Magnesium in PDB 5nfz: Tubulin-Mtc Complex

The structure of Tubulin-Mtc Complex, PDB code: 5nfz 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)	59.78 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.163, 158.787, 180.376, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.8

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

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Mtc Complex (pdb code 5nfz). 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 Complex, PDB code: 5nfz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Mtc 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.9 occ:1.00 O A:HOH630 2.0 41.2 1.0 O1G A:GTP501 2.0 28.4 1.0 O A:HOH663 2.1 33.8 1.0 O A:HOH640 2.1 39.4 1.0 O A:HOH618 2.2 39.9 1.0 O1B A:GTP501 2.2 26.9 1.0 PG A:GTP501 3.2 37.7 1.0 PB A:GTP501 3.3 34.6 1.0 O3B A:GTP501 3.5 41.0 1.0 O2G A:GTP501 3.7 34.0 1.0 O3A A:GTP501 3.8 35.0 1.0 NZ B:LYS254 3.9 42.6 1.0 OE1 A:GLU71 4.1 52.1 1.0 OD1 A:ASP69 4.1 41.8 1.0 CB A:GLN11 4.1 34.3 1.0 OD2 A:ASP69 4.2 40.5 1.0 CB A:ASP98 4.3 44.4 1.0 N A:GLN11 4.3 33.6 1.0 CG A:GLU71 4.3 49.3 1.0 OD2 A:ASP98 4.3 49.0 1.0 O3G A:GTP501 4.4 33.1 1.0 ND2 B:ASN249 4.5 67.5 1.0 O1A A:GTP501 4.5 38.5 1.0 CG A:ASP69 4.6 44.6 1.0 O2B A:GTP501 4.6 42.2 1.0 OE1 A:GLN11 4.7 46.4 1.0 CG A:ASP98 4.7 45.7 1.0 CD A:GLU71 4.7 50.8 1.0 PA A:GTP501 4.7 35.4 1.0 CA A:GLN11 4.8 35.6 1.0 OG1 A:THR145 4.9 36.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Mtc 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:27.1 occ:1.00 O B:HOH647 1.9 31.6 1.0 OE1 B:GLN11 2.1 44.8 1.0 O1A B:GDP502 2.3 32.0 1.0 O C:HOH641 2.3 43.0 1.0 O B:HOH602 2.4 40.7 1.0 O B:HOH630 2.5 36.9 1.0 CD B:GLN11 3.3 42.1 1.0 PA B:GDP502 3.6 30.0 1.0 OD2 B:ASP179 3.8 44.7 1.0 O3A B:GDP502 3.8 31.2 1.0 CB B:GLN11 4.0 34.4 1.0 CG B:GLN11 4.1 36.2 1.0 NE2 B:GLN11 4.4 49.5 1.0 O5' B:GDP502 4.4 29.9 1.0 C5' B:GDP502 4.4 36.3 1.0 OD1 B:ASN101 4.4 39.5 1.0 O C:HOH633 4.5 50.2 1.0 O1B B:GDP502 4.5 30.2 1.0 OE1 C:GLU254 4.5 49.6 1.0 O2A B:GDP502 4.6 29.2 1.0 C8 B:GDP502 4.8 38.2 1.0 CG B:ASP179 4.8 47.3 1.0 PB B:GDP502 4.9 32.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Mtc 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.2 occ:1.00 O1G C:GTP501 2.0 29.4 1.0 O C:HOH718 2.0 30.3 1.0 O C:HOH618 2.1 32.9 1.0 O C:HOH655 2.1 32.1 1.0 O C:HOH634 2.1 31.3 1.0 O1B C:GTP501 2.2 29.2 1.0 PG C:GTP501 3.1 34.5 1.0 PB C:GTP501 3.3 31.8 1.0 O3B C:GTP501 3.5 34.0 1.0 O2G C:GTP501 3.6 31.0 1.0 NZ D:LYS254 3.8 36.5 1.0 O3A C:GTP501 3.8 29.5 1.0 OE1 C:GLU71 4.0 43.2 1.0 OD1 C:ASP69 4.1 36.0 1.0 OD2 C:ASP98 4.1 48.2 1.0 CB C:GLN11 4.2 27.0 1.0 OD2 C:ASP69 4.3 31.7 1.0 CG C:GLU71 4.3 42.5 1.0 CB C:ASP98 4.3 33.6 1.0 O3G C:GTP501 4.4 29.7 1.0 N C:GLN11 4.5 25.7 1.0 ND2 D:ASN249 4.5 61.6 1.0 CG C:ASP98 4.6 41.3 1.0 O1A C:GTP501 4.6 33.2 1.0 O2B C:GTP501 4.6 32.5 1.0 CG C:ASP69 4.6 34.6 1.0 CD C:GLU71 4.7 47.5 1.0 OE1 C:GLN11 4.8 39.5 1.0 PA C:GTP501 4.8 30.9 1.0 CA C:GLN11 4.9 28.0 1.0 CE D:LYS254 5.0 36.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Mtc 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:58.8 occ:1.00 O D:HOH609 2.0 54.3 1.0 OE1 D:GLN11 2.3 78.2 1.0 O D:HOH631 2.4 57.2 1.0 O1A D:GDP501 2.5 60.6 1.0 O D:HOH630 2.7 73.1 1.0 CD D:GLN11 3.3 81.9 1.0 PA D:GDP501 3.7 56.9 1.0 NE2 D:GLN11 4.0 87.8 1.0 O3A D:GDP501 4.1 48.8 1.0 CB D:GLN11 4.1 65.7 1.0 CG D:GLN11 4.3 67.8 1.0 C5' D:GDP501 4.6 61.3 1.0 OD1 D:ASN101 4.6 69.0 1.0 O5' D:GDP501 4.6 62.9 1.0 O1B D:GDP501 4.7 47.2 1.0 O2A D:GDP501 4.7 60.6 1.0 C8 D:GDP501 4.9 47.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Mtc 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:72.3 occ:1.00 OE2 F:GLU331 2.0 0.3 1.0 O1G F:ACP402 2.1 0.8 1.0 O1B F:ACP402 2.4 0.6 1.0 CD F:GLU331 2.9 0.5 1.0 OE1 F:GLU331 3.1 0.4 1.0 ND2 F:ASN333 3.3 0.4 1.0 PG F:ACP402 3.4 0.3 1.0 NZ F:LYS74 3.5 92.0 1.0 PB F:ACP402 3.5 0.2 1.0 OD1 F:ASN333 3.5 0.7 1.0 C3B F:ACP402 3.7 0.3 1.0 CG F:ASN333 3.8 0.2 1.0 O2B F:ACP402 4.0 0.7 1.0 CG F:GLU331 4.3 91.8 1.0 O2G F:ACP402 4.4 0.2 1.0 CE F:LYS74 4.4 89.7 1.0 O3G F:ACP402 4.4 0.4 1.0 O F:HOH502 4.5 81.3 1.0 O3A F:ACP402 4.9 0.8 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