Magnesium in PDB 7z7d: Tubulin-Todalam-Vinblastine-Complex

The structure of Tubulin-Todalam-Vinblastine-Complex, PDB code: 7z7d was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.286, 157.296, 182.526, 90, 90, 90
R / Rfree (%)	20.4 / 23.6

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

Calcium	(Ca)	4 atoms
Fluorine	(F)	3 atoms

The binding sites of Magnesium atom in the Tubulin-Todalam-Vinblastine-Complex (pdb code 7z7d). 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-Todalam-Vinblastine-Complex, PDB code: 7z7d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.0 occ:1.00 O1G A:GTP501 1.9 28.1 1.0 O A:HOH678 2.0 31.6 1.0 O A:HOH712 2.1 31.8 1.0 O A:HOH614 2.1 33.9 1.0 O1B A:GTP501 2.1 28.3 1.0 O A:HOH682 2.2 37.2 1.0 PG A:GTP501 3.1 34.5 1.0 PB A:GTP501 3.2 34.4 1.0 O3B A:GTP501 3.5 43.6 1.0 O3A A:GTP501 3.6 42.2 1.0 O2G A:GTP501 3.7 35.8 1.0 OE1 A:GLU71 3.7 60.2 1.0 NZ B:LYS254 3.8 33.6 1.0 CB A:GLN11 4.2 35.0 1.0 OD1 A:ASP69 4.2 38.2 1.0 O3G A:GTP501 4.4 33.2 1.0 CB A:ASP98 4.4 43.0 1.0 OD2 A:ASP69 4.4 39.3 1.0 OD2 A:ASP98 4.5 39.1 1.0 N A:GLN11 4.5 31.2 1.0 O2B A:GTP501 4.5 39.1 1.0 O1A A:GTP501 4.6 33.7 1.0 OE1 A:GLN11 4.7 42.0 1.0 PA A:GTP501 4.7 37.2 1.0 CG A:ASP98 4.7 34.2 1.0 CG A:ASP69 4.8 39.4 1.0 CD A:GLU71 4.9 51.8 1.0 CE B:LYS254 4.9 39.4 1.0 CA A:GLN11 4.9 42.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.9 occ:1.00 OE1 B:GLN11 2.2 50.6 1.0 O B:HOH609 2.2 50.7 1.0 O1A B:GDP501 2.3 26.9 1.0 O B:HOH774 2.5 52.8 1.0 O B:HOH706 2.9 32.1 1.0 O B:HOH756 2.9 51.5 1.0 O C:HOH701 2.9 60.9 1.0 CD B:GLN11 3.4 56.1 1.0 O B:HOH779 3.4 52.7 1.0 PA B:GDP501 3.6 29.3 1.0 O3A B:GDP501 3.9 29.8 1.0 CB B:GLN11 4.1 30.7 1.0 O B:HOH777 4.2 57.2 1.0 CG B:GLN11 4.2 42.1 1.0 OE2 C:GLU254 4.3 49.9 1.0 NE2 B:GLN11 4.3 46.4 1.0 C5' B:GDP501 4.4 30.1 1.0 O5' B:GDP501 4.5 30.8 1.0 OD1 B:ASN101 4.5 40.9 1.0 O1B B:GDP501 4.7 27.5 1.0 O2A B:GDP501 4.7 28.8 1.0 PB B:GDP501 4.9 28.9 1.0 C8 B:GDP501 4.9 30.8 1.0 O B:HOH793 5.0 57.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:27.8 occ:1.00 O1G C:GTP501 2.0 29.4 1.0 O C:HOH686 2.0 30.6 1.0 O C:HOH750 2.0 26.4 1.0 O1B C:GTP501 2.1 25.6 1.0 O C:HOH691 2.1 29.6 1.0 O C:HOH720 2.2 31.1 1.0 PG C:GTP501 3.1 32.7 1.0 PB C:GTP501 3.2 29.2 1.0 O3B C:GTP501 3.6 32.0 1.0 O2G C:GTP501 3.6 30.7 1.0 O3A C:GTP501 3.8 31.7 1.0 NZ D:LYS254 3.9 32.1 1.0 OE2 C:GLU71 4.0 50.0 1.0 OD1 C:ASP69 4.1 30.7 1.0 OD2 C:ASP98 4.3 38.0 1.0 CB C:GLN11 4.3 30.5 1.0 OD2 C:ASP69 4.3 31.0 1.0 CG C:GLU71 4.3 34.9 1.0 O3G C:GTP501 4.4 28.5 1.0 CB C:ASP98 4.5 34.4 1.0 N C:GLN11 4.5 32.1 1.0 O2B C:GTP501 4.5 31.2 1.0 O1A C:GTP501 4.6 30.7 1.0 O C:HOH615 4.6 45.0 1.0 CD C:GLU71 4.6 53.4 1.0 CG C:ASP69 4.7 36.0 1.0 CG C:ASP98 4.7 36.9 1.0 PA C:GTP501 4.8 30.9 1.0 OE1 C:GLN11 5.0 40.0 1.0 CE D:LYS254 5.0 33.6 1.0 CA C:GLN11 5.0 30.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:61.5 occ:1.00 O1A D:GDP501 2.0 93.6 1.0 OE1 D:GLN11 2.8 64.3 1.0 O D:HOH677 3.5 65.8 1.0 PA D:GDP501 3.5 62.4 1.0 OD1 D:ASN101 3.7 67.5 1.0 CD D:GLN11 4.0 68.6 1.0 C5' D:GDP501 4.1 64.7 1.0 O5' D:GDP501 4.3 55.7 1.0 O2A D:GDP501 4.3 50.3 1.0 O3A D:GDP501 4.5 73.1 1.0 ND2 D:ASN101 4.5 68.5 1.0 CG D:ASN101 4.5 68.0 1.0 O1B D:GDP501 4.7 42.0 1.0 CB D:GLN11 4.8 61.8 1.0 NE2 D:GLN11 4.9 59.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Todalam-Vinblastine-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:70.3 occ:1.00 O F:HOH503 2.2 70.3 1.0 O3G F:ACP401 2.3 89.7 1.0 OE2 F:GLU331 2.4 94.9 1.0 ND2 F:ASN333 2.8 83.3 1.0 O1B F:ACP401 2.9 91.8 1.0 CD F:GLU331 3.3 82.2 1.0 OE1 F:GLU331 3.5 78.8 1.0 PG F:ACP401 3.6 106.3 1.0 PB F:ACP401 3.8 89.4 1.0 O2B F:ACP401 3.8 112.7 1.0 CG F:ASN333 3.9 73.8 1.0 O2G F:ACP401 3.9 88.7 1.0 C3B F:ACP401 4.3 93.2 1.0 OD1 F:ASN333 4.3 79.3 1.0 NZ F:LYS74 4.3 78.7 1.0 CG F:GLU331 4.7 68.2 1.0 O1G F:ACP401 4.8 80.0 1.0

T.Muhlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz. Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052