Magnesium in PDB 6qtn: Tubulin-Cyclostreptin Complex

The structure of Tubulin-Cyclostreptin Complex, PDB code: 6qtn was solved by F.D.A.Balaguer, T.Muehlethaler, J.Estevez-Gallego, E.Calvo, J.F.Gimenez-Abian, A.L.Risinger, E.J.Sorensen, C.D.Vanderwal, K.-H.Altmann, S.L.Mooberry, M.O.Steinmetz, M.A.Oliva, A.E.Prota, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.585, 158.361, 179.946, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

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

Calcium

(Ca)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Cyclostreptin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.4 occ:1.00 O A:HOH636 2.0 38.9 1.0 O A:HOH676 2.0 38.0 1.0 O3G A:GTP501 2.0 30.7 1.0 O A:HOH610 2.1 40.9 1.0 O A:HOH609 2.2 38.9 1.0 O1B A:GTP501 2.2 32.9 1.0 PG A:GTP501 3.3 38.6 1.0 PB A:GTP501 3.3 37.1 1.0 O1G A:GTP501 3.7 36.8 1.0 OE2 A:GLU71 3.7 61.0 1.0 O3B A:GTP501 3.7 40.7 1.0 NZ B:LYS254 3.8 52.6 1.0 O3A A:GTP501 3.9 39.9 1.0 CB A:GLN11 4.1 36.8 1.0 OD1 A:ASP69 4.1 49.0 1.0 OD2 A:ASP69 4.2 47.4 1.0 CG A:GLU71 4.2 64.5 1.0 OD2 A:ASP98 4.3 50.3 1.0 N A:GLN11 4.4 36.0 1.0 CB A:ASP98 4.4 46.4 1.0 CD A:GLU71 4.4 66.1 1.0 O1A A:GTP501 4.5 36.8 1.0 O2G A:GTP501 4.5 37.6 1.0 CG A:ASP69 4.6 49.7 1.0 O2B A:GTP501 4.6 39.9 1.0 CG A:ASP98 4.7 50.0 1.0 PA A:GTP501 4.7 38.6 1.0 OE1 A:GLN11 4.8 50.7 1.0 CA A:GLN11 4.8 39.7 1.0 CE B:LYS254 5.0 44.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Cyclostreptin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.2 occ:1.00 O B:HOH695 2.0 38.5 1.0 OE1 B:GLN11 2.2 44.5 1.0 O1A B:GDP501 2.3 32.6 1.0 O C:HOH628 2.3 46.9 1.0 O B:HOH610 2.5 42.7 1.0 O B:HOH677 2.5 37.0 1.0 CD B:GLN11 3.3 41.6 1.0 PA B:GDP501 3.6 33.4 1.0 O3A B:GDP501 3.9 36.2 1.0 OD2 B:ASP179 4.0 42.0 1.0 CB B:GLN11 4.0 30.9 1.0 CG B:GLN11 4.1 36.6 1.0 NE2 B:GLN11 4.4 47.9 1.0 ND2 B:ASN101 4.4 35.8 1.0 C5' B:GDP501 4.4 31.5 1.0 O5' B:GDP501 4.4 34.4 1.0 OE1 C:GLU254 4.4 45.0 1.0 O1B B:GDP501 4.6 31.8 1.0 O2A B:GDP501 4.7 32.5 1.0 O C:HOH604 4.7 52.5 1.0 C8 B:GDP501 4.7 38.8 1.0 PB B:GDP501 4.9 33.5 1.0 O B:HOH688 4.9 58.7 1.0 CG B:ASP179 4.9 41.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Cyclostreptin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:33.1 occ:1.00 O C:HOH662 2.0 33.4 1.0 O1G C:GTP501 2.0 31.1 1.0 O C:HOH721 2.0 32.8 1.0 O C:HOH654 2.1 36.5 1.0 O1B C:GTP501 2.1 33.0 1.0 O C:HOH687 2.2 34.6 1.0 PG C:GTP501 3.2 32.5 1.0 PB C:GTP501 3.2 30.8 1.0 O2G C:GTP501 3.6 36.3 1.0 O3B C:GTP501 3.6 34.5 1.0 O3A C:GTP501 3.8 33.7 1.0 NZ D:LYS254 3.9 38.1 1.0 OE1 C:GLU71 3.9 53.7 1.0 OD1 C:ASP69 4.1 40.8 1.0 OD2 C:ASP69 4.2 37.4 1.0 OD2 C:ASP98 4.2 49.0 1.0 CB C:GLN11 4.2 30.3 1.0 CG C:GLU71 4.2 47.4 1.0 N C:GLN11 4.4 28.6 1.0 CB C:ASP98 4.4 37.6 1.0 O3G C:GTP501 4.4 31.6 1.0 O2B C:GTP501 4.5 35.6 1.0 O1A C:GTP501 4.5 33.4 1.0 CD C:GLU71 4.6 56.1 1.0 CG C:ASP69 4.6 35.6 1.0 CG C:ASP98 4.7 44.2 1.0 PA C:GTP501 4.8 32.8 1.0 CA C:GLN11 4.9 32.5 1.0 OE1 C:GLN11 4.9 42.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Cyclostreptin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:62.3 occ:1.00 O1A D:GDP501 2.2 64.9 1.0 OE1 D:GLN11 2.3 71.8 1.0 O D:HOH639 2.4 69.0 1.0 O D:HOH664 2.5 61.1 1.0 O D:HOH621 2.6 91.3 1.0 O D:HOH624 2.6 63.0 1.0 PA D:GDP501 3.5 60.1 1.0 CD D:GLN11 3.6 75.6 1.0 O D:HOH667 3.6 77.9 1.0 O3A D:GDP501 3.9 54.7 1.0 O D:HOH652 4.1 81.5 1.0 CB D:GLN11 4.2 67.0 1.0 C5' D:GDP501 4.4 61.5 1.0 OD1 D:ASN101 4.4 86.2 1.0 CG D:GLN11 4.4 70.5 1.0 O5' D:GDP501 4.4 63.0 1.0 NE2 D:GLN11 4.5 70.1 1.0 O1B D:GDP501 4.5 53.1 1.0 O2A D:GDP501 4.6 64.7 1.0 PB D:GDP501 4.9 57.8 1.0 C8 D:GDP501 5.0 55.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Cyclostreptin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:67.4 occ:1.00 OE2 F:GLU331 1.9 0.3 1.0 O1G F:ACP401 2.5 0.8 1.0 O1B F:ACP401 2.5 0.3 1.0 CD F:GLU331 2.8 0.1 1.0 ND2 F:ASN333 2.8 92.2 1.0 OE1 F:GLU331 3.0 0.6 1.0 H3B1 F:ACP401 3.3 0.2 1.0 PB F:ACP401 3.5 0.1 1.0 NZ F:LYS74 3.5 84.5 1.0 C3B F:ACP401 3.5 0.7 1.0 PG F:ACP401 3.5 1.0 1.0 CG F:ASN333 3.8 83.1 1.0 O3A F:ACP401 3.9 0.7 1.0 OD1 F:ASN333 4.2 85.6 1.0 CG F:GLU331 4.2 82.2 1.0 O F:HOH507 4.3 84.2 1.0 O3G F:ACP401 4.5 0.6 1.0 H3B2 F:ACP401 4.5 0.2 1.0 CE F:LYS74 4.6 76.2 1.0 O2G F:ACP401 4.8 0.2 1.0 O2B F:ACP401 4.9 1.0 1.0

F.A.Balaguer, T.Muhlethaler, J.Estevez-Gallego, E.Calvo, J.F.Gimenez-Abian, A.L.Risinger, E.J.Sorensen, C.D.Vanderwal, K.H.Altmann, S.L.Mooberry, M.O.Steinmetz, M.A.Oliva, A.E.Prota, J.F.Diaz. Crystal Structure of the Cyclostreptin-Tubulin Adduct: Implications For Tubulin Activation By Taxane-Site Ligands. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 30897704
DOI: 10.3390/IJMS20061392