Magnesium in PDB 5lov: Dz-2384 Tubulin Complex

The structure of Dz-2384 Tubulin Complex, PDB code: 5lov was solved by A.E.Prota, M.O.Steinmetz, G.C.Shore, G.Brouhard, A.Roulston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.35 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.160, 154.700, 180.320, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.2

The structure of Dz-2384 Tubulin Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Dz-2384 Tubulin Complex (pdb code 5lov). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dz-2384 Tubulin Complex, PDB code: 5lov:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Dz-2384 Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dz-2384 Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:82.9 occ:1.00 O A:HOH610 2.0 45.2 1.0 O2G A:GTP501 2.0 58.0 1.0 O A:HOH613 2.4 43.2 1.0 O A:HOH605 2.6 74.7 1.0 OD2 A:ASP98 2.6 57.1 1.0 OE2 A:GLU71 2.7 98.3 1.0 NZ B:LYS254 3.1 55.2 1.0 PG A:GTP501 3.4 67.8 1.0 CG A:ASP98 3.6 56.4 1.0 O1B A:GTP501 3.7 55.6 1.0 CB A:ASP98 3.8 52.6 1.0 O1G A:GTP501 3.9 58.9 1.0 CD A:GLU71 3.9 91.3 1.0 CE B:LYS254 4.2 53.7 1.0 O3G A:GTP501 4.3 57.5 1.0 O B:HOH609 4.4 83.7 1.0 O3B A:GTP501 4.4 79.9 1.0 CB A:GLU71 4.5 73.9 1.0 PB A:GTP501 4.5 54.6 1.0 OD1 A:ASP98 4.6 54.3 1.0 OE1 A:GLU71 4.7 0.2 1.0 O3A A:GTP501 4.8 67.6 1.0 O A:HOH607 4.8 66.8 1.0 CG A:GLU71 4.8 73.4 1.0 NE2 A:GLN11 4.8 82.2 1.0

Magnesium binding site 2 out of 3 in the Dz-2384 Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dz-2384 Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:84.8 occ:1.00 O B:HOH611 2.3 61.5 1.0 OE1 C:GLU254 2.4 84.3 1.0 OE1 B:GLN11 2.8 69.1 1.0 O B:HOH620 2.9 70.4 1.0 OE2 C:GLU254 3.0 81.2 1.0 CD C:GLU254 3.0 75.8 1.0 OE2 B:GLU71 3.8 0.0 1.0 CD B:GLN11 4.0 68.2 1.0 NZ C:LYS352 4.5 55.7 1.0 CG C:GLU254 4.5 63.1 1.0 CG1 C:VAL250 4.6 81.6 1.0 CG2 C:VAL250 4.6 84.8 1.0 O1A B:GDP501 4.6 48.0 1.0 NE2 B:GLN11 4.7 66.6 1.0 CB B:GLN11 4.8 59.6 1.0 CD B:GLU71 4.9 98.5 1.0 ND2 B:ASN101 4.9 59.2 1.0 CG B:GLN11 5.0 62.1 1.0

Magnesium binding site 3 out of 3 in the Dz-2384 Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dz-2384 Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.9 occ:1.00 O C:HOH601 2.2 40.3 1.0 O C:HOH637 2.2 47.0 1.0 O1G C:GTP501 2.3 49.9 1.0 O1B C:GTP501 2.4 45.8 1.0 O C:HOH611 2.6 42.2 1.0 O3G C:GTP501 2.7 46.4 1.0 PG C:GTP501 2.9 53.7 1.0 OD1 C:ASP69 3.2 58.3 1.0 O3B C:GTP501 3.4 66.2 1.0 PB C:GTP501 3.4 45.4 1.0 CB C:ASP98 3.7 53.8 1.0 OD2 C:ASP69 3.9 53.5 1.0 CG C:ASP69 3.9 52.3 1.0 OD2 C:ASP98 4.0 62.5 1.0 OE1 C:GLU71 4.0 71.9 1.0 OG1 C:THR145 4.0 57.8 1.0 CG C:ASP98 4.3 60.6 1.0 O2G C:GTP501 4.3 38.3 1.0 O3A C:GTP501 4.4 48.3 1.0 NZ D:LYS254 4.5 51.8 1.0 O2B C:GTP501 4.5 62.1 1.0 CB C:THR145 4.5 52.9 1.0 N C:GLN11 4.6 40.5 1.0 CB C:GLU71 4.7 56.5 1.0 CB C:GLN11 5.0 42.2 1.0

M.Wieczorek, J.Tcherkezian, C.Bernier, A.E.Prota, S.Chaaban, Y.Rolland, C.Godbout, M.A.Hancock, J.C.Arezzo, O.Ocal, C.Rocha, N.Olieric, A.Hall, H.Ding, A.Bramoulle, M.G.Annis, G.Zogopoulos, P.G.Harran, T.M.Wilkie, R.A.Brekken, P.M.Siegel, M.O.Steinmetz, G.C.Shore, G.J.Brouhard, A.Roulston. The Synthetic Diazonamide Dz-2384 Has Distinct Effects on Microtubule Curvature and Dynamics Without Neurotoxicity. Sci Transl Med V. 8 RA159 2016.
ISSN: ESSN 1946-6242
PubMed: 27856798
DOI: 10.1126/SCITRANSLMED.AAG1093