Magnesium in PDB 5ca1: Crystal Structure of T2R-Ttl-Nocodazole Complex

The structure of Crystal Structure of T2R-Ttl-Nocodazole Complex, PDB code: 5ca1 was solved by Y.Wang, Y.Yu, Q.Chen, J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.440, 158.362, 180.692, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.5

The structure of Crystal Structure of T2R-Ttl-Nocodazole Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Nocodazole Complex (pdb code 5ca1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Nocodazole Complex, PDB code: 5ca1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T2R-Ttl-Nocodazole 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 T2R-Ttl-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.2 occ:1.00 O A:HOH640 2.0 25.6 1.0 O A:HOH625 2.1 28.9 1.0 O A:HOH611 2.1 28.2 1.0 O2G A:GTP501 2.1 22.0 1.0 O2B A:GTP501 2.2 23.4 1.0 O A:HOH689 2.2 25.9 1.0 PG A:GTP501 3.2 28.1 1.0 PB A:GTP501 3.3 28.4 1.0 OE1 A:GLU71 3.3 56.2 1.0 O3G A:GTP501 3.6 26.7 1.0 O3B A:GTP501 3.6 36.7 1.0 O3A A:GTP501 3.7 33.0 1.0 NZ B:LYS252 3.9 31.4 1.0 OD1 A:ASP69 4.1 29.1 1.0 OD2 A:ASP98 4.1 28.0 1.0 CB A:GLN11 4.2 24.3 1.0 OD2 A:ASP69 4.2 32.0 1.0 CB A:ASP98 4.2 26.5 1.0 N A:GLN11 4.4 29.4 1.0 CD A:GLU71 4.4 41.5 1.0 O1G A:GTP501 4.5 26.5 1.0 CG A:ASP98 4.5 33.9 1.0 CG A:ASP69 4.6 32.4 1.0 O1B A:GTP501 4.6 33.6 1.0 OE1 A:GLN11 4.6 42.9 1.0 O2A A:GTP501 4.7 26.2 1.0 PA A:GTP501 4.8 28.0 1.0 CA A:GLN11 4.9 31.0 1.0 OG1 A:THR145 4.9 25.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T2R-Ttl-Nocodazole 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 T2R-Ttl-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:26.8 occ:1.00 OE1 B:GLN11 2.1 29.9 1.0 O B:HOH617 2.1 33.8 1.0 O2A B:GDP501 2.1 27.6 1.0 O C:HOH610 2.4 28.3 1.0 O B:HOH659 2.5 34.6 1.0 CD B:GLN11 3.3 44.2 1.0 PA B:GDP501 3.5 26.4 1.0 OD2 B:ASP177 3.5 49.0 1.0 O3A B:GDP501 3.9 24.4 1.0 CB B:GLN11 4.0 22.0 1.0 CG B:GLN11 4.2 36.7 1.0 OE1 C:GLU254 4.3 52.8 1.0 C5' B:GDP501 4.3 31.6 1.0 NE2 B:GLN11 4.3 40.4 1.0 O5' B:GDP501 4.4 27.5 1.0 OD1 B:ASN99 4.4 35.0 1.0 O C:HOH707 4.4 38.7 1.0 O2B B:GDP501 4.5 29.0 1.0 O1A B:GDP501 4.5 27.3 1.0 CG B:ASP177 4.7 32.2 1.0 PB B:GDP501 4.8 28.2 1.0 C8 B:GDP501 4.9 26.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T2R-Ttl-Nocodazole 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 T2R-Ttl-Nocodazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:24.9 occ:1.00 O C:HOH676 2.0 24.2 1.0 O C:HOH652 2.1 23.6 1.0 O C:HOH615 2.1 22.6 1.0 O3G C:GTP501 2.1 19.2 1.0 O2B C:GTP501 2.1 20.6 1.0 O C:HOH650 2.2 28.3 1.0 PB C:GTP501 3.3 21.4 1.0 PG C:GTP501 3.3 26.9 1.0 O3B C:GTP501 3.7 30.8 1.0 O3A C:GTP501 3.7 28.0 1.0 OE1 C:GLU71 3.9 37.8 1.0 O2G C:GTP501 3.9 26.9 1.0 NZ D:LYS252 3.9 23.6 1.0 OD1 C:ASP69 4.0 25.4 1.0 OD2 C:ASP69 4.1 23.9 1.0 CB C:GLN11 4.1 22.9 1.0 N C:GLN11 4.3 19.5 1.0 OD2 C:ASP98 4.4 36.8 1.0 OE1 C:GLN11 4.5 36.9 1.0 CG C:ASP69 4.5 23.2 1.0 CB C:ASP98 4.5 27.8 1.0 O1G C:GTP501 4.5 25.1 1.0 O2A C:GTP501 4.6 29.1 1.0 O1B C:GTP501 4.6 24.0 1.0 PA C:GTP501 4.7 24.3 1.0 CA C:GLN11 4.8 22.4 1.0 CG C:ASP98 4.9 33.1 1.0 CD C:GLU71 5.0 37.2 1.0

Y.Wang, H.Zhang, B.Gigant, Y.Yu, Y.Wu, X.Chen, Q.Lai, Z.Yang, Q.Chen, J.Yang. Structures of A Diverse Set of Colchicine Binding Site Inhibitors in Complex with Tubulin Provide A Rationale For Drug Discovery. Febs J. V. 283 102 2016.
ISSN: ISSN 1742-464X
PubMed: 26462166
DOI: 10.1111/FEBS.13555