Magnesium in PDB 5jqg: An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison

The structure of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison, PDB code: 5jqg was solved by Y.X.Wang, J.H.Naismith, X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.22 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.050, 158.120, 180.630, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.2

The structure of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison (pdb code 5jqg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison, PDB code: 5jqg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.9 occ:1.00 O1G A:GTP501 2.0 25.2 1.0 O1B A:GTP501 2.0 26.9 1.0 O A:HOH633 2.0 34.4 1.0 O A:HOH645 2.0 28.5 1.0 O A:HOH647 2.1 29.0 1.0 O A:HOH616 2.2 33.6 1.0 PG A:GTP501 3.1 30.4 1.0 PB A:GTP501 3.2 30.0 1.0 O3B A:GTP501 3.5 32.5 1.0 O2G A:GTP501 3.6 31.3 1.0 O3A A:GTP501 3.7 30.3 1.0 NZ B:LYS252 3.9 39.2 1.0 OD1 A:ASP69 4.1 30.3 1.0 OE2 A:GLU71 4.1 56.9 1.0 CB A:GLN11 4.2 33.0 1.0 OD2 A:ASP98 4.3 35.2 1.0 OD2 A:ASP69 4.3 31.2 1.0 O1A A:GTP501 4.4 27.2 1.0 CG A:GLU71 4.4 47.2 1.0 N A:GLN11 4.4 32.5 1.0 O3G A:GTP501 4.5 29.4 1.0 O2B A:GTP501 4.5 33.3 1.0 CB A:ASP98 4.5 33.4 1.0 CG A:ASP69 4.6 32.6 1.0 PA A:GTP501 4.7 29.5 1.0 CG A:ASP98 4.8 36.1 1.0 CD A:GLU71 4.8 48.7 1.0 CA A:GLN11 4.9 33.6 1.0 OE1 A:GLN11 4.9 44.2 1.0 CE B:LYS252 4.9 36.8 1.0

Magnesium binding site 2 out of 4 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.0 occ:1.00 O1A B:GDP501 2.0 28.4 1.0 O B:HOH643 2.1 41.1 1.0 OE1 B:GLN11 2.2 43.6 1.0 O C:HOH627 2.5 39.4 1.0 O B:HOH602 2.5 40.5 1.0 O B:HOH653 2.5 39.8 1.0 CD B:GLN11 3.4 41.5 1.0 PA B:GDP501 3.4 28.8 1.0 O3A B:GDP501 3.8 29.2 1.0 OD2 B:ASP177 3.9 38.7 1.0 CB B:GLN11 4.2 35.2 1.0 CG B:GLN11 4.3 38.7 1.0 O5' B:GDP501 4.3 28.1 1.0 C5' B:GDP501 4.4 32.2 1.0 NE2 B:GLN11 4.4 46.2 1.0 OD1 B:ASN99 4.5 33.6 1.0 OE1 C:GLU254 4.6 47.5 1.0 O2A B:GDP501 4.7 25.7 1.0 O1B B:GDP501 4.7 25.3 1.0 CG B:ASP177 4.8 40.8 1.0 C8 B:GDP501 4.8 33.8 1.0 PB B:GDP501 4.9 28.6 1.0

Magnesium binding site 3 out of 4 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:28.7 occ:1.00 O1G C:GTP501 1.9 23.5 1.0 O1B C:GTP501 2.0 26.8 1.0 O C:HOH692 2.1 26.7 1.0 O C:HOH607 2.1 29.3 1.0 O C:HOH633 2.1 25.6 1.0 O C:HOH645 2.1 29.5 1.0 PG C:GTP501 3.1 31.0 1.0 PB C:GTP501 3.1 26.5 1.0 O3B C:GTP501 3.5 28.4 1.0 O2G C:GTP501 3.6 31.4 1.0 O3A C:GTP501 3.6 26.1 1.0 NZ D:LYS252 3.9 31.2 1.0 OD1 C:ASP69 4.0 30.7 1.0 OE2 C:GLU71 4.1 47.6 1.0 OD2 C:ASP69 4.2 28.4 1.0 CB C:GLN11 4.2 29.4 1.0 OD2 C:ASP98 4.3 37.5 1.0 N C:GLN11 4.4 29.0 1.0 CG C:GLU71 4.4 40.5 1.0 O3G C:GTP501 4.4 27.4 1.0 O2B C:GTP501 4.5 26.5 1.0 CB C:ASP98 4.5 36.5 1.0 O1A C:GTP501 4.5 24.6 1.0 CG C:ASP69 4.6 30.1 1.0 PA C:GTP501 4.7 26.4 1.0 CG C:ASP98 4.7 35.4 1.0 CD C:GLU71 4.8 43.9 1.0 CA C:GLN11 4.9 28.1 1.0 CE D:LYS252 5.0 31.3 1.0 OE1 C:GLN11 5.0 39.7 1.0

Magnesium binding site 4 out of 4 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.0 occ:1.00 O D:HOH601 1.9 50.5 1.0 O1G D:GTP501 1.9 42.6 1.0 O D:HOH629 2.2 58.8 1.0 O D:HOH605 2.3 56.1 1.0 O1B D:GTP501 2.6 43.2 1.0 PG D:GTP501 3.1 59.5 1.0 PB D:GTP501 3.5 51.4 1.0 O2G D:GTP501 3.5 47.5 1.0 O3B D:GTP501 3.7 54.4 1.0 O3A D:GTP501 3.9 44.9 1.0 CB D:GLN11 4.1 58.4 1.0 OE1 D:GLN11 4.2 70.3 1.0 N D:GLN11 4.4 55.8 1.0 CB D:GLU69 4.4 72.5 1.0 O3G D:GTP501 4.4 46.2 1.0 OD1 D:ASP67 4.5 59.1 1.0 O1A D:GTP501 4.6 55.0 1.0 CG D:GLU69 4.6 75.9 1.0 OD2 D:ASP67 4.7 63.1 1.0 PA D:GTP501 4.8 50.9 1.0 CA D:GLN11 4.8 56.8 1.0 O2B D:GTP501 4.9 60.1 1.0

J.Yang, Y.X.Wang, T.Wang, J.Jiang, C.H.Botting, H.Liu, Q.Chen, J.Yang, J.H.Naismith, X.Zhu, L.Chen. Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule Nat Commun V. 7 12103 2016.
ISSN: ESSN 2041-1723
PubMed: 27357539
DOI: 10.1038/NCOMMS12103