Magnesium in PDB 7ce8: Crystal Structure of T2R-Ttl-COMPOUND11 Complex

The structure of Crystal Structure of T2R-Ttl-COMPOUND11 Complex, PDB code: 7ce8 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)	48.13 / 2.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.25, 157.675, 181.48, 90, 90, 90
R / Rfree (%)	20.7 / 24.2

The structure of Crystal Structure of T2R-Ttl-COMPOUND11 Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-COMPOUND11 Complex (pdb code 7ce8). 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-COMPOUND11 Complex, PDB code: 7ce8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND11 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-COMPOUND11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.5 occ:1.00 O1B A:GTP501 2.1 20.7 1.0 O A:HOH639 2.1 32.3 1.0 O A:HOH604 2.1 30.4 1.0 O A:HOH625 2.2 26.4 1.0 O2G A:GTP501 2.3 16.2 1.0 O A:HOH637 2.4 30.6 1.0 HB2 A:GLN11 3.2 33.4 1.0 HZ1 B:LYS252 3.2 36.7 1.0 PB A:GTP501 3.2 20.5 1.0 PG A:GTP501 3.5 20.2 1.0 O3A A:GTP501 3.7 22.2 1.0 H A:GLN11 3.7 26.3 1.0 O3B A:GTP501 3.8 28.2 1.0 HB2 A:ASP98 3.9 37.8 1.0 NZ B:LYS252 3.9 30.6 1.0 OE1 A:GLU71 3.9 33.6 1.0 HB3 A:GLN11 4.0 33.4 1.0 O1G A:GTP501 4.0 17.6 1.0 CB A:GLN11 4.0 27.8 1.0 HZ2 B:LYS252 4.0 36.7 1.0 HZ3 B:LYS252 4.0 36.7 1.0 HB3 A:GLU71 4.2 47.8 1.0 OD1 A:ASP69 4.2 25.1 1.0 HB3 A:ASP98 4.2 37.8 1.0 OD2 A:ASP69 4.2 30.1 1.0 N A:GLN11 4.4 21.9 1.0 CB A:ASP98 4.5 31.5 1.0 HD21 B:ASN247 4.5 85.9 1.0 O2B A:GTP501 4.5 26.7 1.0 OE1 A:GLN11 4.5 39.1 1.0 O1A A:GTP501 4.6 23.3 1.0 CG A:ASP69 4.7 32.2 1.0 ND2 B:ASN247 4.7 71.6 1.0 O3G A:GTP501 4.7 20.9 1.0 PA A:GTP501 4.7 19.1 1.0 HD22 B:ASN247 4.8 85.9 1.0 CA A:GLN11 4.8 26.8 1.0 HG1 A:THR145 4.8 25.9 1.0 OD2 A:ASP98 4.8 29.9 1.0 HG21 A:VAL74 4.9 48.6 1.0 HA2 A:GLY10 4.9 28.6 1.0 CG A:ASP98 5.0 27.1 1.0 CD A:GLN11 5.0 27.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND11 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-COMPOUND11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.3 occ:1.00 O B:HOH603 2.0 31.0 1.0 O B:HOH626 2.1 33.3 1.0 O C:HOH611 2.1 42.9 1.0 O B:HOH634 2.1 33.6 1.0 OE1 B:GLN11 2.2 35.1 1.0 O1A B:GDP501 2.3 20.0 1.0 CD B:GLN11 3.4 40.7 1.0 PA B:GDP501 3.6 17.5 1.0 HB3 B:GLN11 3.8 37.9 1.0 OE1 C:GLU254 3.9 69.8 1.0 OD2 B:ASP177 3.9 35.0 1.0 HB2 B:GLN11 3.9 37.9 1.0 O3A B:GDP501 3.9 15.2 1.0 OD1 B:ASN99 4.0 18.8 1.0 HE22 B:GLN11 4.1 47.4 1.0 H8 B:GDP501 4.1 32.8 1.0 CB B:GLN11 4.2 31.6 1.0 NE2 B:GLN11 4.2 39.5 1.0 O1B B:GDP501 4.4 20.9 1.0 CG B:GLN11 4.4 34.3 1.0 C5' B:GDP501 4.4 20.9 1.0 HD21 B:ASN99 4.5 29.6 1.0 O5' B:GDP501 4.5 19.0 1.0 O2A B:GDP501 4.7 18.5 1.0 PB B:GDP501 4.7 22.0 1.0 CG B:ASP177 4.8 32.4 1.0 CD C:GLU254 4.9 42.6 1.0 HG2 B:GLN11 4.9 41.2 1.0 HB3 B:ASP177 4.9 36.1 1.0 CG B:ASN99 4.9 21.8 1.0 O C:HOH632 4.9 33.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND11 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-COMPOUND11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.3 occ:1.00 O C:HOH620 1.9 22.2 1.0 O1B C:GTP501 1.9 20.8 1.0 O C:HOH631 2.0 22.2 1.0 O C:HOH624 2.0 23.4 1.0 O1G C:GTP501 2.1 22.0 1.0 O C:HOH640 2.1 36.4 1.0 PB C:GTP501 3.2 16.7 1.0 PG C:GTP501 3.2 16.5 1.0 HZ1 D:LYS252 3.2 44.4 1.0 O3B C:GTP501 3.5 19.4 1.0 HB2 C:GLN11 3.6 20.5 1.0 O2G C:GTP501 3.7 20.2 1.0 HB2 C:ASP98 3.7 29.4 1.0 H C:GLN11 3.7 16.7 1.0 OD1 C:ASP69 3.7 19.8 1.0 O3A C:GTP501 3.8 16.3 1.0 OD2 C:ASP69 3.8 18.7 1.0 OE1 C:GLU71 3.9 27.9 1.0 NZ D:LYS252 3.9 37.0 1.0 HZ3 D:LYS252 4.0 44.4 1.0 HB3 C:GLU71 4.1 30.8 1.0 HB3 C:ASP98 4.1 29.4 1.0 HZ2 D:LYS252 4.2 44.4 1.0 CG C:ASP69 4.2 17.2 1.0 CB C:ASP98 4.3 24.5 1.0 HG1 C:THR145 4.4 22.5 1.0 O2B C:GTP501 4.4 17.0 1.0 N C:GLN11 4.4 13.9 1.0 CB C:GLN11 4.4 17.1 1.0 O3G C:GTP501 4.5 20.6 1.0 HA2 C:GLY10 4.5 22.1 1.0 HB3 C:GLN11 4.5 20.5 1.0 HB C:THR145 4.6 26.1 1.0 OG1 C:THR145 4.7 18.7 1.0 OD2 C:ASP98 4.8 31.5 1.0 HG21 C:VAL74 4.8 33.0 1.0 OE1 C:GLN11 4.8 32.3 1.0 PA C:GTP501 4.9 18.6 1.0 O1A C:GTP501 4.9 22.1 1.0 CG C:ASP98 4.9 28.1 1.0 CA C:GLN11 5.0 16.1 1.0 CB C:GLU71 5.0 25.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-COMPOUND11 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-COMPOUND11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:60.4 occ:1.00 O3G D:GTP501 2.3 67.6 1.0 OE2 D:GLU69 2.4 115.5 1.0 O1G D:GTP501 2.8 76.3 1.0 PG D:GTP501 3.1 70.5 1.0 O1B D:GTP501 3.3 71.5 1.0 HB2 D:GLN11 3.3 95.8 1.0 CD D:GLU69 3.4 115.8 1.0 H D:GLN11 3.7 78.8 1.0 O3A D:GTP501 3.8 63.7 1.0 PB D:GTP501 3.9 52.5 1.0 HB3 D:GLN11 3.9 95.8 1.0 HG2 D:GLU69 4.0 111.1 1.0 O3B D:GTP501 4.0 63.8 1.0 CB D:GLN11 4.1 79.8 1.0 OE1 D:GLU69 4.1 104.3 1.0 CG D:GLU69 4.3 92.6 1.0 O2G D:GTP501 4.3 63.0 1.0 N D:GLN11 4.4 65.7 1.0 OD1 D:ASP67 4.5 57.3 1.0 OD2 D:ASP67 4.5 71.3 1.0 HG3 D:GLU69 4.7 111.1 1.0 HG1 D:THR143 4.8 80.0 1.0 CA D:GLN11 4.8 78.1 1.0 OE1 D:GLN11 4.9 67.0 1.0 HA2 D:GLY10 4.9 80.2 1.0 CG D:ASP67 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.