Magnesium in PDB 5z4p: Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex, PDB code: 5z4p was solved by H.Zhang, C.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.64 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.832, 154.843, 181.024, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28.6

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex (pdb code 5z4p). 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-Stathmin-Ttl-Compound Tca Complex, PDB code: 5z4p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex


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-Stathmin-Ttl-Compound Tca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:59.0 occ:1.00 O3G A:GTP501 2.1 54.6 1.0 O2B A:GTP501 2.2 55.0 1.0 PG A:GTP501 3.2 59.0 1.0 PB A:GTP501 3.5 47.6 1.0 O2G A:GTP501 3.5 55.4 1.0 OE1 A:GLU71 3.6 72.3 1.0 O3B A:GTP501 3.7 60.6 1.0 OD1 A:ASP69 3.7 58.6 1.0 NZ B:LYS254 3.9 67.8 1.0 OD2 A:ASP69 4.0 66.6 1.0 CB A:GLN11 4.1 56.7 1.0 OD2 A:ASP98 4.2 65.2 1.0 CG A:ASP69 4.3 66.6 1.0 O3A A:GTP501 4.3 55.1 1.0 CB A:ASP98 4.3 63.1 1.0 OE1 A:GLN11 4.4 74.4 1.0 N A:GLN11 4.4 56.1 1.0 CG A:ASP98 4.5 59.4 1.0 O1G A:GTP501 4.6 46.7 1.0 O1B A:GTP501 4.6 53.0 1.0 O2A A:GTP501 4.7 52.8 1.0 CA A:GLN11 4.8 60.1 1.0 CD A:GLU71 4.8 74.4 1.0 CB A:GLU71 4.8 67.2 1.0 CG A:GLN11 5.0 55.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex


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-Stathmin-Ttl-Compound Tca Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:51.2 occ:1.00 OE1 B:GLN11 2.2 51.0 1.0 O2A B:GDP501 2.2 48.9 1.0 OD2 B:ASP179 2.3 59.3 1.0 O B:HOH609 2.7 42.0 1.0 CD B:GLN11 3.4 52.7 1.0 CG B:ASP179 3.5 56.9 1.0 PA B:GDP501 3.6 43.1 1.0 O3A B:GDP501 3.8 47.2 1.0 OD1 B:ASN101 4.1 45.3 1.0 C5' B:GDP501 4.1 45.5 1.0 NE2 B:GLN11 4.2 46.5 1.0 O5' B:GDP501 4.3 38.9 1.0 OD1 B:ASP179 4.3 66.5 1.0 OE1 C:GLU254 4.4 61.7 1.0 CB B:GLN11 4.4 50.4 1.0 CB B:ASP179 4.5 52.4 1.0 CG B:GLN11 4.5 53.8 1.0 OE2 C:GLU254 4.7 54.4 1.0 ND2 B:ASN101 4.7 41.0 1.0 O1A B:GDP501 4.7 38.4 1.0 C8 B:GDP501 4.8 46.0 1.0 CG B:ASN101 4.8 43.8 1.0 CD C:GLU254 4.9 52.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex


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-Stathmin-Ttl-Compound Tca Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:50.9 occ:1.00 O C:HOH601 1.9 49.8 1.0 O2B C:GTP503 2.3 51.5 1.0 O3G C:GTP503 2.4 46.7 1.0 OE1 C:GLU71 2.9 64.7 1.0 OD2 C:ASP69 3.2 43.3 1.0 OD1 C:ASP69 3.3 52.0 1.0 PG C:GTP503 3.5 43.9 1.0 PB C:GTP503 3.6 41.0 1.0 CG C:ASP69 3.6 53.2 1.0 O2G C:GTP503 3.7 47.3 1.0 O3B C:GTP503 3.9 47.1 1.0 CD C:GLU71 4.1 58.9 1.0 CB C:ASP98 4.1 38.2 1.0 OD2 C:ASP98 4.2 48.8 1.0 NZ D:LYS254 4.3 55.4 1.0 N C:GLN11 4.3 35.7 1.0 CB C:GLN11 4.4 46.6 1.0 CB C:GLU71 4.4 50.4 1.0 O1B C:GTP503 4.5 48.0 1.0 CG C:ASP98 4.6 48.6 1.0 O3A C:GTP503 4.7 50.2 1.0 OG1 C:THR145 4.7 46.7 1.0 O1G C:GTP503 4.8 42.5 1.0 CA C:GLN11 4.8 43.6 1.0 OE2 C:GLU71 4.9 69.8 1.0 CG C:GLU71 4.9 57.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Tca Complex


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-Stathmin-Ttl-Compound Tca Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:76.9 occ:1.00 O2B D:GDP501 2.1 92.6 1.0 CB D:ALA99 2.9 84.5 1.0 PB D:GDP501 3.1 81.8 1.0 O3B D:GDP501 3.3 80.6 1.0 OD1 D:ASN101 3.4 82.4 1.0 OE2 D:GLU71 3.5 95.4 1.0 OE1 D:GLU71 3.6 92.8 1.0 O3A D:GDP501 3.7 72.8 1.0 OE1 D:GLN11 3.8 93.1 1.0 CD D:GLU71 3.8 0.7 1.0 CA D:ALA99 4.2 90.3 1.0 CG D:ASN101 4.4 82.4 1.0 O1B D:GDP501 4.4 67.3 1.0 N D:ASN101 4.5 85.7 1.0 N D:ALA99 4.6 95.5 1.0 N D:GLY100 4.6 82.7 1.0 O2A D:GDP501 4.7 84.6 1.0 OG1 D:THR145 4.8 84.9 1.0 PA D:GDP501 4.8 73.4 1.0 C D:ALA99 4.8 83.2 1.0 CD D:GLN11 4.9 94.7 1.0 CA D:ASN101 4.9 81.0 1.0

H.Zhang, C.Luo. Discovery and Design of Novel Tubulin Inhibitors To Be Published.