Magnesium in PDB 5c8y: Crystal Structure of T2R-Ttl-Plinabulin Complex

The structure of Crystal Structure of T2R-Ttl-Plinabulin Complex, PDB code: 5c8y 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)	39.70 / 2.59
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 (%)	22.2 / 27.1

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

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Plinabulin Complex (pdb code 5c8y). 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-Plinabulin Complex, PDB code: 5c8y:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:26.7 occ:1.00 O A:HOH629 2.2 26.8 1.0 O B:HOH602 2.2 33.4 1.0 O1B A:GTP501 2.4 21.7 1.0 O1G A:GTP501 2.5 13.7 1.0 HB2 A:GLN11 3.2 43.9 1.0 OD2 A:ASP69 3.4 29.7 1.0 OE1 A:GLU71 3.4 65.9 1.0 OD1 A:ASP69 3.4 56.7 1.0 HB3 A:GLU71 3.6 78.7 1.0 PB A:GTP501 3.6 16.3 1.0 H A:GLN11 3.6 41.4 1.0 OD1 B:ASN247 3.7 0.9 1.0 PG A:GTP501 3.7 35.2 1.0 CG A:ASP69 3.8 45.5 1.0 HB3 A:ASP98 3.9 50.6 1.0 HZ1 B:LYS252 3.9 39.7 1.0 O3B A:GTP501 4.0 79.2 1.0 HB2 A:ASP98 4.0 50.6 1.0 CB A:GLN11 4.1 36.6 1.0 O3A A:GTP501 4.2 48.8 1.0 N A:GLN11 4.2 34.5 1.0 HB3 A:GLN11 4.2 43.9 1.0 CD A:GLU71 4.3 69.3 1.0 HG21 A:VAL74 4.3 71.2 1.0 O2G A:GTP501 4.4 43.3 1.0 CB A:ASP98 4.4 42.2 1.0 HG23 A:VAL74 4.4 71.2 1.0 CB A:GLU71 4.4 65.6 1.0 HA2 A:GLY10 4.4 41.2 1.0 HB2 A:GLU71 4.5 78.7 1.0 OE1 A:GLN11 4.5 52.6 1.0 CA A:GLN11 4.6 34.1 1.0 CG B:ASN247 4.7 90.1 1.0 NZ B:LYS252 4.7 33.1 1.0 HZ2 B:LYS252 4.7 39.7 1.0 HG1 A:THR145 4.7 39.6 1.0 HA A:GLN11 4.8 41.0 1.0 HB A:THR145 4.8 35.8 1.0 HZ3 B:LYS252 4.8 39.7 1.0 OD2 A:ASP98 4.8 62.1 1.0 O2B A:GTP501 4.8 54.0 1.0 CG2 A:VAL74 4.8 59.4 1.0 O3G A:GTP501 4.9 35.5 1.0 OG1 A:THR145 4.9 33.0 1.0 CG A:GLU71 5.0 55.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.5 occ:1.00 O1A B:GDP501 2.1 62.5 1.0 O C:HOH632 2.2 53.0 1.0 OE1 B:GLN11 2.3 78.2 1.0 OD2 B:ASP177 3.3 51.6 1.0 CD B:GLN11 3.4 79.1 1.0 PA B:GDP501 3.6 33.5 1.0 H8 B:GDP501 3.8 68.0 1.0 HB3 B:GLN11 3.9 58.3 1.0 HE22 B:GLN11 4.0 63.2 1.0 OD1 B:ASN99 4.1 39.8 1.0 NE2 B:GLN11 4.2 52.6 1.0 OE1 C:GLU254 4.2 75.8 1.0 HB2 B:GLN11 4.2 58.3 1.0 C5' B:GDP501 4.2 38.7 1.0 HD21 B:ASN99 4.3 29.1 1.0 O5' B:GDP501 4.4 26.1 1.0 CB B:GLN11 4.4 48.6 1.0 O3A B:GDP501 4.4 37.5 1.0 O2A B:GDP501 4.5 18.6 1.0 CG B:ASP177 4.5 59.0 1.0 CG B:GLN11 4.5 50.1 1.0 O C:HOH617 4.5 51.4 1.0 HB3 B:ASP177 4.6 62.5 1.0 O3B B:GDP501 4.6 50.0 1.0 C8 B:GDP501 4.7 56.7 1.0 HG2 B:GLN11 4.9 60.2 1.0 CG B:ASN99 4.9 43.8 1.0 ND2 B:ASN99 5.0 24.2 1.0 CB B:ASP177 5.0 52.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T2R-Ttl-Plinabulin 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-Plinabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.2 occ:1.00 O C:HOH621 2.1 30.3 1.0 O C:HOH626 2.1 25.4 1.0 O1G C:GTP501 2.2 22.2 1.0 O1B C:GTP501 2.2 42.9 1.0 PG C:GTP501 3.3 30.6 1.0 HZ1 D:LYS252 3.4 39.8 1.0 PB C:GTP501 3.4 23.1 1.0 OE1 C:GLU71 3.6 51.9 1.0 O3B C:GTP501 3.6 34.8 1.0 HB3 C:GLU71 3.7 41.5 1.0 HB2 C:GLN11 3.7 46.3 1.0 OD1 C:ASP69 3.7 36.5 1.0 HB2 C:ASP98 3.7 49.2 1.0 O2G C:GTP501 3.8 26.3 1.0 H C:GLN11 3.8 27.2 1.0 HB3 C:ASP98 3.9 49.2 1.0 OD2 C:ASP69 3.9 25.2 1.0 O3A C:GTP501 4.0 45.7 1.0 OD1 D:ASN247 4.1 76.1 1.0 NZ D:LYS252 4.1 33.2 1.0 HZ2 D:LYS252 4.2 39.8 1.0 CB C:ASP98 4.3 41.0 1.0 HZ3 D:LYS252 4.3 39.8 1.0 CG C:ASP69 4.3 36.1 1.0 HB2 C:GLU71 4.3 41.5 1.0 HG1 C:THR145 4.3 28.6 1.0 CB C:GLU71 4.4 34.5 1.0 HB3 C:GLN11 4.5 46.3 1.0 CD C:GLU71 4.5 50.5 1.0 CB C:GLN11 4.5 38.6 1.0 N C:GLN11 4.6 22.7 1.0 O3G C:GTP501 4.6 29.1 1.0 HA2 C:GLY10 4.6 36.2 1.0 O2B C:GTP501 4.6 23.1 1.0 OD2 C:ASP98 4.6 65.5 1.0 OG1 C:THR145 4.7 23.9 1.0 HB C:THR145 4.8 16.4 1.0 HG21 C:VAL74 4.8 48.8 1.0 OE1 C:GLN11 4.8 46.5 1.0 CG C:ASP98 4.9 56.8 1.0 CG D:ASN247 4.9 53.7 1.0 CG C:GLU71 5.0 40.1 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