Magnesium in PDB 7vmk: Crystal Structure of Tubulin with 3

The structure of Crystal Structure of Tubulin with 3, PDB code: 7vmk was solved by Z.Jifa, T.Lun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.831, 157.513, 182.187, 90, 90, 90
R / Rfree (%)	19.4 / 23.2

The structure of Crystal Structure of Tubulin with 3 also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of Tubulin with 3 (pdb code 7vmk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Tubulin with 3, PDB code: 7vmk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.5 occ:1.00 O A:HOH607 1.8 32.1 1.0 O A:HOH613 2.0 27.2 1.0 O A:HOH606 2.0 24.7 1.0 O1G A:GTP501 2.1 24.9 1.0 O A:HOH614 2.2 24.7 1.0 O1B A:GTP501 2.3 21.9 1.0 PG A:GTP501 3.3 29.8 1.0 PB A:GTP501 3.3 23.4 1.0 O3B A:GTP501 3.6 45.9 1.0 OE1 A:GLU71 3.7 52.7 1.0 O2G A:GTP501 3.8 36.0 1.0 O3A A:GTP501 3.9 33.9 1.0 OD2 A:ASP69 4.0 36.9 1.0 CB A:GLN11 4.1 26.3 1.0 OD2 A:ASP98 4.1 38.0 1.0 OD1 A:ASP69 4.1 37.9 1.0 NZ B:LYS252 4.2 38.2 1.0 N A:GLN11 4.3 29.8 1.0 O1A A:GTP501 4.4 30.7 1.0 CB A:ASP98 4.5 33.2 1.0 NE2 A:GLN11 4.5 31.8 1.0 CG A:ASP69 4.5 32.7 1.0 O3G A:GTP501 4.6 26.3 1.0 CG A:ASP98 4.6 41.6 1.0 O2B A:GTP501 4.6 32.1 1.0 PA A:GTP501 4.8 30.8 1.0 CA A:GLN11 4.8 30.5 1.0 OG1 A:THR145 4.8 27.8 1.0 CD A:GLU71 4.9 54.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.3 occ:1.00 OE1 B:GLN11 2.0 43.2 1.0 O B:HOH611 2.1 31.2 1.0 O B:HOH614 2.2 49.1 1.0 O C:HOH650 2.2 36.2 1.0 O1A B:GDP501 2.3 28.0 1.0 O B:HOH630 2.4 35.9 1.0 CD B:GLN11 3.3 46.3 1.0 PA B:GDP501 3.6 24.6 1.0 OD2 B:ASP177 3.7 39.3 1.0 O3A B:GDP501 3.8 28.6 1.0 NE2 B:GLN11 4.2 45.0 1.0 OD1 B:ASN99 4.2 33.0 1.0 CG B:GLN11 4.3 35.1 1.0 CB B:GLN11 4.3 24.2 1.0 C5' B:GDP501 4.4 22.6 1.0 O5' B:GDP501 4.5 20.2 1.0 O1B B:GDP501 4.5 25.5 1.0 OE1 C:GLU254 4.7 43.1 1.0 O2A B:GDP501 4.7 22.2 1.0 CG B:ASP177 4.8 40.3 1.0 PB B:GDP501 4.8 22.9 1.0 C8 B:GDP501 4.9 26.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:66.3 occ:1.00 OD2 B:ASP118 3.7 57.5 1.0 OD1 B:ASP118 3.8 55.5 1.0 CG B:ASP118 4.2 51.3 1.0 CB B:ASP114 4.4 35.4 1.0 OD2 B:ASP114 4.9 77.3 1.0 O B:ASP114 4.9 36.5 1.0 CG B:ASP114 5.0 54.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:33.1 occ:1.00 O1G C:GTP501 2.1 26.4 1.0 O1B C:GTP501 2.2 25.5 1.0 PG C:GTP501 3.3 23.9 1.0 PB C:GTP501 3.4 20.2 1.0 O3B C:GTP501 3.7 25.6 1.0 OE2 C:GLU71 3.7 54.2 1.0 OD2 C:ASP69 3.8 32.7 1.0 O2G C:GTP501 3.8 31.3 1.0 OD1 C:ASP69 3.9 27.7 1.0 O3A C:GTP501 4.0 33.3 1.0 CG C:GLU71 4.1 34.4 1.0 NZ D:LYS252 4.1 33.3 1.0 OD2 C:ASP98 4.3 45.7 1.0 CB C:GLN11 4.3 20.7 1.0 CG C:ASP69 4.3 26.4 1.0 N C:GLN11 4.3 18.4 1.0 CD C:GLU71 4.4 43.9 1.0 CB C:ASP98 4.4 29.8 1.0 O2B C:GTP501 4.6 26.9 1.0 O3G C:GTP501 4.6 27.4 1.0 CG C:ASP98 4.7 34.8 1.0 OE1 C:GLN11 4.8 33.1 1.0 O1A C:GTP501 4.8 26.8 1.0 OG1 C:THR145 4.8 23.1 1.0 CA C:GLN11 4.9 20.8 1.0 PA C:GTP501 5.0 23.7 1.0

Z.Jifa, T.Lun. Crystal Structure of Tubulin with 3 To Be Published.