Magnesium in PDB 6ses: Tubulin-B2 Complex

The structure of Tubulin-B2 Complex, PDB code: 6ses was solved by B.Guo, A.Rodriguez-Gabin, A.E.Prota, T.Muehlethaler, N.Zhang, K.Ye, M.O.Steinmetz, S.Band Horwitz, A.B.Smith Iii, H.M.Mcdaid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.050, 157.170, 178.420, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Tubulin-B2 Complex (pdb code 6ses). 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-B2 Complex, PDB code: 6ses:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-B2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-B2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.5 occ:1.00 O A:HOH614 1.9 37.5 1.0 O A:HOH668 2.1 34.4 1.0 O A:HOH630 2.2 37.6 1.0 O3G A:GTP501 2.2 31.6 1.0 O A:HOH612 2.2 35.9 1.0 O1B A:GTP501 2.2 33.1 1.0 OE1 A:GLU71 3.3 64.8 1.0 PG A:GTP501 3.4 39.6 1.0 PB A:GTP501 3.4 33.6 1.0 O3B A:GTP501 3.8 39.7 1.0 O3A A:GTP501 3.8 39.0 1.0 O1G A:GTP501 3.8 36.8 1.0 CB A:GLN11 3.9 38.6 1.0 OD1 A:ASP69 3.9 46.9 1.0 OD2 A:ASP69 4.0 46.2 1.0 NZ B:LYS254 4.0 47.6 1.0 N A:GLN11 4.2 37.5 1.0 OD2 A:ASP98 4.4 45.8 1.0 CG A:ASP69 4.4 48.4 1.0 OE1 A:GLN11 4.4 55.9 1.0 O1A A:GTP501 4.5 37.4 1.0 CD A:GLU71 4.5 76.8 1.0 CB A:ASP98 4.6 38.9 1.0 CA A:GLN11 4.6 38.6 1.0 O2G A:GTP501 4.7 29.6 1.0 O2B A:GTP501 4.7 36.5 1.0 PA A:GTP501 4.8 39.1 1.0 CG A:ASP98 4.9 42.9 1.0 CB A:GLU71 4.9 66.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-B2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-B2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:32.5 occ:1.00 O B:HOH650 2.1 41.1 1.0 O1A B:GDP501 2.2 39.4 1.0 OE1 B:GLN11 2.3 48.9 1.0 O B:HOH709 2.3 44.9 1.0 O C:HOH662 2.4 52.7 1.0 O B:HOH603 2.6 48.0 1.0 O B:HOH693 2.8 76.1 1.0 CD B:GLN11 3.5 44.1 1.0 PA B:GDP501 3.6 37.4 1.0 OD2 B:ASP179 3.9 64.5 1.0 O3A B:GDP501 4.0 38.3 1.0 CB B:GLN11 4.2 36.6 1.0 OD1 B:ASN101 4.3 41.5 1.0 CG B:GLN11 4.3 38.3 1.0 OE1 C:GLU254 4.4 50.0 1.0 C5' B:GDP501 4.4 42.4 1.0 O5' B:GDP501 4.4 33.0 1.0 NE2 B:GLN11 4.5 45.7 1.0 O B:HOH737 4.6 70.8 1.0 O1B B:GDP501 4.6 26.6 1.0 O2A B:GDP501 4.6 35.7 1.0 C8 B:GDP501 4.8 41.2 1.0 PB B:GDP501 4.9 37.1 1.0 CG B:ASP179 4.9 62.6 1.0 ND2 B:ASN101 5.0 42.3 1.0

Magnesium binding site 3 out of 5 in the Tubulin-B2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-B2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.8 occ:1.00 O1G C:GTP501 2.2 33.4 1.0 O C:HOH679 2.2 31.8 1.0 O C:HOH667 2.2 31.0 1.0 O C:HOH779 2.2 30.5 1.0 O C:HOH723 2.2 36.0 1.0 O1B C:GTP501 2.3 33.4 1.0 PG C:GTP501 3.2 38.3 1.0 PB C:GTP501 3.3 39.3 1.0 O2G C:GTP501 3.5 31.9 1.0 O3B C:GTP501 3.5 39.9 1.0 NZ D:LYS254 3.9 42.5 1.0 O3A C:GTP501 3.9 38.8 1.0 CG C:GLU71 4.0 47.2 1.0 OD1 C:ASP69 4.0 41.0 1.0 OE2 C:GLU71 4.1 60.6 1.0 OD2 C:ASP69 4.3 43.7 1.0 OD2 C:ASP98 4.3 45.3 1.0 CB C:GLN11 4.3 27.1 1.0 O C:HOH714 4.4 65.4 1.0 CB C:ASP98 4.4 38.4 1.0 O3G C:GTP501 4.5 33.0 1.0 N C:GLN11 4.5 32.2 1.0 CD C:GLU71 4.6 58.5 1.0 O2B C:GTP501 4.6 37.2 1.0 CG C:ASP69 4.6 37.5 1.0 O1A C:GTP501 4.7 42.7 1.0 CG C:ASP98 4.7 41.2 1.0 PA C:GTP501 4.8 44.3 1.0 OE1 C:GLN11 5.0 47.8 1.0

Magnesium binding site 4 out of 5 in the Tubulin-B2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-B2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:57.0 occ:1.00 O1A D:GDP501 2.1 69.8 1.0 OE1 D:GLN11 2.4 59.1 1.0 O D:HOH736 2.5 52.0 1.0 O D:HOH684 2.7 49.3 1.0 O D:HOH618 3.0 77.0 1.0 PA D:GDP501 3.5 54.0 1.0 CD D:GLN11 3.6 68.1 1.0 O D:HOH770 3.7 52.6 1.0 C5' D:GDP501 4.1 55.1 1.0 OD1 D:ASN101 4.1 76.2 1.0 O3A D:GDP501 4.3 55.6 1.0 O5' D:GDP501 4.3 59.4 1.0 NE2 D:GLN11 4.5 60.6 1.0 O2A D:GDP501 4.5 49.6 1.0 CB D:GLN11 4.5 54.5 1.0 CG D:GLN11 4.6 63.8 1.0 O1B D:GDP501 4.8 48.5 1.0 C8 D:GDP501 4.9 40.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-B2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-B2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:76.0 occ:1.00 O1G F:ACP401 2.4 0.5 1.0 OE1 F:GLU331 2.4 1.0 1.0 ND2 F:ASN333 2.6 0.6 1.0 O1B F:ACP401 2.7 0.2 1.0 CD F:GLU331 3.2 99.5 1.0 OE2 F:GLU331 3.3 0.6 1.0 PG F:ACP401 3.6 1.0 1.0 O3G F:ACP401 3.8 0.8 1.0 CG F:ASN333 3.8 94.2 1.0 PB F:ACP401 3.9 0.7 1.0 NZ F:LYS74 4.3 0.3 1.0 OD1 F:ASN333 4.4 94.2 1.0 C3B F:ACP401 4.4 0.3 1.0 CG F:GLU331 4.5 81.3 1.0 O2B F:ACP401 4.5 0.9 1.0 O F:HOH566 4.6 77.1 1.0 O2G F:ACP401 4.8 0.4 1.0 CB F:ASN333 5.0 74.5 1.0

B.Guo, A.Rodriguez-Gabin, A.E.Prota, T.Muhlethaler, N.Zhang, K.Ye, M.O.Steinmetz, S.B.Horwitz, A.B.Smith 3Rd, H.M.Mcdaid. Structural Refinement of the Tubulin Ligand (+)-Discodermolide to Attenuate Chemotherapy-Mediated Senescence. Mol.Pharmacol. V. 98 156 2020.
ISSN: ESSN 1521-0111
PubMed: 32591477
DOI: 10.1124/MOL.119.117457