Magnesium in PDB 5o7a: Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin

The structure of Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin, PDB code: 5o7a was solved by A.Sharma, N.Olieric, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.907, 157.474, 180.678, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.6

The binding sites of Magnesium atom in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin (pdb code 5o7a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin, PDB code: 5o7a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:56.4 occ:1.00 O A:HOH615 2.0 51.6 1.0 O2G A:GTP501 2.1 45.0 1.0 O A:HOH608 2.2 43.8 1.0 O A:HOH610 2.3 50.9 1.0 O1B A:GTP501 2.7 43.8 1.0 PG A:GTP501 3.2 54.2 1.0 NZ B:LYS254 3.3 50.2 1.0 ND2 B:ASN249 3.7 80.8 1.0 PB A:GTP501 3.7 57.1 1.0 O1G A:GTP501 3.7 52.5 1.0 OE1 A:GLU71 3.7 68.7 1.0 O3B A:GTP501 3.7 65.9 1.0 OD2 A:ASP98 4.2 69.4 1.0 CG A:GLU71 4.2 67.2 1.0 O3A A:GTP501 4.2 62.1 1.0 CB A:ASP98 4.2 65.9 1.0 CD A:GLU71 4.3 68.7 1.0 O3G A:GTP501 4.4 48.7 1.0 OD1 A:ASP69 4.4 56.6 1.0 CB A:GLN11 4.5 51.9 1.0 OE1 A:GLN11 4.5 57.0 1.0 CE B:LYS254 4.5 49.0 1.0 CG B:ASN249 4.5 79.9 1.0 OD2 A:ASP69 4.5 58.2 1.0 O1A A:GTP501 4.6 43.6 1.0 CG A:ASP98 4.6 68.1 1.0 O B:ASN249 4.7 74.8 1.0 N A:GLN11 4.8 48.1 1.0 CG A:ASP69 4.9 57.3 1.0 O2B A:GTP501 4.9 60.1 1.0

Magnesium binding site 2 out of 4 in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:49.1 occ:1.00 OE1 B:GLN11 2.1 50.9 1.0 O1A B:GDP501 2.6 56.0 1.0 O B:HOH615 2.7 44.6 1.0 OD2 B:ASP179 3.1 66.9 1.0 CD B:GLN11 3.3 51.9 1.0 H5' B:GDP501 3.4 50.9 1.0 PA B:GDP501 3.6 51.0 1.0 O3A B:GDP501 3.7 54.9 1.0 H8 B:GDP501 3.8 65.3 1.0 O C:HOH637 3.9 63.1 1.0 ND2 B:ASN101 3.9 43.5 1.0 OE1 C:GLU254 4.1 61.5 1.0 C5' B:GDP501 4.1 43.0 1.0 NE2 B:GLN11 4.1 54.2 1.0 O5' B:GDP501 4.2 40.5 1.0 H5'' B:GDP501 4.2 50.9 1.0 CB B:GLN11 4.3 48.8 1.0 CG B:ASP179 4.3 67.6 1.0 CG B:GLN11 4.4 51.5 1.0 OD1 B:ASN101 4.5 45.5 1.0 C8 B:GDP501 4.7 55.1 1.0 CG B:ASN101 4.7 44.4 1.0 O2A B:GDP501 4.8 54.0 1.0 CB B:ASP179 4.9 66.6 1.0 PB B:GDP501 4.9 50.5 1.0 O1B B:GDP501 5.0 46.4 1.0 CD C:GLU254 5.0 60.4 1.0

Magnesium binding site 3 out of 4 in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:56.3 occ:1.00 O C:HOH608 2.2 37.2 1.0 O C:HOH605 2.2 45.8 1.0 O1G C:GTP501 2.7 36.2 1.0 O1B C:GTP501 2.9 39.7 1.0 O1A C:GTP501 3.2 48.7 1.0 NZ D:LYS254 3.3 52.2 1.0 O3A C:GTP501 3.4 53.5 1.0 O C:HOH606 3.5 41.5 1.0 OE1 C:GLN11 3.5 53.1 1.0 PB C:GTP501 3.6 51.3 1.0 CB C:GLN11 3.7 48.3 1.0 PA C:GTP501 3.9 53.6 1.0 PG C:GTP501 4.0 53.7 1.0 O3B C:GTP501 4.3 58.6 1.0 OE1 C:GLU71 4.3 64.2 1.0 CD C:GLN11 4.3 52.5 1.0 O D:ASN249 4.6 0.1 1.0 O2A C:GTP501 4.6 43.0 1.0 CE D:LYS254 4.6 49.9 1.0 CG C:GLN11 4.6 50.7 1.0 CB D:ASN249 4.7 0.3 1.0 N C:GLN11 4.7 42.2 1.0 ND2 D:ASN249 4.8 0.9 1.0 O2G C:GTP501 4.8 49.0 1.0 CA C:GLN11 4.8 45.2 1.0 O3G C:GTP501 4.9 49.1 1.0 O2B C:GTP501 4.9 40.4 1.0

Magnesium binding site 4 out of 4 in the Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:31.9 occ:1.00 O1A D:GDP501 2.4 0.4 1.0 O D:HOH611 2.5 31.9 1.0 O D:HOH612 2.5 31.9 1.0 OE1 D:GLN11 2.7 86.7 1.0 O D:HOH617 2.9 31.9 1.0 CD D:GLN11 3.3 84.5 1.0 PA D:GDP501 3.6 83.1 1.0 O2A D:GDP501 3.7 74.7 1.0 CB D:GLN11 3.9 80.0 1.0 H8 D:GDP501 3.9 0.7 1.0 H5' D:GDP501 3.9 78.3 1.0 NE2 D:GLN11 3.9 85.5 1.0 CG D:GLN11 4.1 82.2 1.0 OD1 D:ASN101 4.3 94.7 1.0 O1B D:GDP501 4.5 90.8 1.0 C5' D:GDP501 4.6 65.9 1.0 O5' D:GDP501 4.6 72.2 1.0 O3A D:GDP501 4.7 90.8 1.0 C8 D:GDP501 4.7 85.4 1.0 H5'' D:GDP501 4.8 78.3 1.0 PB D:GDP501 4.9 76.1 1.0

A.Sharma, G.Saez-Calvo, N.Olieric, F.De Asis Balaguer, I.Barasoain, C.Lamberth, J.F.Diaz, M.O.Steinmetz. Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin. Int J Mol Sci V. 18 2017.
ISSN: ESSN 1422-0067
PubMed: 28640209
DOI: 10.3390/IJMS18071336