Magnesium in PDB 5njh: Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin

The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh was solved by A.Sharma, G.S.Calvo, A.E.Prota, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.09 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.430, 158.353, 173.458, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.7

The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin (pdb code 5njh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor 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 Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.3 occ:1.00 O1B A:GTP501 1.9 41.1 1.0 O1G A:GTP501 2.0 38.3 1.0 O A:HOH622 2.0 47.4 1.0 O A:HOH635 2.1 43.1 1.0 O A:HOH616 2.1 47.4 1.0 O A:HOH636 2.2 43.4 1.0 PB A:GTP501 3.1 41.4 1.0 PG A:GTP501 3.1 46.0 1.0 O3B A:GTP501 3.4 55.1 1.0 O3G A:GTP501 3.5 43.2 1.0 O3A A:GTP501 3.7 44.1 1.0 NZ B:LYS254 3.8 46.4 1.0 CB A:GLN11 4.0 42.1 1.0 OD1 A:ASP69 4.0 47.5 1.0 OE1 A:GLU71 4.1 62.6 1.0 OD2 A:ASP69 4.3 51.3 1.0 N A:GLN11 4.3 39.5 1.0 OE1 A:GLN11 4.4 46.1 1.0 O2B A:GTP501 4.4 45.2 1.0 OD2 A:ASP98 4.4 52.9 1.0 O2G A:GTP501 4.4 41.4 1.0 CG A:GLU71 4.4 59.0 1.0 O1A A:GTP501 4.4 49.2 1.0 CB A:ASP98 4.5 49.9 1.0 NE2 B:GLN247 4.6 0.2 1.0 CG A:ASP69 4.6 49.1 1.0 PA A:GTP501 4.6 46.7 1.0 CG A:ASP98 4.8 51.1 1.0 CD A:GLU71 4.8 62.0 1.0 CA A:GLN11 4.8 41.6 1.0

Magnesium binding site 2 out of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor 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 Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:73.7 occ:1.00 O C:HOH603 3.2 47.9 1.0 NE2 B:GLN11 3.3 51.3 1.0 OE2 B:GLU71 3.6 74.5 1.0 O1B B:GDP501 3.7 42.8 1.0 O1A B:GDP501 3.8 51.5 1.0 O3A B:GDP501 4.2 50.4 1.0 O B:HOH635 4.2 50.0 1.0 CB B:GLN11 4.3 48.2 1.0 CD B:GLN11 4.3 50.4 1.0 O B:HOH620 4.3 50.7 1.0 PB B:GDP501 4.4 40.4 1.0 CD B:GLU71 4.5 75.4 1.0 PA B:GDP501 4.6 59.1 1.0 O3B B:GDP501 4.7 56.0 1.0 OE1 C:GLU254 4.8 48.5 1.0 ND2 B:ASN101 4.8 43.0 1.0 OE1 B:GLU71 4.9 76.8 1.0 CG B:GLN11 4.9 48.6 1.0 OE2 C:GLU254 5.0 48.4 1.0

Magnesium binding site 3 out of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor 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 Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:44.6 occ:1.00 O C:HOH644 2.0 47.8 1.0 O C:HOH614 2.0 43.4 1.0 O1B C:GTP501 2.0 38.7 1.0 O1G C:GTP501 2.1 44.7 1.0 O C:HOH628 2.1 43.6 1.0 O C:HOH646 2.3 47.0 1.0 PB C:GTP501 3.2 42.8 1.0 PG C:GTP501 3.2 41.8 1.0 O3B C:GTP501 3.5 61.4 1.0 NZ D:LYS254 3.8 53.3 1.0 O2G C:GTP501 3.8 42.6 1.0 O3A C:GTP501 3.9 56.5 1.0 OE1 C:GLU71 4.0 56.3 1.0 OD1 C:ASP69 4.1 41.6 1.0 CB C:GLN11 4.2 45.8 1.0 CG C:GLU71 4.2 55.3 1.0 OD2 C:ASP69 4.3 42.1 1.0 O2B C:GTP501 4.4 46.3 1.0 O3G C:GTP501 4.5 47.4 1.0 OE1 C:GLN11 4.5 48.4 1.0 N C:GLN11 4.5 44.3 1.0 CB C:ASP98 4.6 52.7 1.0 OD2 C:ASP98 4.6 54.3 1.0 O1A C:GTP501 4.6 55.3 1.0 CG C:ASP69 4.6 42.1 1.0 CD C:GLU71 4.6 56.5 1.0 PA C:GTP501 4.7 59.5 1.0 OG1 C:THR145 4.8 38.3 1.0 CE D:LYS254 4.9 50.6 1.0 CG C:ASP98 4.9 53.6 1.0 CA C:GLN11 4.9 45.1 1.0 O2A C:GTP501 5.0 58.7 1.0

Magnesium binding site 4 out of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor 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 Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.4 occ:1.00 OE1 D:GLN11 2.1 63.7 1.0 O D:HOH620 2.3 61.2 1.0 O1A D:GDP501 2.3 57.9 1.0 O D:HOH638 2.4 57.7 1.0 O D:HOH652 3.2 66.1 1.0 CD D:GLN11 3.4 62.5 1.0 PA D:GDP501 3.7 56.7 1.0 O3A D:GDP501 4.0 59.8 1.0 NE2 D:GLN11 4.2 64.3 1.0 CB D:GLN11 4.2 56.5 1.0 CG D:GLN11 4.3 58.9 1.0 C5' D:GDP501 4.3 56.2 1.0 O D:HOH636 4.4 64.6 1.0 O5' D:GDP501 4.5 51.2 1.0 OD1 D:ASN101 4.7 70.4 1.0 O2A D:GDP501 4.7 50.6 1.0 O1B D:GDP501 4.9 53.0 1.0 C8 D:GDP501 5.0 55.4 1.0

Magnesium binding site 5 out of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.6 occ:1.00 O1B F:ACP402 2.4 0.1 1.0 O1G F:ACP402 2.5 0.9 1.0 OE1 F:GLU331 2.5 77.0 1.0 NZ F:LYS74 2.8 75.2 1.0 O F:HOH505 3.1 97.1 1.0 O2B F:ACP402 3.3 0.2 1.0 PB F:ACP402 3.3 0.6 1.0 CD F:GLU331 3.4 76.0 1.0 PG F:ACP402 3.7 0.7 1.0 OE2 F:GLU331 3.7 76.7 1.0 C3B F:ACP402 4.0 0.7 1.0 CE F:LYS74 4.1 74.5 1.0 OD1 F:ASN333 4.4 82.3 1.0 O3G F:ACP402 4.6 0.3 1.0 ND2 F:ASN333 4.6 83.0 1.0 O3A F:ACP402 4.7 0.2 1.0 CG F:GLU331 4.8 74.9 1.0 O2G F:ACP402 4.8 0.6 1.0 CG F:ASN333 4.9 82.1 1.0

G.Saez-Calvo, A.Sharma, F.A.Balaguer, I.Barasoain, J.Rodriguez-Salarichs, N.Olieric, H.Munoz-Hernandez, M.A.Berbis, S.Wendeborn, M.A.Penalva, R.Matesanz, A.Canales, A.E.Prota, J.Jimenez-Barbero, J.M.Andreu, C.Lamberth, M.O.Steinmetz, J.F.Diaz. Triazolopyrimidines Are Microtubule-Stabilizing Agents That Bind the Vinca Inhibitor Site of Tubulin. Cell Chem Biol V. 24 737 2017.
ISSN: ESSN 2451-9456
PubMed: 28579361
DOI: 10.1016/J.CHEMBIOL.2017.05.016