Magnesium in PDB 7cda: Crystal Structure of T2R-Ttl-Pac Complex

The structure of Crystal Structure of T2R-Ttl-Pac Complex, PDB code: 7cda 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)	39.76 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.086, 156.826, 182.407, 90, 90, 90
R / Rfree (%)	22.2 / 25.7

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

Calcium

(Ca)

2 atoms

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

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Pac 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-Pac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.9 occ:1.00 O A:HOH616 2.0 29.5 1.0 O A:HOH612 2.1 32.6 1.0 O2G A:GTP501 2.1 22.2 1.0 O A:HOH660 2.2 27.9 1.0 O A:HOH682 2.3 32.7 1.0 O1B A:GTP501 2.3 21.5 1.0 HZ1 B:LYS252 3.2 36.8 1.0 HB2 A:GLN11 3.2 31.6 1.0 PG A:GTP501 3.4 17.6 1.0 PB A:GTP501 3.5 19.1 1.0 H A:GLN11 3.7 30.1 1.0 O3B A:GTP501 3.8 29.3 1.0 NZ B:LYS252 3.8 30.7 1.0 HB2 A:ASP98 3.9 39.3 1.0 O3A A:GTP501 3.9 24.4 1.0 HZ2 B:LYS252 3.9 36.8 1.0 HE21 A:GLN11 4.0 37.7 1.0 HZ3 B:LYS252 4.0 36.8 1.0 CB A:GLN11 4.0 26.3 1.0 HB3 A:GLN11 4.1 31.6 1.0 OE1 A:GLU71 4.1 43.3 1.0 HB3 A:GLU71 4.1 49.5 1.0 O1G A:GTP501 4.1 24.1 1.0 OD1 A:ASP69 4.1 34.9 1.0 HB3 A:ASP98 4.2 39.3 1.0 OD2 A:ASP69 4.3 32.3 1.0 NE2 A:GLN11 4.4 31.4 1.0 N A:GLN11 4.4 25.1 1.0 CB A:ASP98 4.5 32.8 1.0 HG21 A:VAL74 4.5 58.8 1.0 O3G A:GTP501 4.6 21.6 1.0 HE22 A:GLN11 4.6 37.7 1.0 CG A:ASP69 4.7 37.2 1.0 O1A A:GTP501 4.7 22.2 1.0 O2B A:GTP501 4.7 24.1 1.0 HB2 A:GLU71 4.8 49.5 1.0 CA A:GLN11 4.8 27.6 1.0 HG1 A:THR145 4.8 28.1 1.0 PA A:GTP501 4.8 16.8 1.0 CB A:GLU71 4.8 41.3 1.0 HA2 A:GLY10 4.9 31.2 1.0 HG3 A:GLU71 4.9 48.3 1.0 HG23 A:VAL74 4.9 58.8 1.0 HB A:THR145 5.0 29.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Pac 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-Pac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:23.7 occ:1.00 O C:HOH608 2.1 35.4 1.0 OE1 B:GLN11 2.1 50.4 1.0 O1A B:GDP501 2.2 27.1 1.0 O B:HOH606 2.2 53.4 1.0 O B:HOH648 2.3 30.6 1.0 O B:HOH625 2.4 29.9 1.0 CD B:GLN11 3.3 44.1 1.0 HD21 B:ASN99 3.4 26.2 1.0 PA B:GDP501 3.7 15.8 1.0 OD2 B:ASP177 3.7 29.1 1.0 HB3 B:GLN11 3.7 39.1 1.0 H8 B:GDP501 3.8 30.7 1.0 HE22 B:GLN11 4.0 59.7 1.0 HB2 B:GLN11 4.1 39.1 1.0 OE1 C:GLU254 4.1 42.4 1.0 NE2 B:GLN11 4.2 49.7 1.0 ND2 B:ASN99 4.2 21.8 1.0 CB B:GLN11 4.2 32.6 1.0 CG B:GLN11 4.3 40.7 1.0 C5' B:GDP501 4.3 21.4 1.0 O3A B:GDP501 4.4 17.6 1.0 O5' B:GDP501 4.5 17.5 1.0 O C:HOH671 4.5 27.6 1.0 O2A B:GDP501 4.5 19.1 1.0 O3B B:GDP501 4.6 22.6 1.0 HD22 B:ASN99 4.6 26.2 1.0 CG B:ASP177 4.6 29.6 1.0 HG2 B:GLN11 4.7 48.9 1.0 C8 B:GDP501 4.7 25.6 1.0 HB3 B:ASP177 4.9 36.5 1.0 CD C:GLU254 5.0 29.4 1.0 HE21 B:GLN11 5.0 59.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Pac 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-Pac Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.1 occ:1.00 O C:HOH623 2.0 25.3 1.0 O C:HOH626 2.0 24.7 1.0 O C:HOH634 2.1 29.7 1.0 O C:HOH624 2.1 22.6 1.0 O1B C:GTP501 2.2 19.4 1.0 O1G C:GTP501 2.3 21.6 1.0 HZ1 D:LYS252 3.1 53.8 1.0 PB C:GTP501 3.4 15.1 1.0 PG C:GTP501 3.5 13.8 1.0 HB2 C:GLN11 3.5 24.3 1.0 OE1 C:GLU71 3.5 34.9 1.0 OD2 C:ASP69 3.6 21.3 1.0 OD1 C:ASP69 3.6 19.6 1.0 H C:GLN11 3.7 18.9 1.0 O3B C:GTP501 3.8 19.9 1.0 HB2 C:ASP98 3.8 34.0 1.0 HB3 C:GLU71 3.8 41.1 1.0 O2G C:GTP501 3.9 21.7 1.0 NZ D:LYS252 4.0 44.8 1.0 O3A C:GTP501 4.0 21.3 1.0 HB3 C:ASP98 4.0 34.0 1.0 CG C:ASP69 4.0 20.4 1.0 HZ2 D:LYS252 4.3 53.8 1.0 CB C:GLN11 4.3 20.3 1.0 CB C:ASP98 4.4 28.3 1.0 N C:GLN11 4.4 15.7 1.0 HB3 C:GLN11 4.4 24.3 1.0 HZ3 D:LYS252 4.4 53.8 1.0 HG1 C:THR145 4.5 21.9 1.0 CD C:GLU71 4.6 33.7 1.0 HA2 C:GLY10 4.6 20.2 1.0 O2B C:GTP501 4.6 20.0 1.0 HG21 C:VAL74 4.7 33.7 1.0 OE1 C:GLN11 4.7 36.0 1.0 HE3 D:LYS252 4.7 40.7 1.0 O3G C:GTP501 4.7 21.0 1.0 CB C:GLU71 4.8 34.3 1.0 OG1 C:THR145 4.8 18.2 1.0 CE D:LYS252 4.8 33.9 1.0 HD22 D:ASN247 4.8 87.1 1.0 HE2 D:LYS252 4.8 40.7 1.0 HB C:THR145 4.9 23.8 1.0 CA C:GLN11 4.9 18.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Pac 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-Pac Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:107.9 occ:1.00 HG3 D:GLN11 1.8 121.4 1.0 OE2 D:GLU69 2.1 141.6 1.0 O3G D:GTP501 2.1 98.8 1.0 HG2 D:GLN11 2.2 121.4 1.0 CG D:GLN11 2.4 101.2 1.0 HB2 D:GLN11 3.2 104.6 1.0 CD D:GLU69 3.3 122.1 1.0 CB D:GLN11 3.3 87.2 1.0 PG D:GTP501 3.3 136.5 1.0 HE21 D:GLN11 3.3 121.7 1.0 O1G D:GTP501 3.4 95.2 1.0 CD D:GLN11 3.6 97.5 1.0 HA D:GLN11 3.6 98.1 1.0 H D:GLN11 3.6 92.1 1.0 NE2 D:GLN11 3.8 101.4 1.0 CA D:GLN11 3.8 81.7 1.0 HG2 D:GLU69 3.9 107.7 1.0 HG21 D:THR72 3.9 109.8 1.0 N D:GLN11 4.0 76.8 1.0 HG23 D:THR72 4.1 109.8 1.0 O1B D:GTP501 4.1 83.4 1.0 CG D:GLU69 4.1 89.7 1.0 HB3 D:GLN11 4.1 104.6 1.0 OE1 D:GLU69 4.1 115.5 1.0 OD2 D:ASP67 4.2 76.1 1.0 HG3 D:GLU69 4.3 107.7 1.0 O2G D:GTP501 4.3 95.3 1.0 O3B D:GTP501 4.4 90.7 1.0 CG2 D:THR72 4.5 91.5 1.0 O1A D:GTP501 4.5 92.5 1.0 OD1 D:ASP67 4.6 69.8 1.0 HE22 D:GLN11 4.6 121.7 1.0 OE1 D:GLN11 4.6 112.0 1.0 PB D:GTP501 4.8 67.2 1.0 CG D:ASP67 4.9 76.5 1.0 HG22 D:THR72 4.9 109.8 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.