Magnesium in PDB 7ce6: Crystal Structure of T2R-Ttl-COMPOUND9 Complex

The structure of Crystal Structure of T2R-Ttl-COMPOUND9 Complex, PDB code: 7ce6 was solved by L.J.Chen, Q.Chen, Y.Yu, J.H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.305, 157.529, 182.426, 90, 90, 90
R / Rfree (%)	22.4 / 24.9

The structure of Crystal Structure of T2R-Ttl-COMPOUND9 Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-COMPOUND9 Complex (pdb code 7ce6). 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-COMPOUND9 Complex, PDB code: 7ce6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND9 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-COMPOUND9 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.7 occ:1.00 O A:HOH649 2.0 32.9 1.0 O A:HOH611 2.0 29.6 1.0 O A:HOH623 2.0 27.2 1.0 O2G A:GTP501 2.2 26.8 1.0 O1B A:GTP501 2.2 21.9 1.0 HZ1 B:LYS252 3.2 47.2 1.0 HB2 A:GLN11 3.3 36.2 1.0 PB A:GTP501 3.3 20.3 1.0 PG A:GTP501 3.4 19.3 1.0 O3B A:GTP501 3.7 28.9 1.0 H A:GLN11 3.7 32.6 1.0 O3A A:GTP501 3.8 23.5 1.0 NZ B:LYS252 3.9 39.3 1.0 HZ3 B:LYS252 3.9 47.2 1.0 HZ2 B:LYS252 3.9 47.2 1.0 HB2 A:ASP98 3.9 37.5 1.0 O1G A:GTP501 4.0 25.0 1.0 HB3 A:GLN11 4.0 36.2 1.0 CB A:GLN11 4.1 30.2 1.0 OD1 A:ASP69 4.1 31.6 1.0 OD2 A:ASP69 4.2 30.7 1.0 HB3 A:ASP98 4.3 37.5 1.0 HD22 B:ASN247 4.3 120.1 1.0 HD21 B:ASN247 4.3 120.1 1.0 N A:GLN11 4.4 27.1 1.0 ND2 B:ASN247 4.4 100.1 1.0 O1A A:GTP501 4.5 26.4 1.0 CB A:ASP98 4.5 31.2 1.0 HB3 A:GLU71 4.5 49.5 1.0 OE1 A:GLN11 4.5 38.6 1.0 O3G A:GTP501 4.6 25.5 1.0 HG21 A:VAL74 4.6 46.7 1.0 CG A:ASP69 4.6 31.6 1.0 O2B A:GTP501 4.6 24.1 1.0 OD2 A:ASP98 4.7 34.4 1.0 PA A:GTP501 4.7 22.0 1.0 CA A:GLN11 4.8 27.1 1.0 HG1 A:THR145 4.8 29.9 1.0 HB A:THR145 4.9 30.4 1.0 CG A:ASP98 4.9 30.6 1.0 HA2 A:GLY10 4.9 31.4 1.0 OE1 A:GLU71 4.9 45.4 1.0 O A:HOH655 4.9 41.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND9 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-COMPOUND9 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:23.5 occ:1.00 O B:HOH642 1.9 25.2 1.0 OE1 B:GLN11 2.0 27.5 1.0 O C:HOH610 2.1 28.6 1.0 O1A B:GDP501 2.3 20.3 1.0 O B:HOH641 2.4 30.0 1.0 CD B:GLN11 3.2 28.9 1.0 OD2 B:ASP177 3.5 26.0 1.0 PA B:GDP501 3.6 15.3 1.0 HB3 B:GLN11 3.6 29.8 1.0 H8 B:GDP501 3.7 28.4 1.0 OE1 C:GLU254 3.9 45.8 1.0 HB2 B:GLN11 4.0 29.8 1.0 O B:HOH671 4.0 40.0 1.0 HE22 B:GLN11 4.0 33.7 1.0 O3A B:GDP501 4.1 20.7 1.0 NE2 B:GLN11 4.1 28.1 1.0 CB B:GLN11 4.1 24.8 1.0 CG B:GLN11 4.1 27.3 1.0 OD1 B:ASN99 4.3 22.2 1.0 C5' B:GDP501 4.4 21.3 1.0 HG2 B:GLN11 4.4 32.7 1.0 CG B:ASP177 4.5 26.2 1.0 O5' B:GDP501 4.5 18.3 1.0 HD21 B:ASN99 4.6 28.9 1.0 O2A B:GDP501 4.7 21.5 1.0 C8 B:GDP501 4.7 23.6 1.0 O3B B:GDP501 4.7 21.5 1.0 HB3 B:ASP177 4.8 30.0 1.0 HE21 B:GLN11 4.9 33.7 1.0 CD C:GLU254 4.9 33.7 1.0 HG3 B:GLN11 5.0 32.7 1.0 PB B:GDP501 5.0 16.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND9 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-COMPOUND9 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.8 occ:1.00 O1B C:GTP501 1.9 20.7 1.0 O C:HOH643 2.0 22.4 1.0 O C:HOH654 2.1 29.4 1.0 O C:HOH648 2.1 25.7 1.0 O1G C:GTP501 2.1 22.5 1.0 PB C:GTP501 3.1 15.1 1.0 PG C:GTP501 3.1 16.4 1.0 HZ1 D:LYS252 3.2 48.2 1.0 O3B C:GTP501 3.4 20.2 1.0 O2G C:GTP501 3.5 20.2 1.0 HB2 C:ASP98 3.5 33.0 1.0 HB2 C:GLN11 3.7 30.5 1.0 OD1 C:ASP69 3.7 21.4 1.0 OE1 C:GLU71 3.7 34.5 1.0 O3A C:GTP501 3.7 20.7 1.0 H C:GLN11 3.8 36.2 1.0 OD2 C:ASP69 4.0 24.9 1.0 NZ D:LYS252 4.1 40.2 1.0 HB3 C:ASP98 4.1 33.0 1.0 HB3 C:GLU71 4.1 36.3 1.0 CB C:ASP98 4.2 27.5 1.0 CG C:ASP69 4.3 22.3 1.0 O2B C:GTP501 4.3 20.4 1.0 HZ3 D:LYS252 4.4 48.2 1.0 HG1 C:THR145 4.4 21.7 1.0 HZ2 D:LYS252 4.4 48.2 1.0 O3G C:GTP501 4.5 21.7 1.0 CB C:GLN11 4.5 25.4 1.0 N C:GLN11 4.5 30.2 1.0 HB3 C:GLN11 4.5 30.5 1.0 HA2 C:GLY10 4.6 26.2 1.0 HB C:THR145 4.6 24.1 1.0 OD2 C:ASP98 4.6 31.1 1.0 OG1 C:THR145 4.7 18.1 1.0 CG C:ASP98 4.8 29.4 1.0 PA C:GTP501 4.9 16.8 1.0 HE2 D:LYS252 4.9 44.1 1.0 CD C:GLU71 4.9 34.9 1.0 HE3 D:LYS252 4.9 44.1 1.0 O1A C:GTP501 4.9 22.2 1.0 CE D:LYS252 4.9 36.7 1.0 H C:ALA99 5.0 28.1 1.0 OE1 C:GLN11 5.0 38.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND9 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-COMPOUND9 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:89.7 occ:1.00 OE2 D:GLU69 2.3 107.8 1.0 O3B D:GTP501 2.6 89.5 1.0 O3G D:GTP501 2.6 87.2 1.0 HG2 D:GLU69 3.0 101.8 1.0 PG D:GTP501 3.0 128.5 1.0 CD D:GLU69 3.1 100.6 1.0 HB2 D:GLN11 3.1 103.6 1.0 H D:GLN11 3.2 75.7 1.0 OD2 D:ASP67 3.2 61.1 1.0 CG D:GLU69 3.6 84.8 1.0 O2G D:GTP501 3.6 90.9 1.0 HB3 D:GLN11 3.7 103.6 1.0 OD1 D:ASP67 3.7 64.1 1.0 CB D:GLN11 3.8 86.3 1.0 N D:GLN11 3.8 63.1 1.0 CG D:ASP67 3.8 63.7 1.0 PB D:GTP501 3.9 68.4 1.0 O1B D:GTP501 4.0 68.8 1.0 OE1 D:GLU69 4.0 89.6 1.0 HG21 D:THR72 4.1 102.2 1.0 HG3 D:GLU69 4.1 101.8 1.0 HA2 D:GLY10 4.2 69.5 1.0 HG1 D:THR143 4.2 92.3 1.0 HG23 D:THR72 4.2 102.2 1.0 CA D:GLN11 4.2 73.2 1.0 HA D:GLN11 4.2 87.9 1.0 O1G D:GTP501 4.4 80.8 1.0 HB3 D:GLU69 4.5 96.6 1.0 CG2 D:THR72 4.5 85.2 1.0 HG22 D:THR72 4.6 102.2 1.0 C D:GLY10 4.7 57.8 1.0 O2B D:GTP501 4.7 70.6 1.0 CB D:GLU69 4.7 80.5 1.0 OG1 D:THR143 4.8 76.9 1.0 HB D:THR143 4.8 79.3 1.0 CA D:GLY10 4.8 57.9 1.0 H D:GLU69 4.8 88.4 1.0 HA3 D:GLY10 5.0 69.5 1.0 O3A D:GTP501 5.0 66.2 1.0

L.J.Chen, Q.Chen, J.H.Yang, Y.Yu. Small Molecular Promote Selective Destabilization and Degradation of Tubular Heterodimers By Specific Charging of GLU198 of Beta-Tubulin Through A Low Barrier Hydrogen Bond To Be Published.