Magnesium in PDB 4tv8: Tubulin-Maytansine Complex

The structure of Tubulin-Maytansine Complex, PDB code: 4tv8 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)	62.42 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.860, 155.570, 180.620, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.9

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

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Tubulin-Maytansine Complex (pdb code 4tv8). 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-Maytansine Complex, PDB code: 4tv8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Maytansine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Maytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.2 occ:1.00 O A:HOH732 2.0 40.1 1.0 O2G A:GTP501 2.0 37.4 1.0 O A:HOH733 2.1 40.2 1.0 O A:HOH731 2.1 40.9 1.0 O A:HOH734 2.1 46.9 1.0 O1B A:GTP501 2.2 41.0 1.0 PG A:GTP501 3.2 42.7 1.0 PB A:GTP501 3.4 39.7 1.0 O3B A:GTP501 3.7 74.9 1.0 O1G A:GTP501 3.7 45.9 1.0 OE1 A:GLU71 3.7 72.6 1.0 NZ B:LYS254 3.8 50.3 1.0 O3A A:GTP501 4.0 53.4 1.0 OD1 A:ASP69 4.1 53.6 1.0 OD2 A:ASP69 4.2 52.2 1.0 CB A:GLN11 4.2 41.1 1.0 OD2 A:ASP98 4.2 57.6 1.0 CB A:ASP98 4.2 49.2 1.0 N A:GLN11 4.4 42.1 1.0 O A:HOH705 4.5 61.8 1.0 O3G A:GTP501 4.5 39.1 1.0 OE1 A:GLN11 4.6 56.8 1.0 CG A:ASP69 4.6 53.2 1.0 O1A A:GTP501 4.6 43.2 1.0 CG A:ASP98 4.7 52.4 1.0 O2B A:GTP501 4.7 48.0 1.0 CD A:GLU71 4.8 79.5 1.0 CB A:GLU71 4.8 71.1 1.0 CE B:LYS254 4.8 44.4 1.0 PA A:GTP501 4.9 43.0 1.0 CA A:GLN11 4.9 43.3 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Maytansine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Maytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.1 occ:1.00 O1A B:GDP501 2.3 43.6 1.0 OE1 B:GLN11 2.3 47.9 1.0 O C:HOH817 2.3 63.9 1.0 O B:HOH611 2.5 58.2 1.0 O B:HOH686 2.6 50.0 1.0 O C:HOH740 3.0 70.3 1.0 CD B:GLN11 3.5 52.1 1.0 PA B:GDP501 3.6 40.2 1.0 OD2 B:ASP179 3.8 61.5 1.0 O3A B:GDP501 3.9 50.1 1.0 OE1 C:GLU254 4.0 60.1 1.0 CB B:GLN11 4.2 42.6 1.0 OD1 B:ASN101 4.2 48.4 1.0 C5' B:GDP501 4.4 39.4 1.0 CG B:GLN11 4.4 44.5 1.0 NE2 B:GLN11 4.4 54.0 1.0 O5' B:GDP501 4.4 43.1 1.0 O C:HOH724 4.5 64.5 1.0 O1B B:GDP501 4.5 32.9 1.0 O2A B:GDP501 4.7 41.1 1.0 CG B:ASP179 4.8 58.5 1.0 C8 B:GDP501 4.8 42.0 1.0 PB B:GDP501 5.0 40.4 1.0 ND2 B:ASN101 5.0 50.5 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Maytansine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Maytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:41.1 occ:1.00 O C:HOH850 2.0 44.2 1.0 O1G C:GTP501 2.0 30.9 1.0 O1B C:GTP501 2.1 37.7 1.0 O C:HOH849 2.1 45.1 1.0 O C:HOH624 2.1 38.4 1.0 O C:HOH627 2.1 39.4 1.0 PG C:GTP501 3.2 40.3 1.0 PB C:GTP501 3.3 40.0 1.0 O3B C:GTP501 3.6 46.8 1.0 O2G C:GTP501 3.7 38.6 1.0 O3A C:GTP501 3.8 41.0 1.0 NZ D:LYS254 3.9 49.5 1.0 OD1 C:ASP69 4.1 40.5 1.0 OE1 C:GLU71 4.2 59.5 1.0 CB C:GLN11 4.2 32.5 1.0 OD2 C:ASP69 4.3 45.3 1.0 CB C:ASP98 4.4 45.7 1.0 OD2 C:ASP98 4.4 51.5 1.0 N C:GLN11 4.4 36.9 1.0 O3G C:GTP501 4.4 34.3 1.0 O1A C:GTP501 4.5 41.0 1.0 O2B C:GTP501 4.6 36.7 1.0 CG C:ASP69 4.6 46.0 1.0 CB C:GLU71 4.7 64.4 1.0 PA C:GTP501 4.7 40.4 1.0 CG C:ASP98 4.8 47.9 1.0 NE2 C:GLN11 4.9 48.1 1.0 CA C:GLN11 4.9 41.6 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Maytansine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Maytansine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:62.1 occ:1.00 O1A D:GDP501 2.1 85.8 1.0 OE1 D:GLN11 2.2 76.7 1.0 O D:HOH636 2.4 61.5 1.0 O D:HOH682 2.6 61.7 1.0 O D:HOH683 2.7 87.1 1.0 CD D:GLN11 3.4 78.5 1.0 PA D:GDP501 3.6 75.7 1.0 C5' D:GDP501 4.2 69.1 1.0 CB D:GLN11 4.2 72.8 1.0 NE2 D:GLN11 4.3 78.0 1.0 O3A D:GDP501 4.3 61.3 1.0 CG D:GLN11 4.3 75.4 1.0 O5' D:GDP501 4.3 70.9 1.0 O1B D:GDP501 4.5 65.4 1.0 OD1 D:ASN101 4.5 95.0 1.0 O2A D:GDP501 4.6 73.0 1.0 C8 D:GDP501 5.0 58.1 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