Magnesium in PDB 5bmv: Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex, PDB code: 5bmv was solved by Y.Wang, Q.Chen, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.470, 157.420, 183.180, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.5

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

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

Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.0 occ:1.00 O1G A:GTP501 1.9 25.9 1.0 O1B A:GTP501 1.9 26.9 1.0 O A:HOH605 2.0 20.3 1.0 O A:HOH609 2.0 17.4 1.0 O A:HOH631 2.1 21.2 1.0 O A:HOH608 2.1 30.0 1.0 PG A:GTP501 2.9 29.5 1.0 PB A:GTP501 2.9 29.6 1.0 O3B A:GTP501 3.2 29.2 1.0 O2G A:GTP501 3.4 29.6 1.0 O3A A:GTP501 3.7 29.5 1.0 NZ B:LYS254 3.9 34.5 1.0 OD1 A:ASP69 4.1 34.6 1.0 OE1 A:GLU71 4.2 53.9 1.0 O3G A:GTP501 4.3 29.3 1.0 OD2 A:ASP69 4.3 33.3 1.0 CB A:GLN11 4.3 41.0 1.0 O2B A:GTP501 4.3 30.1 1.0 OD2 A:ASP98 4.4 37.5 1.0 O1A A:GTP501 4.4 32.0 1.0 N A:GLN11 4.4 39.7 1.0 CB A:ASP98 4.4 39.2 1.0 CG A:GLU71 4.4 51.6 1.0 PA A:GTP501 4.6 30.2 1.0 CG A:ASP69 4.7 34.4 1.0 CG A:ASP98 4.7 38.5 1.0 OG1 A:THR145 4.8 34.0 1.0 CD A:GLU71 4.8 54.0 1.0 CA A:GLN11 4.9 38.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:74.9 occ:1.00 O B:HOH653 2.3 41.9 1.0 O B:HOH604 2.4 53.8 1.0 O B:HOH622 2.5 33.6 1.0 NE2 B:GLN11 2.8 58.3 1.0 O1A B:GDP501 2.9 29.9 1.0 CD B:GLN11 3.4 60.8 1.0 OE1 B:GLN11 3.8 63.4 1.0 CB B:GLN11 4.1 41.6 1.0 PA B:GDP501 4.2 24.8 1.0 CG B:GLN11 4.3 51.3 1.0 O3A B:GDP501 4.4 24.5 1.0 O1B B:GDP501 4.5 27.6 1.0 OE2 B:GLU71 4.7 91.3 1.0 OE1 C:GLU254 4.9 82.5 1.0 OD1 B:ASN101 4.9 34.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.2 occ:1.00 O1G C:GTP501 1.7 25.9 1.0 O1B C:GTP501 1.9 27.7 1.0 O C:HOH613 2.0 26.8 1.0 O C:HOH627 2.0 21.7 1.0 O C:HOH649 2.0 19.3 1.0 O C:HOH662 2.1 23.2 1.0 PG C:GTP501 2.8 28.1 1.0 PB C:GTP501 3.0 28.3 1.0 O3B C:GTP501 3.3 25.8 1.0 O2G C:GTP501 3.3 30.3 1.0 O3A C:GTP501 3.6 31.9 1.0 NZ D:LYS254 4.0 41.8 1.0 OE1 C:GLU71 4.0 59.8 1.0 OD1 C:ASP69 4.1 29.7 1.0 O3G C:GTP501 4.2 27.2 1.0 OD2 C:ASP98 4.3 35.8 1.0 OD2 C:ASP69 4.3 34.8 1.0 O2B C:GTP501 4.3 32.9 1.0 CB C:GLN11 4.4 37.8 1.0 O1A C:GTP501 4.4 30.0 1.0 N C:GLN11 4.5 34.2 1.0 CB C:ASP98 4.5 34.1 1.0 PA C:GTP501 4.6 28.6 1.0 CG C:ASP69 4.6 33.2 1.0 OG1 C:THR145 4.7 30.0 1.0 CG C:ASP98 4.8 34.1 1.0 OE1 C:GLN11 4.9 36.2 1.0 CE D:LYS254 5.0 38.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin-Stathmin-Ttl-Vinblastine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:53.9 occ:1.00 O3B D:GDP501 1.8 65.5 1.0 PB D:GDP501 2.9 60.2 1.0 O1B D:GDP501 3.3 44.5 1.0 O3A D:GDP501 3.8 55.9 1.0 CB D:ALA99 3.8 76.5 1.0 OG1 D:THR145 3.9 72.2 1.0 O2B D:GDP501 4.1 67.5 1.0 N D:ALA99 4.1 78.9 1.0 N D:GLY100 4.2 63.0 1.0 CA D:ALA99 4.4 70.8 1.0 OD1 D:ASN101 4.5 62.8 1.0 CB D:THR145 4.6 65.3 1.0 N D:ASN101 4.6 70.1 1.0 N D:THR145 4.6 55.2 1.0 N D:GLY144 4.6 53.2 1.0 CG D:GLU71 4.7 84.1 1.0 C D:ALA99 4.7 62.7 1.0 CA D:GLY100 4.9 62.4 1.0 PA D:GDP501 5.0 54.5 1.0

Y.Wang, F.W.Benz, Y.Wu, Q.Wang, Y.Chen, X.Chen, H.Li, Y.Zhang, R.Zhang, J.Yang. Structural Insights Into the Pharmacophore of Vinca Domain Inhibitors of Microtubules. Mol.Pharmacol. V. 89 233 2016.
ISSN: ESSN 1521-0111
PubMed: 26660762
DOI: 10.1124/MOL.115.100149