Magnesium in PDB 5cb4: Crystal Structure of T2R-Ttl-Tivantinib Complex

The structure of Crystal Structure of T2R-Ttl-Tivantinib Complex, PDB code: 5cb4 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)	39.82 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.060, 158.444, 181.825, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.2

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Tivantinib Complex (pdb code 5cb4). 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-Tivantinib Complex, PDB code: 5cb4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T2R-Ttl-Tivantinib 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-Tivantinib Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.9 occ:1.00 O A:HOH743 2.1 34.3 1.0 O A:HOH623 2.1 34.0 1.0 O A:HOH675 2.1 34.4 1.0 O2G A:GTP501 2.1 25.9 1.0 O2B A:GTP501 2.2 31.9 1.0 O A:HOH742 2.3 35.0 1.0 PG A:GTP501 3.3 36.2 1.0 PB A:GTP501 3.4 30.0 1.0 HZ1 B:LYS252 3.4 57.0 1.0 HB2 A:GLN11 3.4 32.3 1.0 O3G A:GTP501 3.7 32.8 1.0 HB2 A:ASP98 3.7 40.7 1.0 O3B A:GTP501 3.8 36.2 1.0 O3A A:GTP501 3.8 35.9 1.0 H A:GLN11 3.8 38.1 1.0 HB3 A:ASP98 3.9 40.7 1.0 OE1 A:GLU71 4.0 45.9 1.0 OD1 A:ASP69 4.0 33.1 1.0 HB3 A:GLU71 4.1 48.5 1.0 HB3 A:GLN11 4.1 32.3 1.0 OD2 A:ASP69 4.1 30.9 1.0 NZ B:LYS252 4.2 47.5 1.0 CB A:GLN11 4.2 26.9 1.0 HZ2 B:LYS252 4.2 57.0 1.0 CB A:ASP98 4.2 33.9 1.0 CG A:ASP69 4.5 31.6 1.0 N A:GLN11 4.5 31.7 1.0 OE1 A:GLN11 4.5 43.5 1.0 HG1 A:THR145 4.5 46.2 1.0 HZ3 B:LYS252 4.5 57.0 1.0 O1G A:GTP501 4.6 33.9 1.0 OD2 A:ASP98 4.6 45.0 1.0 O1B A:GTP501 4.7 40.1 1.0 HB A:THR145 4.7 39.1 1.0 CD A:GLU71 4.8 57.9 1.0 HG21 A:VAL74 4.8 49.8 1.0 CG A:ASP98 4.9 39.2 1.0 HA2 A:GLY10 4.9 30.2 1.0 OG1 A:THR145 4.9 38.5 1.0 CB A:GLU71 4.9 40.4 1.0 HB2 A:GLU71 4.9 48.5 1.0 CA A:GLN11 4.9 32.9 1.0 PA A:GTP501 4.9 29.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T2R-Ttl-Tivantinib 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-Tivantinib Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:28.4 occ:1.00 O B:HOH617 2.1 34.8 1.0 O2A B:GDP501 2.1 35.6 1.0 OE1 B:GLN11 2.3 34.8 1.0 O C:HOH613 2.3 46.2 1.0 O B:HOH610 2.6 46.3 1.0 O B:HOH706 2.6 39.0 1.0 OD2 B:ASP177 3.3 60.4 1.0 CD B:GLN11 3.5 47.0 1.0 PA B:GDP501 3.5 31.3 1.0 H8 B:GDP501 3.6 40.9 1.0 HB3 B:GLN11 3.6 38.6 1.0 O3A B:GDP501 4.0 33.2 1.0 HB2 B:GLN11 4.1 38.6 1.0 OE1 C:GLU254 4.2 65.1 1.0 C5' B:GDP501 4.2 29.3 1.0 OD1 B:ASN99 4.2 33.8 1.0 CB B:GLN11 4.2 32.2 1.0 HE22 B:GLN11 4.4 60.2 1.0 O5' B:GDP501 4.4 29.8 1.0 CG B:GLN11 4.4 42.8 1.0 NE2 B:GLN11 4.4 50.2 1.0 CG B:ASP177 4.5 45.7 1.0 HD21 B:ASN99 4.5 41.9 1.0 O1A B:GDP501 4.6 29.6 1.0 C8 B:GDP501 4.6 34.1 1.0 O2B B:GDP501 4.6 30.0 1.0 HG2 B:GLN11 4.7 51.3 1.0 HB3 B:ASP177 4.9 66.5 1.0 O C:HOH800 4.9 44.5 1.0 PB B:GDP501 5.0 32.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T2R-Ttl-Tivantinib 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-Tivantinib Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.7 occ:1.00 O3G C:GTP501 2.0 21.7 1.0 O C:HOH774 2.1 30.2 1.0 O C:HOH624 2.1 20.9 1.0 O C:HOH644 2.1 27.9 1.0 O2B C:GTP501 2.1 34.9 1.0 O C:HOH725 2.1 29.7 1.0 PB C:GTP501 3.2 41.0 1.0 PG C:GTP501 3.3 31.9 1.0 HZ1 D:LYS252 3.4 42.6 1.0 HB2 C:GLN11 3.4 29.9 1.0 OE1 C:GLU71 3.6 58.7 1.0 O3B C:GTP501 3.6 33.7 1.0 O3A C:GTP501 3.7 37.8 1.0 H C:GLN11 3.7 31.9 1.0 HB2 C:ASP98 3.8 37.6 1.0 O2G C:GTP501 4.0 38.4 1.0 OD1 C:ASP69 4.0 29.5 1.0 HB3 C:ASP98 4.0 37.6 1.0 HB3 C:GLU71 4.1 58.2 1.0 HB3 C:GLN11 4.1 29.9 1.0 OD2 C:ASP69 4.1 32.2 1.0 NZ D:LYS252 4.2 35.5 1.0 CB C:GLN11 4.2 24.9 1.0 HZ2 D:LYS252 4.3 42.6 1.0 CB C:ASP98 4.4 31.4 1.0 N C:GLN11 4.4 26.6 1.0 O1G C:GTP501 4.4 32.3 1.0 HZ3 D:LYS252 4.5 42.6 1.0 O1B C:GTP501 4.5 31.3 1.0 CG C:ASP69 4.5 36.3 1.0 OE1 C:GLN11 4.6 32.4 1.0 CD C:GLU71 4.6 46.6 1.0 HG21 C:VAL74 4.7 45.5 1.0 HG1 C:THR145 4.7 36.7 1.0 OD2 C:ASP98 4.7 36.4 1.0 HB C:THR145 4.8 30.8 1.0 PA C:GTP501 4.8 44.1 1.0 HA2 C:GLY10 4.8 30.5 1.0 O2A C:GTP501 4.8 36.7 1.0 CA C:GLN11 4.9 29.7 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