Magnesium in PDB 5xi5: Crystal Structure of T2R-Ttl-PO5 Complex

The structure of Crystal Structure of T2R-Ttl-PO5 Complex, PDB code: 5xi5 was solved by Y.Chu, Y.Wang, J.Yang, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	119.17 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.251, 157.375, 182.467, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.5

The structure of Crystal Structure of T2R-Ttl-PO5 Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-PO5 Complex (pdb code 5xi5). 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-PO5 Complex, PDB code: 5xi5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-PO5 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-PO5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.8 occ:1.00 O B:HOH607 2.0 50.3 1.0 O A:HOH609 2.1 23.3 1.0 O2B A:GTP501 2.2 24.9 1.0 O A:HOH606 2.3 12.2 1.0 O3G A:GTP501 2.3 26.7 1.0 O2G A:GTP501 2.8 27.2 1.0 PG A:GTP501 2.9 26.8 1.0 PB A:GTP501 3.3 26.2 1.0 O3B A:GTP501 3.4 27.1 1.0 NZ B:LYS252 3.6 37.2 1.0 OD1 A:ASP69 4.0 43.5 1.0 O3A A:GTP501 4.0 26.8 1.0 OD1 B:ASN247 4.0 60.5 1.0 CG A:GLU71 4.3 44.7 1.0 CB A:ASP98 4.3 44.9 1.0 OE2 A:GLU71 4.4 47.6 1.0 O1G A:GTP501 4.4 26.5 1.0 CB A:GLN11 4.5 32.1 1.0 OG1 A:THR145 4.6 29.3 1.0 O1B A:GTP501 4.6 26.3 1.0 OD2 A:ASP69 4.6 45.8 1.0 N A:GLN11 4.7 32.6 1.0 CG A:ASP69 4.8 44.7 1.0 CG A:ASP98 4.8 46.8 1.0 CG B:ASN247 4.8 60.5 1.0 CE B:LYS252 4.8 36.5 1.0 O2A A:GTP501 4.8 27.5 1.0 CD A:GLU71 4.9 45.7 1.0 OE1 A:GLN11 4.9 31.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-PO5 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-PO5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.9 occ:1.00 O B:HOH603 2.1 37.8 1.0 O2A B:GDP501 2.2 23.8 1.0 O C:HOH636 2.3 31.9 1.0 OE1 B:GLN11 2.4 41.3 1.0 O B:HOH614 2.5 41.5 1.0 O B:HOH616 3.2 26.2 1.0 CD B:GLN11 3.4 38.3 1.0 OD2 B:ASP177 3.5 41.3 1.0 PA B:GDP501 3.6 23.1 1.0 O3A B:GDP501 4.0 23.7 1.0 CB B:GLN11 4.1 34.9 1.0 NE2 B:GLN11 4.2 39.0 1.0 CG B:GLN11 4.3 36.7 1.0 OD1 B:ASN99 4.4 30.6 1.0 C5' B:GDP501 4.4 24.3 1.0 O5' B:GDP501 4.4 23.0 1.0 CG B:ASP177 4.7 40.1 1.0 O2B B:GDP501 4.7 23.2 1.0 O1A B:GDP501 4.8 23.2 1.0 OE1 C:GLU254 4.8 51.0 1.0 C8 B:GDP501 4.9 26.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-PO5 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-PO5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.3 occ:1.00 O C:HOH623 2.0 29.1 1.0 O3G C:GTP501 2.0 22.5 1.0 O2B C:GTP501 2.1 24.8 1.0 O C:HOH628 2.1 30.6 1.0 O C:HOH615 2.2 17.4 1.0 O C:HOH601 2.2 15.1 1.0 PB C:GTP501 3.1 24.8 1.0 PG C:GTP501 3.2 22.9 1.0 O3B C:GTP501 3.5 23.2 1.0 O3A C:GTP501 3.5 24.9 1.0 NZ D:LYS252 3.7 42.6 1.0 O2G C:GTP501 3.7 23.2 1.0 CB C:GLN11 4.2 26.2 1.0 OD1 C:ASP69 4.2 28.3 1.0 OE2 C:GLU71 4.2 32.3 1.0 OD2 C:ASP69 4.3 29.1 1.0 O2A C:GTP501 4.4 24.9 1.0 N C:GLN11 4.4 24.8 1.0 O1G C:GTP501 4.5 22.6 1.0 O1B C:GTP501 4.5 24.9 1.0 PA C:GTP501 4.5 24.7 1.0 CG C:GLU71 4.5 31.9 1.0 OD2 C:ASP98 4.5 38.6 1.0 OE1 C:GLN11 4.6 28.0 1.0 CE D:LYS252 4.6 42.2 1.0 CB C:ASP98 4.7 39.2 1.0 CG C:ASP69 4.7 29.5 1.0 CA C:GLN11 4.9 25.7 1.0 CD C:GLU71 4.9 32.1 1.0 CG C:ASP98 5.0 39.3 1.0 ND2 D:ASN247 5.0 62.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-PO5 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-PO5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:67.1 occ:1.00 O2G D:GTP501 2.8 67.9 1.0 O3G D:GTP501 2.9 69.6 1.0 O2B D:GTP501 3.2 62.8 1.0 PG D:GTP501 3.4 72.6 1.0 CB D:GLN11 3.9 67.3 1.0 CB D:GLU69 3.9 81.4 1.0 OD2 D:ASP67 4.1 63.6 1.0 OE2 D:GLU69 4.1 79.4 1.0 PB D:GTP501 4.3 63.5 1.0 N D:GLN11 4.3 60.7 1.0 O3B D:GTP501 4.3 67.0 1.0 OD1 D:ASP67 4.3 61.4 1.0 CG D:GLU69 4.4 82.0 1.0 OE1 D:GLN11 4.4 67.5 1.0 CA D:GLN11 4.6 64.3 1.0 O3A D:GTP501 4.6 61.7 1.0 CG D:ASP67 4.6 63.5 1.0 CG D:GLN11 4.7 68.7 1.0 CD D:GLU69 4.8 82.1 1.0 O1G D:GTP501 4.8 67.8 1.0 CG2 D:THR72 4.8 0.1 1.0 O2A D:GTP501 4.9 62.5 1.0 CD D:GLN11 5.0 68.3 1.0

Y.Chu, Y.Wang, J.Yang, W.Li. Synthesis, Biological Evaluation and X-Ray Structure of Anti-Microtubule Agents To Be Published.