Magnesium in PDB 4tuy: Tubulin-Rhizoxin Complex

The structure of Tubulin-Rhizoxin Complex, PDB code: 4tuy was solved by A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.70 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.310, 156.920, 181.120, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.7

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

Calcium

(Ca)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Rhizoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.2 occ:1.00 O2G A:GTP501 2.0 22.8 1.0 O A:HOH844 2.0 28.1 1.0 O A:HOH620 2.1 25.0 1.0 O A:HOH624 2.1 32.5 1.0 O1B A:GTP501 2.1 25.6 1.0 O A:HOH623 2.2 33.0 1.0 PG A:GTP501 3.2 28.7 1.0 PB A:GTP501 3.3 24.9 1.0 O3B A:GTP501 3.6 37.4 1.0 O1G A:GTP501 3.7 33.3 1.0 OE1 A:GLU71 3.8 55.5 1.0 NZ B:LYS254 3.9 33.4 1.0 O3A A:GTP501 3.9 35.9 1.0 OD1 A:ASP69 4.1 35.1 1.0 CB A:GLN11 4.2 27.7 1.0 CB A:ASP98 4.3 31.2 1.0 OD2 A:ASP69 4.4 39.2 1.0 OD2 A:ASP98 4.4 37.8 1.0 O A:HOH784 4.4 53.0 1.0 N A:GLN11 4.4 33.2 1.0 O3G A:GTP501 4.5 26.3 1.0 O1A A:GTP501 4.5 32.1 1.0 O2B A:GTP501 4.6 31.4 1.0 OE1 A:GLN11 4.7 40.9 1.0 CG A:ASP69 4.7 36.7 1.0 CG A:ASP98 4.8 34.1 1.0 PA A:GTP501 4.8 29.2 1.0 CE B:LYS254 4.9 32.7 1.0 CA A:GLN11 4.9 30.9 1.0 CB A:GLU71 4.9 55.6 1.0 CD A:GLU71 4.9 61.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Rhizoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.0 occ:1.00 O B:HOH620 2.1 32.0 1.0 OE1 B:GLN11 2.1 36.3 1.0 O1A B:GDP501 2.2 30.1 1.0 O C:HOH693 2.4 40.3 1.0 O B:HOH630 2.6 34.0 1.0 O B:HOH698 2.6 62.8 1.0 O B:HOH624 2.7 30.8 1.0 CD B:GLN11 3.3 37.1 1.0 PA B:GDP501 3.6 27.1 1.0 O3A B:GDP501 4.0 32.2 1.0 CB B:GLN11 4.1 26.8 1.0 OD2 B:ASP179 4.1 36.3 1.0 CG B:GLN11 4.2 32.6 1.0 NE2 B:GLN11 4.3 36.7 1.0 C5' B:GDP501 4.3 34.2 1.0 O B:HOH757 4.3 56.2 1.0 OD1 B:ASN101 4.4 34.5 1.0 O5' B:GDP501 4.4 29.2 1.0 O C:HOH821 4.4 46.1 1.0 O1B B:GDP501 4.5 23.9 1.0 OE1 C:GLU254 4.6 39.4 1.0 O B:HOH758 4.6 58.1 1.0 O2A B:GDP501 4.7 25.1 1.0 C8 B:GDP501 4.9 31.5 1.0 PB B:GDP501 5.0 27.6 1.0 CG B:ASP179 5.0 37.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Rhizoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:25.7 occ:1.00 O1G C:GTP501 2.0 20.5 1.0 O C:HOH652 2.0 28.2 1.0 O1B C:GTP501 2.0 23.6 1.0 O C:HOH977 2.1 24.9 1.0 O C:HOH658 2.1 31.5 1.0 O C:HOH659 2.2 24.7 1.0 PG C:GTP501 3.2 26.9 1.0 PB C:GTP501 3.2 23.8 1.0 O3B C:GTP501 3.6 34.5 1.0 O2G C:GTP501 3.7 26.9 1.0 O3A C:GTP501 3.9 32.3 1.0 NZ D:LYS254 4.0 37.4 1.0 OE1 C:GLU71 4.0 46.8 1.0 OD1 C:ASP69 4.0 33.9 1.0 CG C:GLU71 4.1 38.1 1.0 OD2 C:ASP69 4.2 25.7 1.0 CB C:GLN11 4.2 22.1 1.0 N C:GLN11 4.4 21.8 1.0 CB C:ASP98 4.4 32.9 1.0 O3G C:GTP501 4.5 24.1 1.0 OD2 C:ASP98 4.5 39.1 1.0 CG C:ASP69 4.5 26.2 1.0 O1A C:GTP501 4.5 27.0 1.0 O2B C:GTP501 4.5 25.2 1.0 O C:HOH813 4.6 48.5 1.0 CD C:GLU71 4.6 43.5 1.0 OE1 C:GLN11 4.8 41.3 1.0 PA C:GTP501 4.8 29.5 1.0 CG C:ASP98 4.9 36.5 1.0 CA C:GLN11 4.9 27.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Rhizoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:46.0 occ:1.00 O D:HOH770 2.1 43.7 1.0 OE1 D:GLN11 2.1 63.9 1.0 O1A D:GDP501 2.2 60.5 1.0 O D:HOH764 2.3 43.2 1.0 O D:HOH763 2.5 53.4 1.0 CD D:GLN11 3.3 74.1 1.0 PA D:GDP501 3.7 54.5 1.0 CB D:GLN11 4.2 58.2 1.0 NE2 D:GLN11 4.3 64.9 1.0 CG D:GLN11 4.3 69.3 1.0 C5' D:GDP501 4.3 54.5 1.0 O3A D:GDP501 4.3 46.2 1.0 O5' D:GDP501 4.5 60.6 1.0 O1B D:GDP501 4.5 37.9 1.0 O D:HOH689 4.7 49.2 1.0 O2A D:GDP501 4.7 58.0 1.0 C8 D:GDP501 4.9 42.4 1.0 OD1 D:ASN101 4.9 67.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Rhizoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:61.1 occ:1.00 O2B F:ACP401 2.2 0.0 1.0 OE2 F:GLU331 2.5 84.3 1.0 O1G F:ACP401 2.7 0.8 1.0 OE1 F:GLU331 2.7 72.2 1.0 CD F:GLU331 3.0 74.2 1.0 OD1 F:ASN333 3.1 89.1 1.0 PB F:ACP401 3.5 88.0 1.0 O1B F:ACP401 3.8 92.6 1.0 PG F:ACP401 3.8 0.6 1.0 CG F:ASN333 4.1 78.3 1.0 O3G F:ACP401 4.1 0.9 1.0 NZ F:LYS74 4.2 66.3 1.0 C3B F:ACP401 4.4 90.0 1.0 CG F:GLU331 4.5 61.2 1.0 CE F:LYS74 4.5 72.6 1.0 ND2 F:ASN333 4.5 79.0 1.0 O3A F:ACP401 4.8 68.3 1.0 O1A F:ACP401 4.8 78.9 1.0

A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz. A New Tubulin-Binding Site and Pharmacophore For Microtubule-Destabilizing Anticancer Drugs. Proc.Natl.Acad.Sci.Usa V. 111 13817 2014.
ISSN: ESSN 1091-6490
PubMed: 25114240
DOI: 10.1073/PNAS.1408124111