Magnesium in PDB 6qqn: Tubulin-TH588 Complex

The structure of Tubulin-TH588 Complex, PDB code: 6qqn was solved by J.C.Patterson, B.A.Joughin, A.E.Prota, T.Muehlethaler, O.H.Jonas, M.A.Whitman, S.Varmeh, S.Chen, S.P.Balk, M.O.Steinmetz, D.A.Lauffenburger, M.B.Yaffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.832, 156.186, 179.432, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Tubulin-TH588 Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Tubulin-TH588 Complex (pdb code 6qqn). 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-TH588 Complex, PDB code: 6qqn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.8 occ:1.00 O3G A:GTP501 2.0 42.0 1.0 O A:HOH625 2.1 51.4 1.0 O A:HOH621 2.1 41.1 1.0 O A:HOH607 2.1 47.3 1.0 O A:HOH610 2.1 47.3 1.0 O1B A:GTP501 2.2 38.7 1.0 PG A:GTP501 3.1 49.4 1.0 PB A:GTP501 3.3 45.9 1.0 O1G A:GTP501 3.5 48.1 1.0 O3B A:GTP501 3.6 59.4 1.0 O3A A:GTP501 3.6 51.6 1.0 OE2 A:GLU71 3.8 72.6 1.0 NZ B:LYS254 4.0 56.2 1.0 CB A:GLN11 4.1 46.5 1.0 OD1 A:ASP69 4.3 52.3 1.0 CG A:GLU71 4.3 72.5 1.0 OD2 A:ASP98 4.3 60.3 1.0 OE1 A:GLN11 4.4 56.4 1.0 CB A:ASP98 4.4 50.0 1.0 O2G A:GTP501 4.4 46.0 1.0 N A:GLN11 4.4 51.0 1.0 OD2 A:ASP69 4.4 53.0 1.0 O1A A:GTP501 4.5 53.9 1.0 CD A:GLU71 4.5 74.4 1.0 O2B A:GTP501 4.6 53.4 1.0 CG A:ASP98 4.6 55.8 1.0 PA A:GTP501 4.7 48.4 1.0 CG A:ASP69 4.8 52.9 1.0 CA A:GLN11 4.9 49.3 1.0 NE2 B:GLN247 4.9 0.8 1.0 CE B:LYS254 5.0 56.8 1.0

Magnesium binding site 2 out of 5 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:45.8 occ:1.00 O B:HOH614 2.1 45.1 1.0 O B:HOH604 2.1 50.9 1.0 O C:HOH664 2.1 41.3 1.0 OE1 B:GLN11 2.1 61.4 1.0 O B:HOH630 2.1 40.2 1.0 O1A B:GDP501 2.2 38.9 1.0 CD B:GLN11 3.3 53.3 1.0 PA B:GDP501 3.5 36.6 1.0 OD2 B:ASP179 3.6 64.6 1.0 O3A B:GDP501 3.9 48.2 1.0 CB B:GLN11 4.1 49.8 1.0 CG B:GLN11 4.2 51.2 1.0 NE2 B:GLN11 4.3 60.6 1.0 OD1 B:ASN101 4.3 42.8 1.0 C5' B:GDP501 4.4 46.1 1.0 O5' B:GDP501 4.4 38.2 1.0 O1B B:GDP501 4.5 47.9 1.0 O2A B:GDP501 4.6 40.9 1.0 OE1 C:GLU254 4.6 58.5 1.0 CG B:ASP179 4.7 58.9 1.0 C8 B:GDP501 4.8 44.7 1.0 PB B:GDP501 4.9 42.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.2 occ:1.00 O C:HOH645 2.1 42.8 1.0 O C:HOH628 2.1 40.9 1.0 O C:HOH603 2.1 41.1 1.0 O C:HOH627 2.1 46.5 1.0 O1B C:GTP501 2.1 42.5 1.0 O3G C:GTP501 2.1 37.7 1.0 PG C:GTP501 3.2 45.7 1.0 PB C:GTP501 3.3 42.2 1.0 O1G C:GTP501 3.6 40.5 1.0 O3B C:GTP501 3.7 51.5 1.0 NZ D:LYS254 3.8 48.0 1.0 O3A C:GTP501 3.9 50.7 1.0 OE2 C:GLU71 4.1 67.1 1.0 OD2 C:ASP98 4.1 45.1 1.0 OD1 C:ASP69 4.1 52.4 1.0 CG C:GLU71 4.2 51.8 1.0 CB C:GLN11 4.3 39.8 1.0 OD2 C:ASP69 4.3 47.2 1.0 CB C:ASP98 4.5 41.6 1.0 O2G C:GTP501 4.5 41.1 1.0 N C:GLN11 4.5 42.8 1.0 O2B C:GTP501 4.5 46.8 1.0 NE2 C:GLN11 4.6 51.0 1.0 CD C:GLU71 4.6 61.1 1.0 CG C:ASP69 4.7 52.5 1.0 O1A C:GTP501 4.7 49.5 1.0 CG C:ASP98 4.7 46.1 1.0 PA C:GTP501 4.9 45.7 1.0 OG1 C:THR145 5.0 40.9 1.0 CE D:LYS254 5.0 46.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:71.1 occ:1.00 O D:HOH602 2.1 74.8 1.0 O D:HOH621 2.1 74.7 1.0 OE1 D:GLN11 2.1 0.0 1.0 O1A D:GDP501 2.5 86.7 1.0 CD D:GLN11 3.3 0.5 1.0 NE2 D:GLN11 4.0 98.0 1.0 PA D:GDP501 4.0 73.2 1.0 C5' D:GDP501 4.3 73.0 1.0 CG D:GLN11 4.4 84.0 1.0 CB D:GLN11 4.4 74.6 1.0 O2A D:GDP501 4.6 67.7 1.0 O5' D:GDP501 4.7 74.5 1.0 C8 D:GDP501 4.7 65.5 1.0 OD1 D:ASN101 5.0 0.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:83.6 occ:1.00 OE2 F:GLU331 2.1 0.6 1.0 OE1 F:GLU331 2.1 0.1 1.0 OD1 F:ASN333 2.2 0.4 1.0 CD F:GLU331 2.4 0.3 1.0 O3G F:ACP701 2.6 1.0 1.0 O1B F:ACP701 2.7 0.6 1.0 CG F:ASN333 3.2 0.9 1.0 PG F:ACP701 3.6 0.7 1.0 ND2 F:ASN333 3.7 0.2 1.0 PB F:ACP701 3.8 0.1 1.0 O1G F:ACP701 3.8 0.8 1.0 CG F:GLU331 3.9 0.7 1.0 C3B F:ACP701 4.0 0.3 1.0 NZ F:LYS74 4.3 0.9 1.0 O2B F:ACP701 4.4 0.8 1.0 CB F:ASN333 4.6 0.4 1.0 O1A F:ACP701 4.6 0.6 1.0 CB F:GLU331 4.7 0.2 1.0 CE F:LYS74 4.8 0.3 1.0 CA F:ASN333 4.9 90.3 1.0 O F:VAL332 4.9 85.7 1.0

J.C.Patterson, B.A.Joughin, A.E.Prota, T.Muhlethaler, O.H.Jonas, M.A.Whitman, S.Varmeh, S.Chen, S.P.Balk, M.O.Steinmetz, D.A.Lauffenburger, M.B.Yaffe. Visage Reveals A Targetable Mitotic Spindle Vulnerability in Cancer Cells. Cell Syst V. 9 74 2019.
ISSN: ISSN 2405-4720
PubMed: 31302152
DOI: 10.1016/J.CELS.2019.05.009