Magnesium in PDB 5yl4: Crystal Structure of T2R-Ttl-8WR Complex

The structure of Crystal Structure of T2R-Ttl-8WR Complex, PDB code: 5yl4 was solved by Z.Y.Fu, W.B.Li, Y.Y.Chu, Y.W.Hou, C.P.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.461, 157.730, 182.147, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.6

The structure of Crystal Structure of T2R-Ttl-8WR Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-8WR Complex (pdb code 5yl4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-8WR Complex, PDB code: 5yl4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-8WR 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-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.5 occ:1.00 O A:HOH603 2.0 30.0 1.0 O A:HOH618 2.1 27.7 1.0 O2G A:GTP501 2.1 23.6 1.0 O B:HOH614 2.1 33.8 1.0 O A:HOH609 2.1 27.2 1.0 O1B A:GTP501 2.3 22.5 1.0 PG A:GTP501 3.0 24.4 1.0 PB A:GTP501 3.3 22.9 1.0 O1G A:GTP501 3.3 24.2 1.0 O3B A:GTP501 3.4 24.5 1.0 NZ B:LYS252 3.5 36.9 1.0 O3A A:GTP501 3.9 22.7 1.0 OD1 A:ASP69 4.1 38.9 1.0 OE2 A:GLU71 4.4 41.1 1.0 CB A:ASP98 4.4 38.9 1.0 CB A:GLN11 4.4 29.5 1.0 CG A:GLU71 4.4 40.1 1.0 O3G A:GTP501 4.5 24.1 1.0 OD2 A:ASP69 4.6 43.1 1.0 O1A A:GTP501 4.6 22.4 1.0 O2B A:GTP501 4.6 23.9 1.0 OD2 A:ASP98 4.6 41.6 1.0 N A:GLN11 4.6 29.1 1.0 OE1 A:GLN11 4.7 29.0 1.0 CG A:ASP98 4.7 39.9 1.0 OD1 B:ASN247 4.7 65.5 1.0 CE B:LYS252 4.8 35.4 1.0 CG A:ASP69 4.8 41.1 1.0 OG1 A:THR145 4.8 25.2 1.0 PA A:GTP501 4.9 22.1 1.0 CG B:ASN247 4.9 64.8 1.0 CD A:GLU71 4.9 40.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-8WR 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-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.3 occ:1.00 O B:HOH619 1.9 37.5 1.0 OE1 B:GLN11 2.2 35.4 1.0 O1A B:GDP501 2.2 20.5 1.0 O C:HOH647 2.3 34.1 1.0 O B:HOH618 2.6 39.8 1.0 O B:HOH637 2.8 36.0 1.0 O B:HOH631 2.8 27.9 1.0 CD B:GLN11 3.4 35.3 1.0 PA B:GDP501 3.5 19.7 1.0 OD2 B:ASP177 3.8 38.8 1.0 O3A B:GDP501 3.9 20.6 1.0 CB B:GLN11 4.1 31.2 1.0 CG B:GLN11 4.3 34.0 1.0 NE2 B:GLN11 4.3 36.4 1.0 C5' B:GDP501 4.3 19.7 1.0 OD1 B:ASN99 4.3 22.9 1.0 O5' B:GDP501 4.4 19.1 1.0 O1B B:GDP501 4.6 21.0 1.0 CG B:ASP177 4.6 37.7 1.0 O2A B:GDP501 4.7 20.1 1.0 OE1 C:GLU254 4.9 32.9 1.0 PB B:GDP501 4.9 21.1 1.0 C8 B:GDP501 4.9 21.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-8WR 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-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:20.7 occ:1.00 O C:HOH627 1.9 27.2 1.0 O1G C:GTP501 2.0 19.2 1.0 O C:HOH628 2.0 17.1 1.0 O C:HOH610 2.1 19.7 1.0 O1B C:GTP501 2.1 19.3 1.0 O C:HOH613 2.2 17.3 1.0 PB C:GTP501 3.1 19.7 1.0 PG C:GTP501 3.2 20.2 1.0 O3A C:GTP501 3.5 19.9 1.0 O3B C:GTP501 3.5 19.1 1.0 NZ D:LYS252 3.8 37.1 1.0 O2G C:GTP501 3.8 20.4 1.0 CB C:GLN11 4.2 23.9 1.0 OD2 C:ASP69 4.2 24.0 1.0 OD1 C:ASP69 4.2 25.0 1.0 OE2 C:GLU71 4.3 35.5 1.0 O1A C:GTP501 4.4 21.6 1.0 N C:GLN11 4.4 21.9 1.0 O3G C:GTP501 4.5 20.4 1.0 CG C:GLU71 4.5 32.7 1.0 O2B C:GTP501 4.5 19.7 1.0 PA C:GTP501 4.5 20.6 1.0 OD2 C:ASP98 4.6 31.5 1.0 OE1 C:GLN11 4.7 27.1 1.0 CG C:ASP69 4.7 24.8 1.0 CB C:ASP98 4.7 32.8 1.0 O C:HOH635 4.9 26.2 1.0 CE D:LYS252 4.9 37.4 1.0 CA C:GLN11 4.9 22.7 1.0 CG C:ASP98 5.0 32.3 1.0 CD C:GLU71 5.0 32.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-8WR Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T2R-Ttl-8WR Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:50.7 occ:1.00 O2G D:GTP501 2.4 54.2 1.0 O1B D:GTP501 2.9 53.7 1.0 O1G D:GTP501 2.9 56.7 1.0 PG D:GTP501 3.2 60.2 1.0 PB D:GTP501 3.9 54.3 1.0 O3B D:GTP501 3.9 57.1 1.0 CB D:GLU69 4.0 81.8 1.0 OE2 D:GLU69 4.1 87.2 1.0 CB D:GLN11 4.2 66.0 1.0 OD2 D:ASP67 4.4 52.7 1.0 O3A D:GTP501 4.4 53.2 1.0 OD1 D:ASP67 4.4 49.1 1.0 CG D:GLU69 4.4 83.0 1.0 N D:GLN11 4.4 58.6 1.0 O3G D:GTP501 4.5 54.8 1.0 OE1 D:GLN11 4.6 66.5 1.0 CD D:GLU69 4.8 85.5 1.0 CG D:ASP67 4.8 52.0 1.0 CA D:GLN11 4.8 61.3 1.0 O1A D:GTP501 4.9 52.1 1.0

Z.Y.Fu, W.B.Li. Design, Synthesis and Biological Activity Evaluation of Plinabulin Derivatives Based on Co-Crystal Structure To Be Published.