Magnesium in PDB 6fkj: Tubulin-TUB075 Complex

The structure of Tubulin-TUB075 Complex, PDB code: 6fkj 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)	49.45 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.670, 157.562, 180.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.6

The structure of Tubulin-TUB075 Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-TUB075 Complex (pdb code 6fkj). 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-TUB075 Complex, PDB code: 6fkj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.8 occ:1.00 O A:HOH662 2.0 36.7 1.0 O A:HOH623 2.0 33.2 1.0 O A:HOH681 2.1 33.3 1.0 O2G A:GTP501 2.1 28.8 1.0 O1B A:GTP501 2.1 29.5 1.0 O A:HOH643 2.1 34.9 1.0 PG A:GTP501 3.2 36.5 1.0 PB A:GTP501 3.3 34.6 1.0 O3B A:GTP501 3.5 48.5 1.0 O1G A:GTP501 3.7 38.4 1.0 O3A A:GTP501 3.8 44.8 1.0 OE1 A:GLU71 3.9 52.5 1.0 NZ B:LYS254 3.9 39.9 1.0 OD1 A:ASP69 3.9 41.4 1.0 CB A:GLN11 4.1 33.0 1.0 OD2 A:ASP69 4.2 44.2 1.0 OD2 A:ASP98 4.2 51.0 1.0 N A:GLN11 4.3 37.1 1.0 CB A:ASP98 4.3 39.1 1.0 CG A:ASP69 4.5 41.6 1.0 O3G A:GTP501 4.5 30.6 1.0 O1A A:GTP501 4.5 40.4 1.0 O2B A:GTP501 4.6 38.7 1.0 CG A:ASP98 4.7 49.5 1.0 PA A:GTP501 4.7 37.4 1.0 ND2 B:ASN249 4.7 93.0 1.0 CA A:GLN11 4.8 36.7 1.0 OE1 A:GLN11 4.8 46.0 1.0 OG1 A:THR145 4.9 38.7 1.0 O B:HOH683 5.0 50.5 1.0

Magnesium binding site 2 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:27.8 occ:1.00 OE1 B:GLN11 2.1 38.1 1.0 O B:HOH647 2.1 34.4 1.0 O1A B:GDP502 2.3 35.9 1.0 O C:HOH675 2.3 44.0 1.0 O B:HOH698 2.4 33.5 1.0 O B:HOH607 2.5 38.8 1.0 CD B:GLN11 3.3 44.2 1.0 PA B:GDP502 3.6 34.2 1.0 O3A B:GDP502 3.8 37.0 1.0 CB B:GLN11 4.0 33.7 1.0 OD2 B:ASP179 4.0 39.7 1.0 CG B:GLN11 4.1 37.8 1.0 NE2 B:GLN11 4.3 38.7 1.0 OD1 B:ASN101 4.4 40.8 1.0 OE1 C:GLU254 4.4 47.6 1.0 C5' B:GDP502 4.4 36.0 1.0 O5' B:GDP502 4.5 37.0 1.0 O C:HOH640 4.5 43.5 1.0 O1B B:GDP502 4.5 29.7 1.0 O2A B:GDP502 4.6 32.9 1.0 C8 B:GDP502 4.7 33.8 1.0 PB B:GDP502 4.8 35.9 1.0 ND2 B:ASN101 5.0 33.9 1.0

Magnesium binding site 3 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.8 occ:1.00 O1G C:GTP501 2.0 27.1 1.0 O C:HOH684 2.0 34.2 1.0 O C:HOH642 2.0 29.0 1.0 O C:HOH611 2.1 32.5 1.0 O1B C:GTP501 2.1 29.5 1.0 O C:HOH731 2.1 32.9 1.0 PG C:GTP501 3.1 30.7 1.0 PB C:GTP501 3.2 29.2 1.0 O3B C:GTP501 3.5 39.6 1.0 O2G C:GTP501 3.6 33.4 1.0 NZ D:LYS254 3.7 33.0 1.0 O3A C:GTP501 3.7 35.0 1.0 OE1 C:GLU71 4.0 43.9 1.0 OD2 C:ASP98 4.0 47.5 1.0 OD1 C:ASP69 4.2 40.2 1.0 CB C:GLN11 4.2 27.1 1.0 OD2 C:ASP69 4.3 34.4 1.0 CG C:GLU71 4.3 35.1 1.0 N C:GLN11 4.4 32.9 1.0 O3G C:GTP501 4.4 31.6 1.0 CB C:ASP98 4.5 39.1 1.0 O1A C:GTP501 4.5 35.5 1.0 O2B C:GTP501 4.5 31.1 1.0 ND2 D:ASN249 4.5 54.4 1.0 CG C:ASP69 4.7 41.0 1.0 CG C:ASP98 4.7 44.1 1.0 PA C:GTP501 4.7 32.2 1.0 CD C:GLU71 4.7 40.5 1.0 OE1 C:GLN11 4.7 39.5 1.0 CE D:LYS254 4.9 35.1 1.0 CA C:GLN11 4.9 27.6 1.0 O C:HOH737 4.9 49.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:66.0 occ:1.00 O D:HOH640 2.1 75.2 1.0 O1A D:GDP501 2.4 59.5 1.0 OE1 D:GLN11 2.6 63.0 1.0 O D:HOH602 2.6 70.2 1.0 O D:HOH641 2.7 60.7 1.0 OD2 D:ASP179 3.5 98.7 1.0 PA D:GDP501 3.5 57.1 1.0 O3A D:GDP501 3.7 51.6 1.0 CD D:GLN11 3.8 70.0 1.0 OD1 D:ASN101 4.0 67.9 1.0 C5' D:GDP501 4.3 52.0 1.0 CB D:GLN11 4.3 63.3 1.0 O5' D:GDP501 4.3 57.5 1.0 CG D:GLN11 4.5 66.8 1.0 CG D:ASP179 4.6 0.1 1.0 O1B D:GDP501 4.6 51.8 1.0 O2A D:GDP501 4.7 57.7 1.0 NE2 D:GLN11 4.8 70.8 1.0 PB D:GDP501 4.8 53.6 1.0 CG D:ASN101 4.9 71.7 1.0 ND2 D:ASN101 4.9 76.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:78.8 occ:1.00 OE2 F:GLU331 2.1 1.0 1.0 O1B F:ACP402 2.3 0.4 1.0 O1G F:ACP402 2.4 0.7 1.0 ND2 F:ASN333 2.6 98.0 1.0 CD F:GLU331 3.0 0.7 1.0 OE1 F:GLU331 3.3 0.2 1.0 PG F:ACP402 3.5 0.2 1.0 PB F:ACP402 3.6 0.3 1.0 CG F:ASN333 3.7 93.6 1.0 NZ F:LYS74 3.7 86.4 1.0 O3G F:ACP402 3.8 0.2 1.0 O2B F:ACP402 3.9 1.0 1.0 OD1 F:ASN333 4.0 0.6 1.0 C3B F:ACP402 4.1 0.9 1.0 CG F:GLU331 4.4 86.3 1.0 O2G F:ACP402 4.8 0.5 1.0 O3A F:ACP402 4.9 0.4 1.0 O1A F:ACP402 4.9 0.6 1.0 CE F:LYS74 4.9 84.6 1.0 CB F:ASN333 4.9 74.2 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