Magnesium in PDB 5iyz: Tubulin-Mmae Complex

The structure of Tubulin-Mmae Complex, PDB code: 5iyz was solved by A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.96 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.510, 156.610, 182.420, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.2

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

Calcium

(Ca)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.6 occ:1.00 O A:HOH751 2.0 34.0 1.0 O3G A:GTP501 2.0 32.3 1.0 O1B A:GTP501 2.1 30.5 1.0 O A:HOH647 2.3 40.3 1.0 O A:HOH627 2.3 36.2 1.0 O A:HOH732 2.4 37.7 1.0 PB A:GTP501 3.2 33.1 1.0 PG A:GTP501 3.3 32.8 1.0 O3B A:GTP501 3.6 37.2 1.0 O1G A:GTP501 3.7 36.5 1.0 O3A A:GTP501 3.8 34.4 1.0 NZ B:LYS254 3.9 38.4 1.0 CB A:GLN11 4.0 37.5 1.0 OE1 A:GLU71 4.0 65.2 1.0 OD1 A:ASP69 4.1 47.4 1.0 OD2 A:ASP69 4.2 51.4 1.0 N A:GLN11 4.3 36.7 1.0 OD2 A:ASP98 4.4 49.4 1.0 O1A A:GTP501 4.5 30.8 1.0 CB A:ASP98 4.6 42.8 1.0 O2B A:GTP501 4.6 33.9 1.0 O2G A:GTP501 4.6 32.2 1.0 CG A:ASP69 4.6 47.6 1.0 O A:HOH652 4.7 59.5 1.0 OE1 A:GLN11 4.7 45.3 1.0 PA A:GTP501 4.7 34.9 1.0 CA A:GLN11 4.7 38.7 1.0 CG A:ASP98 4.8 48.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:63.0 occ:1.00 O B:HOH611 2.3 51.0 1.0 O C:HOH603 2.5 73.2 1.0 O1A B:GDP501 2.6 29.2 1.0 O B:HOH852 2.6 75.2 1.0 O B:HOH739 2.9 35.2 1.0 O B:HOH851 3.1 72.3 1.0 OE1 B:GLN11 3.2 55.5 1.0 O B:HOH874 3.6 52.2 1.0 CD B:GLN11 3.6 51.3 1.0 O B:HOH812 3.6 61.9 1.0 PA B:GDP501 3.8 28.1 1.0 NE2 B:GLN11 4.0 63.8 1.0 O3A B:GDP501 4.0 26.8 1.0 CB B:GLN11 4.3 28.3 1.0 CG B:GLN11 4.5 40.1 1.0 OD1 B:ASN101 4.5 36.7 1.0 C5' B:GDP501 4.6 28.5 1.0 O5' B:GDP501 4.6 28.2 1.0 O1B B:GDP501 4.6 26.5 1.0 OE1 C:GLU254 4.7 62.9 1.0 O B:HOH696 4.9 45.8 1.0 O2A B:GDP501 5.0 29.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.2 occ:1.00 O1G C:GTP501 2.1 31.0 1.0 O C:HOH657 2.1 26.3 1.0 O1B C:GTP501 2.1 28.5 1.0 O C:HOH845 2.2 29.6 1.0 O C:HOH742 2.2 29.2 1.0 O C:HOH613 2.4 37.4 1.0 PB C:GTP501 3.2 28.5 1.0 PG C:GTP501 3.2 30.9 1.0 O3B C:GTP501 3.5 29.3 1.0 O2G C:GTP501 3.6 32.7 1.0 O3A C:GTP501 3.8 30.1 1.0 NZ D:LYS254 3.9 32.4 1.0 OD1 C:ASP69 4.0 31.6 1.0 OE1 C:GLU71 4.0 46.6 1.0 CB C:GLN11 4.1 27.5 1.0 OD2 C:ASP69 4.2 34.9 1.0 CG C:GLU71 4.3 38.9 1.0 OD2 C:ASP98 4.3 43.4 1.0 N C:GLN11 4.3 25.8 1.0 CB C:ASP98 4.5 37.2 1.0 O1A C:GTP501 4.5 31.5 1.0 O3G C:GTP501 4.5 30.4 1.0 O2B C:GTP501 4.5 28.5 1.0 O C:HOH756 4.6 54.9 1.0 CG C:ASP69 4.6 34.4 1.0 CD C:GLU71 4.6 54.2 1.0 O C:HOH815 4.8 63.3 1.0 OE1 C:GLN11 4.8 38.4 1.0 CG C:ASP98 4.8 38.5 1.0 PA C:GTP501 4.8 32.1 1.0 CA C:GLN11 4.8 29.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:64.8 occ:1.00 O1A D:GDP501 2.4 56.9 1.0 OE1 D:GLN11 2.6 61.1 1.0 O D:HOH717 2.7 64.7 1.0 O D:HOH688 2.7 72.0 1.0 O D:HOH739 2.7 0.6 1.0 O D:HOH770 3.3 78.5 1.0 O D:HOH751 3.4 70.8 1.0 PA D:GDP501 3.6 51.8 1.0 O3A D:GDP501 3.8 45.9 1.0 CD D:GLN11 3.9 64.9 1.0 OD1 D:ASN101 4.1 76.4 1.0 C5' D:GDP501 4.3 50.5 1.0 O5' D:GDP501 4.3 42.2 1.0 CB D:GLN11 4.5 55.0 1.0 CG D:GLN11 4.7 56.6 1.0 O1B D:GDP501 4.7 42.6 1.0 O2A D:GDP501 4.8 53.5 1.0 NE2 D:GLN11 4.8 68.7 1.0 PB D:GDP501 4.9 48.6 1.0 CG D:ASN101 5.0 81.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Mmae Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:78.5 occ:1.00 O2B F:ACP402 2.5 1.0 1.0 O1G F:ACP402 2.6 91.1 1.0 OE2 F:GLU331 2.9 0.6 1.0 ND2 F:ASN333 2.9 83.4 1.0 OE1 F:GLU331 3.1 90.5 1.0 CD F:GLU331 3.4 89.5 1.0 NZ F:LYS74 3.6 84.6 1.0 PB F:ACP402 3.6 97.8 1.0 O1B F:ACP402 3.6 0.3 1.0 O F:HOH509 3.9 58.4 1.0 PG F:ACP402 3.9 0.7 1.0 CG F:ASN333 4.2 81.9 1.0 C3B F:ACP402 4.3 88.6 1.0 O3G F:ACP402 4.6 65.8 1.0 OD1 F:ASN333 4.8 89.7 1.0 CG F:GLU331 4.9 72.2 1.0 CE F:LYS74 4.9 83.0 1.0 O3A F:ACP402 5.0 0.5 1.0

A.B.Waight, K.Bargsten, S.Doronina, M.O.Steinmetz, D.Sussman, A.E.Prota. Structural Basis of Microtubule Destabilization By Potent Auristatin Anti-Mitotics. Plos One V. 11 60890 2016.
ISSN: ESSN 1932-6203
PubMed: 27518442
DOI: 10.1371/JOURNAL.PONE.0160890