Magnesium in PDB 5j2t: Tubulin-Vinblastine Complex

The structure of Tubulin-Vinblastine Complex, PDB code: 5j2t was solved by A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.250, 157.740, 182.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.4

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

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Tubulin-Vinblastine Complex (pdb code 5j2t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tubulin-Vinblastine Complex, PDB code: 5j2t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.8 occ:1.00 O A:HOH601 2.0 38.2 1.0 OD2 A:ASP69 2.7 50.6 1.0 O A:HOH627 2.7 52.8 1.0 O A:HOH618 2.9 39.4 1.0 OE1 A:GLU71 2.9 77.1 1.0 O1B A:GTP501 3.2 44.4 1.0 CB A:GLN11 3.3 45.2 1.0 CG A:GLU71 3.4 74.5 1.0 CD A:GLU71 3.6 71.2 1.0 CG A:ASP69 3.6 59.5 1.0 CG2 A:VAL74 3.7 50.9 1.0 OD1 A:ASP69 3.7 59.0 1.0 NE2 A:GLN11 3.9 48.9 1.0 N A:GLN11 3.9 49.9 1.0 O2G A:GTP501 4.0 42.2 1.0 CA A:GLN11 4.0 52.8 1.0 CG A:GLN11 4.4 46.9 1.0 CD A:GLN11 4.6 47.8 1.0 PB A:GTP501 4.6 53.9 1.0 CB A:VAL74 4.8 56.5 1.0 OE2 A:GLU71 4.8 68.0 1.0 CB A:GLU71 4.8 78.8 1.0 O A:HOH606 4.9 57.8 1.0 C A:GLY10 4.9 44.7 1.0

Magnesium binding site 2 out of 3 in the Tubulin-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:42.2 occ:1.00 O1G C:GTP501 1.9 35.8 1.0 O C:HOH622 2.1 40.3 1.0 O C:HOH612 2.1 34.5 1.0 O C:HOH681 2.1 41.6 1.0 O1B C:GTP501 2.2 32.4 1.0 PG C:GTP501 3.1 42.4 1.0 PB C:GTP501 3.2 42.9 1.0 O3G C:GTP501 3.5 43.3 1.0 O3B C:GTP501 3.5 47.3 1.0 O3A C:GTP501 3.7 49.1 1.0 NZ D:LYS254 3.9 49.3 1.0 OD1 C:ASP69 4.1 42.1 1.0 OD2 C:ASP98 4.1 56.0 1.0 OE1 C:GLU71 4.1 66.2 1.0 CG C:GLU71 4.3 49.7 1.0 CB C:GLN11 4.3 45.1 1.0 OD2 C:ASP69 4.3 41.3 1.0 CB C:ASP98 4.4 53.6 1.0 O2G C:GTP501 4.4 33.1 1.0 N C:GLN11 4.4 42.1 1.0 O2B C:GTP501 4.5 38.2 1.0 CG C:ASP98 4.6 43.2 1.0 O1A C:GTP501 4.6 41.2 1.0 CG C:ASP69 4.6 43.5 1.0 CD C:GLU71 4.7 63.5 1.0 PA C:GTP501 4.7 67.1 1.0 OE1 C:GLN11 4.9 51.9 1.0 CA C:GLN11 5.0 46.2 1.0

Magnesium binding site 3 out of 3 in the Tubulin-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:85.4 occ:1.00 OE1 B:GLN11 2.3 81.9 1.0 O1A B:GDP501 2.4 45.1 1.0 O C:HOH714 2.8 63.2 1.0 O B:HOH664 2.9 44.1 1.0 O B:HOH673 3.2 54.9 1.0 O B:HOH672 3.3 54.7 1.0 CD B:GLN11 3.4 82.7 1.0 PA B:GDP501 3.7 42.0 1.0 O B:HOH663 3.9 64.6 1.0 O3A B:GDP501 4.1 39.4 1.0 NE2 B:GLN11 4.2 82.9 1.0 CB B:GLN11 4.3 36.5 1.0 CG B:GLN11 4.3 69.2 1.0 C5' B:GDP501 4.4 39.8 1.0 OD1 B:ASN101 4.4 51.4 1.0 O5' B:GDP501 4.5 35.2 1.0 O1B B:GDP501 4.8 38.3 1.0 O2A B:GDP501 4.8 39.5 1.0 C8 B:GDP501 4.9 42.5 1.0

A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota. Structural Basis of Microtubule Destabilization By Potent Auristatin Anti-Mitotics. Plos One V. 11 60890 2016.
ISSN: ESSN 1932-6203
PubMed: 27518442
DOI: 10.1371/JOURNAL.PONE.0160890