Magnesium in PDB 5lxs: Tubulin-Ks-1-199-32 Complex

The structure of Tubulin-Ks-1-199-32 Complex, PDB code: 5lxs 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)	72.23 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.580, 157.800, 179.440, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

The structure of Tubulin-Ks-1-199-32 Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Ks-1-199-32 Complex (pdb code 5lxs). 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-Ks-1-199-32 Complex, PDB code: 5lxs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.4 occ:1.00 O2G A:GTP501 2.0 26.7 1.0 O A:HOH655 2.0 27.7 1.0 O A:HOH626 2.1 24.2 1.0 O A:HOH686 2.2 30.3 1.0 O1B A:GTP501 2.2 22.7 1.0 O A:HOH692 2.2 32.2 1.0 PG A:GTP501 3.2 27.4 1.0 PB A:GTP501 3.3 26.3 1.0 O3B A:GTP501 3.6 36.2 1.0 O1G A:GTP501 3.6 27.7 1.0 O3A A:GTP501 3.8 29.4 1.0 NZ B:LYS254 3.9 44.2 1.0 OE2 A:GLU71 4.0 51.4 1.0 OD1 A:ASP69 4.0 34.1 1.0 CB A:GLN11 4.0 25.5 1.0 CG A:GLU71 4.3 50.6 1.0 OD2 A:ASP69 4.3 40.3 1.0 N A:GLN11 4.3 30.1 1.0 OD2 A:ASP98 4.3 36.7 1.0 O1A A:GTP501 4.4 31.6 1.0 CB A:ASP98 4.5 31.1 1.0 O3G A:GTP501 4.5 22.2 1.0 O B:HOH634 4.5 57.7 1.0 OE1 A:GLN11 4.6 45.3 1.0 CG A:ASP69 4.6 36.6 1.0 CD A:GLU71 4.6 48.8 1.0 O2B A:GTP501 4.6 26.2 1.0 PA A:GTP501 4.7 29.8 1.0 CG A:ASP98 4.7 33.7 1.0 CA A:GLN11 4.8 29.3 1.0 CE B:LYS254 5.0 41.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:51.2 occ:1.00 O B:HOH611 2.4 56.9 1.0 O B:HOH741 2.4 62.8 1.0 O B:HOH601 2.4 17.4 1.0 O1B B:GDP501 2.8 30.4 1.0 O1A B:GDP501 3.1 30.1 1.0 OE1 B:GLN11 3.1 48.4 1.0 O3A B:GDP501 3.1 31.7 1.0 PB B:GDP501 3.4 29.4 1.0 CB B:GLN11 3.4 35.4 1.0 O C:HOH684 3.5 38.2 1.0 PA B:GDP501 3.6 31.1 1.0 O3B B:GDP501 3.8 27.4 1.0 CD B:GLN11 3.9 36.7 1.0 O B:HOH640 4.0 28.8 1.0 O B:HOH656 4.0 38.9 1.0 CG B:GLN11 4.3 39.1 1.0 OE2 B:GLU71 4.3 81.0 1.0 O B:HOH676 4.4 35.0 1.0 O2A B:GDP501 4.5 31.9 1.0 O B:HOH628 4.5 46.7 1.0 N B:GLN11 4.5 26.8 1.0 CA B:GLN11 4.6 35.5 1.0 OD1 B:ASN101 4.6 49.7 1.0 O2B B:GDP501 4.8 23.9 1.0 O5' B:GDP501 4.9 32.2 1.0 O B:HOH617 4.9 53.0 1.0 NE2 B:GLN11 4.9 46.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:27.4 occ:1.00 O1G C:GTP501 2.0 27.6 1.0 O C:HOH635 2.1 29.5 1.0 O C:HOH743 2.1 25.9 1.0 O1B C:GTP501 2.1 23.7 1.0 O C:HOH704 2.1 29.3 1.0 O C:HOH641 2.2 24.1 1.0 PG C:GTP501 3.2 28.6 1.0 PB C:GTP501 3.3 26.1 1.0 O3B C:GTP501 3.6 48.9 1.0 O2G C:GTP501 3.6 28.4 1.0 O3A C:GTP501 3.9 33.5 1.0 NZ D:LYS254 3.9 38.0 1.0 OD1 C:ASP69 4.2 31.2 1.0 OD2 C:ASP98 4.2 42.7 1.0 OD2 C:ASP69 4.3 33.7 1.0 CB C:GLN11 4.3 22.7 1.0 O C:HOH622 4.4 42.9 1.0 O3G C:GTP501 4.5 25.9 1.0 CB C:ASP98 4.5 33.0 1.0 N C:GLN11 4.5 21.5 1.0 OE1 C:GLU71 4.6 55.2 1.0 O2B C:GTP501 4.6 28.4 1.0 O1A C:GTP501 4.6 33.8 1.0 CG C:ASP98 4.7 38.7 1.0 CG C:ASP69 4.7 31.7 1.0 CB C:GLU71 4.7 52.3 1.0 PA C:GTP501 4.8 30.3 1.0 OE1 C:GLN11 5.0 36.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.2 occ:1.00 OE1 D:GLN11 2.3 74.4 1.0 O1A D:GDP501 2.4 53.8 1.0 O D:HOH689 2.7 73.2 1.0 CD D:GLN11 3.5 67.6 1.0 PA D:GDP501 3.8 43.8 1.0 CB D:GLN11 4.3 46.5 1.0 O3A D:GDP501 4.4 39.5 1.0 NE2 D:GLN11 4.4 74.0 1.0 CG D:GLN11 4.5 54.7 1.0 C5' D:GDP501 4.6 41.8 1.0 O1B D:GDP501 4.7 37.4 1.0 O5' D:GDP501 4.7 42.1 1.0 OD1 D:ASN101 4.8 59.2 1.0 O2A D:GDP501 4.9 41.5 1.0 O D:HOH713 5.0 66.3 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:79.4 occ:1.00 OE2 F:GLU331 2.5 81.1 1.0 O1B F:ACP401 2.6 0.4 1.0 OE1 F:GLU331 3.0 83.9 1.0 CD F:GLU331 3.1 75.7 1.0 ND2 F:ASN333 3.3 96.7 1.0 O1G F:ACP401 3.6 1.0 1.0 PB F:ACP401 3.8 90.8 1.0 NZ F:LYS74 3.9 76.2 1.0 O3A F:ACP401 4.1 92.5 1.0 C3B F:ACP401 4.2 96.0 1.0 PG F:ACP401 4.5 0.5 1.0 CG F:ASN333 4.6 91.7 1.0 CG F:GLU331 4.6 64.1 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