Magnesium in PDB 6fkl: Tubulin-TUB015 Complex

The structure of Tubulin-TUB015 Complex, PDB code: 6fkl was solved by A.E.Prota, M.O.Steinmetz, E.-M.Priego, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.44 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.748, 157.764, 179.971, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.7

The structure of Tubulin-TUB015 Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-TUB015 Complex (pdb code 6fkl). 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-TUB015 Complex, PDB code: 6fkl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.6 occ:1.00 O1G A:GTP501 2.0 24.4 1.0 O A:HOH616 2.1 31.7 1.0 O A:HOH662 2.1 34.5 1.0 O1B A:GTP501 2.1 27.4 1.0 O A:HOH690 2.1 32.9 1.0 O A:HOH631 2.2 36.6 1.0 PB A:GTP501 3.2 30.1 1.0 PG A:GTP501 3.2 32.9 1.0 O3B A:GTP501 3.5 43.0 1.0 O3A A:GTP501 3.7 38.6 1.0 O2G A:GTP501 3.8 34.9 1.0 NZ B:LYS254 3.9 35.0 1.0 OD1 A:ASP69 4.0 39.6 1.0 OE1 A:GLU71 4.0 52.1 1.0 CB A:GLN11 4.1 30.3 1.0 OD2 A:ASP98 4.2 49.2 1.0 OD2 A:ASP69 4.2 41.2 1.0 N A:GLN11 4.3 34.0 1.0 CB A:ASP98 4.4 38.1 1.0 CG A:GLU71 4.4 45.1 1.0 O3G A:GTP501 4.5 29.6 1.0 O2B A:GTP501 4.5 36.8 1.0 O1A A:GTP501 4.5 34.9 1.0 CG A:ASP69 4.6 40.5 1.0 PA A:GTP501 4.7 35.4 1.0 CG A:ASP98 4.7 43.5 1.0 CD A:GLU71 4.7 50.8 1.0 ND2 B:ASN249 4.7 93.2 1.0 CA A:GLN11 4.8 34.1 1.0 OE1 A:GLN11 4.8 43.5 1.0 OG1 A:THR145 4.9 36.5 1.0 O B:HOH666 4.9 44.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.1 occ:1.00 O B:HOH668 2.0 30.9 1.0 OE1 B:GLN11 2.0 35.1 1.0 O C:HOH671 2.3 37.4 1.0 O1A B:GDP501 2.3 33.0 1.0 O B:HOH712 2.4 55.9 1.0 O B:HOH669 2.4 33.0 1.0 O B:HOH612 2.5 33.0 1.0 CD B:GLN11 3.3 42.1 1.0 PA B:GDP501 3.6 27.9 1.0 O3A B:GDP501 3.8 36.1 1.0 CB B:GLN11 4.0 28.6 1.0 OD2 B:ASP179 4.0 37.9 1.0 CG B:GLN11 4.1 33.8 1.0 NE2 B:GLN11 4.2 35.1 1.0 OE1 C:GLU254 4.3 42.0 1.0 OD1 B:ASN101 4.4 35.5 1.0 O C:HOH624 4.4 47.4 1.0 C5' B:GDP501 4.5 28.3 1.0 O5' B:GDP501 4.5 31.4 1.0 O1B B:GDP501 4.6 29.5 1.0 O2A B:GDP501 4.7 28.7 1.0 C8 B:GDP501 4.8 33.9 1.0 PB B:GDP501 4.9 31.0 1.0 ND2 B:ASN101 5.0 30.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.3 occ:1.00 O1G C:GTP501 2.0 21.4 1.0 O C:HOH662 2.0 30.2 1.0 O1B C:GTP501 2.1 27.0 1.0 O C:HOH655 2.1 31.9 1.0 O C:HOH732 2.1 27.8 1.0 O C:HOH616 2.2 31.0 1.0 PG C:GTP501 3.1 30.2 1.0 PB C:GTP501 3.2 25.5 1.0 O3B C:GTP501 3.5 38.4 1.0 O2G C:GTP501 3.6 31.6 1.0 O3A C:GTP501 3.7 31.1 1.0 NZ D:LYS254 3.7 38.6 1.0 OE1 C:GLU71 4.1 44.2 1.0 OD1 C:ASP69 4.1 38.1 1.0 CB C:GLN11 4.2 25.9 1.0 OD2 C:ASP98 4.2 43.5 1.0 CG C:GLU71 4.3 37.2 1.0 OD2 C:ASP69 4.3 34.2 1.0 N C:GLN11 4.4 26.4 1.0 O3G C:GTP501 4.4 29.5 1.0 CB C:ASP98 4.4 39.1 1.0 ND2 D:ASN249 4.5 64.8 1.0 O2B C:GTP501 4.5 28.9 1.0 O1A C:GTP501 4.5 31.1 1.0 CG C:ASP69 4.6 36.6 1.0 OE1 C:GLN11 4.7 41.0 1.0 CD C:GLU71 4.7 40.7 1.0 PA C:GTP501 4.7 27.9 1.0 CG C:ASP98 4.7 42.7 1.0 O C:HOH736 4.9 43.5 1.0 CA C:GLN11 4.9 30.1 1.0 CE D:LYS254 5.0 36.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.8 occ:1.00 O D:HOH616 2.0 52.4 1.0 OE1 D:GLN11 2.1 79.8 1.0 O1A D:GDP501 2.5 55.2 1.0 O D:HOH639 2.5 60.9 1.0 O D:HOH604 2.6 68.4 1.0 CD D:GLN11 3.3 66.8 1.0 PA D:GDP501 3.7 54.1 1.0 O3A D:GDP501 3.8 48.7 1.0 CB D:GLN11 3.8 58.0 1.0 OD2 D:ASP179 4.0 94.0 1.0 CG D:GLN11 4.1 61.4 1.0 NE2 D:GLN11 4.3 63.9 1.0 O1B D:GDP501 4.4 46.5 1.0 O D:HOH640 4.6 67.6 1.0 OD1 D:ASN101 4.6 67.2 1.0 C5' D:GDP501 4.7 52.2 1.0 O5' D:GDP501 4.7 54.0 1.0 O2A D:GDP501 4.7 58.8 1.0 PB D:GDP501 4.8 51.5 1.0 C8 D:GDP501 5.0 49.1 1.0

Magnesium binding site 5 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:76.5 occ:1.00 OE2 F:GLU331 2.1 0.2 1.0 O1B F:ACP402 2.2 95.8 1.0 O1G F:ACP402 2.5 0.5 1.0 OD1 F:ASN333 2.8 93.7 1.0 CD F:GLU331 3.0 0.8 1.0 OE1 F:GLU331 3.1 0.6 1.0 ND2 F:ASN333 3.5 95.4 1.0 CG F:ASN333 3.5 87.1 1.0 PG F:ACP402 3.5 0.4 1.0 PB F:ACP402 3.5 98.7 1.0 O3G F:ACP402 3.6 91.2 1.0 NZ F:LYS74 3.8 88.6 1.0 O2B F:ACP402 4.0 1.0 1.0 C3B F:ACP402 4.2 0.6 1.0 CG F:GLU331 4.4 83.9 1.0 O3A F:ACP402 4.8 96.4 1.0 CE F:LYS74 4.9 84.2 1.0 O1A F:ACP402 4.9 95.3 1.0 O2G F:ACP402 4.9 0.8 1.0 CB F:ASN333 4.9 69.4 1.0

O.Bueno, J.Estevez Gallego, S.Martins, A.E.Prota, F.Gago, A.Gomez-Sanjuan, M.J.Camarasa, I.Barasoain, M.O.Steinmetz, J.F.Diaz, M.J.Perez-Perez, S.Liekens, E.M.Priego. High-Affinity Ligands of the Colchicine Domain in Tubulin Based on A Structure-Guided Design. Sci Rep V. 8 4242 2018.
ISSN: ESSN 2045-2322
PubMed: 29523799
DOI: 10.1038/S41598-018-22382-X