Magnesium in PDB 8r67: Tubulin-Cryptophycin Complex

The structure of Tubulin-Cryptophycin Complex, PDB code: 8r67 was solved by A.C.Abel, T.Muehlethaler, C.Dessin, M.O.Steinmetz, N.Sewald, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.75, 158.66, 180.28, 90, 90, 90
R / Rfree (%)	19.4 / 22.9

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

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

The binding sites of Magnesium atom in the Tubulin-Cryptophycin Complex (pdb code 8r67). 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-Cryptophycin Complex, PDB code: 8r67:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.9 occ:1.00 O A:HOH643 2.0 46.7 1.0 O3G A:GTP501 2.0 46.8 1.0 O A:HOH611 2.1 48.2 1.0 O1B A:GTP501 2.2 50.5 1.0 O A:HOH604 2.2 48.6 1.0 O A:HOH630 2.2 48.3 1.0 PG A:GTP501 3.1 49.3 1.0 PB A:GTP501 3.3 47.6 1.0 OE1 A:GLU71 3.4 75.5 1.0 O3B A:GTP501 3.6 57.4 1.0 O2G A:GTP501 3.6 47.6 1.0 O3A A:GTP501 3.7 48.1 1.0 NZ B:LYS254 3.9 52.5 1.0 OD1 A:ASP69 4.1 50.3 1.0 CB A:GLN11 4.2 48.0 1.0 OD2 A:ASP69 4.3 49.7 1.0 CB A:ASP98 4.4 47.7 1.0 OD2 A:ASP98 4.4 53.1 1.0 O1G A:GTP501 4.4 46.5 1.0 N A:GLN11 4.4 48.9 1.0 O1A A:GTP501 4.5 51.7 1.0 O2B A:GTP501 4.6 48.5 1.0 CG A:ASP69 4.6 54.4 1.0 CD A:GLU71 4.6 72.7 1.0 CG A:ASP98 4.7 50.4 1.0 PA A:GTP501 4.7 46.8 1.0 OE1 A:GLN11 4.7 68.0 1.0 CA A:GLN11 4.9 52.2 1.0 CE B:LYS254 4.9 51.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.0 occ:1.00 O B:HOH648 2.0 48.4 1.0 O B:HOH668 2.1 67.2 1.0 OE1 B:GLN11 2.1 49.1 1.0 O1A B:GDP501 2.3 44.5 1.0 O B:HOH622 2.3 52.5 1.0 O C:HOH675 2.4 57.0 1.0 O B:HOH666 2.6 45.1 1.0 CD B:GLN11 3.4 60.4 1.0 PA B:GDP501 3.5 43.4 1.0 O3A B:GDP501 3.7 46.2 1.0 OD2 B:ASP179 4.0 51.5 1.0 CB B:GLN11 4.1 40.6 1.0 CG B:GLN11 4.2 52.0 1.0 OD1 B:ASN101 4.3 53.6 1.0 NE2 B:GLN11 4.3 60.0 1.0 C5' B:GDP501 4.4 45.3 1.0 O5' B:GDP501 4.4 42.6 1.0 O C:HOH666 4.4 62.7 1.0 OE1 C:GLU254 4.6 51.2 1.0 O2A B:GDP501 4.6 45.0 1.0 O1B B:GDP501 4.7 43.1 1.0 C8 B:GDP501 4.8 50.5 1.0 PB B:GDP501 4.8 41.6 1.0 ND2 B:ASN101 4.9 49.4 1.0 CG B:ASP179 5.0 51.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.7 occ:1.00 O C:HOH618 2.0 46.9 1.0 O C:HOH713 2.0 46.8 1.0 O C:HOH637 2.1 47.0 1.0 O2B C:GTP501 2.1 50.2 1.0 O1G C:GTP501 2.1 46.9 1.0 O C:HOH614 2.3 47.6 1.0 PB C:GTP501 3.2 46.0 1.0 PG C:GTP501 3.3 46.8 1.0 OE1 C:GLU71 3.4 74.4 1.0 O3B C:GTP501 3.6 48.0 1.0 O2G C:GTP501 3.8 47.0 1.0 O3A C:GTP501 3.8 47.5 1.0 OD1 C:ASP69 3.9 49.0 1.0 OD2 C:ASP69 4.0 46.9 1.0 NZ D:LYS254 4.1 47.6 1.0 CB C:GLN11 4.2 46.2 1.0 N C:GLN11 4.3 45.8 1.0 OD2 C:ASP98 4.3 54.1 1.0 CG C:ASP69 4.4 46.8 1.0 CB C:ASP98 4.4 48.0 1.0 O1B C:GTP501 4.5 46.1 1.0 CD C:GLU71 4.5 66.6 1.0 CB C:GLU71 4.5 57.3 1.0 O3G C:GTP501 4.6 47.0 1.0 O1A C:GTP501 4.7 50.5 1.0 PA C:GTP501 4.8 45.8 1.0 CA C:GLN11 4.8 46.0 1.0 CG C:ASP98 4.8 48.2 1.0 OE1 C:GLN11 4.9 57.5 1.0 OG1 C:THR145 5.0 46.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:72.9 occ:1.00 O D:HOH629 2.0 72.0 1.0 O D:HOH638 2.1 69.1 1.0 OE1 D:GLN11 2.1 84.5 1.0 O D:HOH617 2.2 66.1 1.0 O1A D:GDP501 2.4 76.2 1.0 CD D:GLN11 3.3 85.8 1.0 PA D:GDP501 3.6 71.1 1.0 O3A D:GDP501 3.8 72.9 1.0 CB D:GLN11 3.9 71.5 1.0 CG D:GLN11 4.1 79.2 1.0 O D:HOH651 4.1 78.8 1.0 NE2 D:GLN11 4.3 69.2 1.0 O1B D:GDP501 4.5 86.7 1.0 C5' D:GDP501 4.5 70.0 1.0 O5' D:GDP501 4.6 76.4 1.0 O2A D:GDP501 4.6 73.2 1.0 PB D:GDP501 4.8 73.1 1.0 OE2 D:GLU71 4.9 108.6 1.0 C8 D:GDP501 4.9 74.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:106.8 occ:1.00 O1B F:ACP402 2.2 129.6 1.0 OE2 F:GLU331 2.4 109.7 1.0 O3G F:ACP402 2.8 118.4 1.0 ND2 F:ASN333 3.1 113.0 1.0 CD F:GLU331 3.1 115.1 1.0 OE1 F:GLU331 3.1 125.0 1.0 PB F:ACP402 3.5 122.4 1.0 PG F:ACP402 3.5 134.0 1.0 NZ F:LYS74 3.7 121.4 1.0 O1G F:ACP402 3.7 116.7 1.0 C3B F:ACP402 3.8 129.8 1.0 O F:HOH507 4.1 102.2 1.0 CG F:ASN333 4.1 95.7 1.0 OD1 F:ASN333 4.5 96.8 1.0 O3A F:ACP402 4.5 115.7 1.0 O2B F:ACP402 4.5 128.8 1.0 CG F:GLU331 4.6 93.1 1.0 CE F:LYS74 4.8 102.9 1.0 O2G F:ACP402 5.0 128.4 1.0

A.C.Abel, T.Muhlethaler, C.Dessin, T.Schachtsiek, B.Sammet, T.Sharpe, M.O.Steinmetz, N.Sewald, A.E.Prota. Bridging the Maytansine and Vinca Sites: Cryptophycins Target Beta-Tubulin'S T5-Loop. J.Biol.Chem. 07363 2024.
ISSN: ESSN 1083-351X
PubMed: 38735475
DOI: 10.1016/J.JBC.2024.107363