Magnesium in PDB 5ng1: Tubulin-Mtc-Zampanolide Complex

The structure of Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1 was solved by J.J.Field, B.Pera, J.Estevez Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, A.E.Prota, G.Menchon, J.H.Miller, K.-H.Altmann, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.69 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.237, 157.418, 178.858, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-Mtc-Zampanolide Complex (pdb code 5ng1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.5 occ:1.00 O1G A:GTP501 2.0 37.3 1.0 O A:HOH622 2.0 39.7 1.0 O A:HOH631 2.0 38.6 1.0 O A:HOH615 2.0 35.7 1.0 O A:HOH634 2.1 39.5 1.0 O1B A:GTP501 2.2 31.7 1.0 PG A:GTP501 3.1 45.4 1.0 PB A:GTP501 3.2 36.9 1.0 O2G A:GTP501 3.4 42.1 1.0 O3B A:GTP501 3.5 49.5 1.0 O3A A:GTP501 3.8 40.0 1.0 NZ B:LYS254 3.9 52.6 1.0 OD1 A:ASP69 4.0 44.0 1.0 OE1 A:GLU71 4.0 65.0 1.0 OD2 A:ASP98 4.1 50.8 1.0 OD2 A:ASP69 4.1 41.9 1.0 CB A:GLN11 4.1 39.2 1.0 N A:GLN11 4.3 36.3 1.0 O3G A:GTP501 4.4 35.7 1.0 CB A:ASP98 4.4 37.1 1.0 CG A:ASP69 4.4 48.3 1.0 CG A:ASP98 4.5 49.7 1.0 O2B A:GTP501 4.5 45.4 1.0 ND2 B:ASN249 4.6 0.1 1.0 O1A A:GTP501 4.7 38.3 1.0 CA A:GLN11 4.8 42.8 1.0 PA A:GTP501 4.8 39.5 1.0 OG1 A:THR145 4.8 39.2 1.0 CE B:LYS254 5.0 39.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.9 occ:1.00 O1A B:GDP501 2.3 36.3 1.0 OE1 B:GLN11 2.3 43.8 1.0 O C:HOH657 2.3 44.0 1.0 O B:HOH664 2.3 42.2 1.0 O B:HOH651 2.4 65.5 1.0 O B:HOH603 2.6 47.5 1.0 PA B:GDP501 3.5 35.9 1.0 CD B:GLN11 3.5 44.9 1.0 O3A B:GDP501 3.7 40.1 1.0 OD2 B:ASP179 3.9 52.5 1.0 CB B:GLN11 4.2 32.0 1.0 OD1 B:ASN101 4.2 46.3 1.0 CG B:GLN11 4.3 39.6 1.0 O5' B:GDP501 4.3 37.8 1.0 C5' B:GDP501 4.4 39.0 1.0 O C:HOH652 4.4 46.6 1.0 OE1 C:GLU254 4.4 56.7 1.0 NE2 B:GLN11 4.5 45.5 1.0 O2A B:GDP501 4.6 36.8 1.0 O1B B:GDP501 4.6 31.5 1.0 C8 B:GDP501 4.8 36.1 1.0 PB B:GDP501 4.8 35.5 1.0 ND2 B:ASN101 4.8 34.4 1.0 CG B:ASP179 4.9 50.0 1.0 CG B:ASN101 4.9 44.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:35.0 occ:1.00 O1G C:GTP501 2.0 33.0 1.0 O C:HOH717 2.0 32.2 1.0 O C:HOH625 2.0 32.0 1.0 O C:HOH610 2.1 34.8 1.0 O1B C:GTP501 2.1 30.6 1.0 O C:HOH607 2.2 37.0 1.0 PG C:GTP501 3.1 36.5 1.0 PB C:GTP501 3.2 30.0 1.0 O3B C:GTP501 3.6 39.9 1.0 O2G C:GTP501 3.6 34.5 1.0 O3A C:GTP501 3.7 34.0 1.0 NZ D:LYS254 3.8 47.3 1.0 OE1 C:GLU71 3.9 64.3 1.0 CB C:GLN11 4.1 28.5 1.0 OD1 C:ASP69 4.1 47.2 1.0 OD2 C:ASP98 4.2 55.0 1.0 OD2 C:ASP69 4.3 33.7 1.0 CG C:GLU71 4.3 47.9 1.0 N C:GLN11 4.4 31.7 1.0 O1A C:GTP501 4.4 35.6 1.0 O3G C:GTP501 4.4 33.5 1.0 O2B C:GTP501 4.5 34.3 1.0 CB C:ASP98 4.5 38.5 1.0 OE1 C:GLN11 4.6 50.3 1.0 CD C:GLU71 4.6 57.0 1.0 ND2 D:ASN249 4.6 78.5 1.0 CG C:ASP69 4.6 36.0 1.0 PA C:GTP501 4.7 35.4 1.0 CG C:ASP98 4.7 46.5 1.0 CA C:GLN11 4.8 34.2 1.0 CE D:LYS254 5.0 45.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.0 occ:1.00 O D:HOH606 2.1 57.6 1.0 OE1 D:GLN11 2.2 72.4 1.0 O D:HOH676 2.5 65.4 1.0 O1A D:GDP501 2.5 64.0 1.0 CD D:GLN11 3.4 66.9 1.0 PA D:GDP501 3.6 56.4 1.0 O3A D:GDP501 3.7 56.5 1.0 CB D:GLN11 4.0 60.5 1.0 O D:HOH683 4.1 59.7 1.0 CG D:GLN11 4.2 63.7 1.0 OD1 D:ASN101 4.3 68.6 1.0 NE2 D:GLN11 4.4 67.2 1.0 C5' D:GDP501 4.4 51.8 1.0 O5' D:GDP501 4.4 56.3 1.0 O1B D:GDP501 4.6 44.5 1.0 O2A D:GDP501 4.7 55.1 1.0 PB D:GDP501 4.8 55.4 1.0 C8 D:GDP501 4.9 47.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Mtc-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:61.2 occ:1.00 O1G F:ACP701 2.2 94.9 1.0 O1B F:ACP701 2.3 0.8 1.0 OE2 F:GLU331 2.4 81.4 1.0 ND2 F:ASN333 2.4 95.3 1.0 OE1 F:GLU331 3.0 82.8 1.0 CD F:GLU331 3.1 73.8 1.0 NZ F:LYS74 3.2 89.1 1.0 CG F:ASN333 3.6 87.0 1.0 PG F:ACP701 3.6 0.7 1.0 PB F:ACP701 3.7 0.5 1.0 OD1 F:ASN333 4.1 92.8 1.0 O2B F:ACP701 4.1 0.8 1.0 CE F:LYS74 4.2 83.7 1.0 C3B F:ACP701 4.2 0.3 1.0 O2G F:ACP701 4.3 86.8 1.0 CG F:GLU331 4.6 61.0 1.0 O3G F:ACP701 4.7 0.7 1.0 CB F:ASN333 4.8 70.4 1.0 O3A F:ACP701 5.0 0.5 1.0

J.J.Field, B.Pera, J.E.Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, J.M.Andreu, A.E.Prota, G.Menchon, J.H.Miller, K.H.Altmann, J.F.Diaz. Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704