Magnesium in PDB 5lxt: Tubulin-Discodermolide Complex

The structure of Tubulin-Discodermolide Complex, PDB code: 5lxt was solved by A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.25 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.500, 157.790, 180.230, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.8

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

Calcium

(Ca)

4 atoms

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

Magnesium binding site 1 out of 5 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.0 occ:1.00 O A:HOH640 2.0 26.3 1.0 O1G A:GTP501 2.1 23.9 1.0 O1B A:GTP501 2.1 25.8 1.0 O A:HOH678 2.1 31.5 1.0 O A:HOH686 2.2 28.1 1.0 O A:HOH780 2.2 26.5 1.0 PG A:GTP501 3.2 27.4 1.0 PB A:GTP501 3.3 25.9 1.0 O3B A:GTP501 3.6 27.8 1.0 O2G A:GTP501 3.7 28.8 1.0 NZ B:LYS254 3.9 32.4 1.0 O3A A:GTP501 3.9 31.6 1.0 OE1 A:GLU71 4.0 57.2 1.0 OD1 A:ASP69 4.0 33.7 1.0 CB A:GLN11 4.1 26.6 1.0 OD2 A:ASP69 4.1 37.3 1.0 N A:GLN11 4.3 27.3 1.0 OD2 A:ASP98 4.3 38.7 1.0 CB A:ASP98 4.4 33.6 1.0 CG A:ASP69 4.5 34.2 1.0 O1A A:GTP501 4.5 26.8 1.0 O3G A:GTP501 4.5 25.5 1.0 O B:HOH746 4.6 48.7 1.0 O2B A:GTP501 4.6 28.3 1.0 CG A:ASP98 4.7 35.7 1.0 PA A:GTP501 4.8 27.6 1.0 CA A:GLN11 4.8 29.3 1.0 NE2 A:GLN11 4.8 34.2 1.0 CE B:LYS254 4.9 30.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.4 occ:1.00 O B:HOH727 2.1 31.0 1.0 OE1 B:GLN11 2.2 34.1 1.0 O1A B:GDP501 2.2 25.8 1.0 O C:HOH701 2.4 43.0 1.0 O B:HOH620 2.4 35.3 1.0 O B:HOH692 2.5 32.2 1.0 O B:HOH866 3.1 75.8 1.0 CD B:GLN11 3.4 37.1 1.0 PA B:GDP501 3.6 23.5 1.0 O3A B:GDP501 3.9 24.5 1.0 OD2 B:ASP179 3.9 34.9 1.0 CB B:GLN11 4.0 25.3 1.0 CG B:GLN11 4.2 28.8 1.0 NE2 B:GLN11 4.4 42.1 1.0 OE1 C:GLU254 4.4 41.4 1.0 O5' B:GDP501 4.4 26.0 1.0 C5' B:GDP501 4.4 27.0 1.0 OD1 B:ASN101 4.4 34.2 1.0 O1B B:GDP501 4.5 23.7 1.0 O C:HOH643 4.6 42.9 1.0 O2A B:GDP501 4.7 22.1 1.0 C8 B:GDP501 4.7 30.6 1.0 PB B:GDP501 4.9 25.0 1.0 CG B:ASP179 4.9 37.5 1.0 O B:HOH808 4.9 61.9 1.0 O B:HOH773 5.0 48.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:25.0 occ:1.00 O1G C:GTP501 2.0 23.7 1.0 O C:HOH657 2.1 24.0 1.0 O C:HOH712 2.1 25.0 1.0 O1B C:GTP501 2.1 20.6 1.0 O C:HOH724 2.2 25.8 1.0 O C:HOH868 2.2 25.0 1.0 PG C:GTP501 3.2 24.3 1.0 PB C:GTP501 3.2 24.7 1.0 O3B C:GTP501 3.6 23.7 1.0 O2G C:GTP501 3.6 24.7 1.0 O3A C:GTP501 3.8 23.3 1.0 NZ D:LYS254 4.0 29.4 1.0 OE1 C:GLU71 4.0 42.5 1.0 OD1 C:ASP69 4.0 27.4 1.0 CB C:GLN11 4.2 19.6 1.0 OD2 C:ASP69 4.2 27.2 1.0 CG C:GLU71 4.3 35.6 1.0 N C:GLN11 4.3 18.8 1.0 OD2 C:ASP98 4.4 36.1 1.0 CB C:ASP98 4.4 28.9 1.0 O3G C:GTP501 4.5 22.7 1.0 O C:HOH661 4.5 49.6 1.0 O1A C:GTP501 4.5 25.0 1.0 CG C:ASP69 4.6 27.5 1.0 O2B C:GTP501 4.6 23.2 1.0 CD C:GLU71 4.6 43.1 1.0 O C:HOH708 4.7 44.0 1.0 CG C:ASP98 4.7 30.1 1.0 PA C:GTP501 4.8 23.8 1.0 CA C:GLN11 4.8 22.2 1.0 OE1 C:GLN11 5.0 32.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:59.1 occ:1.00 O D:HOH703 2.0 58.4 1.0 OE1 D:GLN11 2.1 60.8 1.0 O1A D:GDP501 2.3 47.1 1.0 O D:HOH792 2.5 52.5 1.0 O D:HOH770 2.6 74.5 1.0 CD D:GLN11 3.3 61.1 1.0 PA D:GDP501 3.7 47.1 1.0 CB D:GLN11 3.9 48.8 1.0 CG D:GLN11 4.0 56.7 1.0 O3A D:GDP501 4.1 37.8 1.0 NE2 D:GLN11 4.3 60.8 1.0 O D:HOH791 4.4 55.6 1.0 O1B D:GDP501 4.5 34.9 1.0 C5' D:GDP501 4.6 43.0 1.0 O5' D:GDP501 4.6 40.9 1.0 O2A D:GDP501 4.7 48.6 1.0 C8 D:GDP501 4.8 34.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:65.5 occ:1.00 O1B F:ACP401 2.1 0.9 1.0 OE2 F:GLU331 2.3 64.8 1.0 O3G F:ACP401 2.5 0.9 1.0 OD1 F:ASN333 2.6 56.6 1.0 CD F:GLU331 3.3 71.6 1.0 PB F:ACP401 3.5 81.2 1.0 PG F:ACP401 3.6 96.8 1.0 CG F:ASN333 3.7 55.4 1.0 OE1 F:GLU331 3.7 83.1 1.0 CB A:GLU450 3.7 0.7 1.0 O1G F:ACP401 4.0 0.1 1.0 O2B F:ACP401 4.1 84.8 1.0 C3B F:ACP401 4.1 86.5 1.0 ND2 F:ASN333 4.2 55.7 1.0 NZ F:LYS74 4.5 68.3 1.0 CG F:GLU331 4.5 60.9 1.0 CA A:GLU450 4.6 0.3 1.0 CG A:GLU450 4.7 0.1 1.0 O3A F:ACP401 4.8 76.4 1.0 OD2 F:ASP318 4.8 66.0 1.0 O2G F:ACP401 4.9 95.7 1.0 CB F:ASN333 5.0 49.9 1.0 O1A F:ACP401 5.0 68.5 1.0 C A:GLU450 5.0 0.8 1.0

A.E.Prota, K.Bargsten, M.Redondo-Horcajo, A.B.Smith, C.H.Yang, H.M.Mcdaid, I.Paterson, S.B.Horwitz, J.Fernando Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Discodermolide. Chembiochem V. 18 905 2017.
ISSN: ESSN 1439-7633
PubMed: 28207984
DOI: 10.1002/CBIC.201600696