.7 0.3 1.0 O1B F:ACP500 2.7 0.4 1.0 OD2 F:ASP318 2.7 63.3 1.0 NH1 F:ARG222 3.4 76.3 1.0 NH2 F:ARG202 3.6 48.2 1.0 NH2 F:ARG222 3.7 77.6 1.0 OE1 F:GLU331 3.7 93.5 1.0 PB F:ACP500 3.8 0.8 1.0 CG F:ASP318 3.8 60.8 1.0 PG F:ACP500 3.9 0.7 1.0 OD1 F:ASN333 3.9 89.3 1.0 CZ F:ARG222 3.9 76.7 1.0 O3G F:ACP500 4.1 0.6 1.0 O2B F:ACP500 4.1 84.0 1.0 OD1 F:ASP318 4.2 61.5 1.0 C3B F:ACP500 4.5 0.5 1.0 ND2 F:ASN333 4.6 88.4 1.0 CG F:ASN333 4.6 82.6 1.0 ND2 F:ASN242 4.8 0.9 1.0 CZ F:ARG202 4.8 46.8 1.0 CD F:GLU331 4.9 89.5 1.0 OD1 F:ASN242 4.9 0.4 1.0 O1A F:ACP500 4.9 0.0 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