Magnesium in PDB 5yz3: Crystal Structure of T2R-Ttl-28 Complex

The structure of Crystal Structure of T2R-Ttl-28 Complex, PDB code: 5yz3 was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.62 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.887, 157.496, 180.904, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.4

The structure of Crystal Structure of T2R-Ttl-28 Complex also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-28 Complex (pdb code 5yz3). 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-28 Complex, PDB code: 5yz3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.9 occ:1.00 O A:HOH630 2.1 23.9 1.0 O A:HOH676 2.1 19.8 1.0 O A:HOH683 2.1 22.8 1.0 O1G A:GTP501 2.3 22.1 1.0 O1B A:GTP501 2.4 20.5 1.0 O A:HOH604 2.6 41.4 1.0 OE1 A:GLU71 2.9 43.7 1.0 HZ1 B:LYS252 3.2 40.6 1.0 HB2 A:GLN11 3.3 31.6 1.0 PG A:GTP501 3.5 23.5 1.0 PB A:GTP501 3.5 18.2 1.0 H A:GLN11 3.8 30.1 1.0 HB2 A:ASP98 3.8 36.3 1.0 O3A A:GTP501 3.8 30.7 1.0 O3B A:GTP501 3.9 28.1 1.0 O2G A:GTP501 4.0 24.9 1.0 NZ B:LYS252 4.0 33.8 1.0 OD1 A:ASP69 4.0 27.6 1.0 HB3 A:ASP98 4.0 36.3 1.0 HB3 A:GLU71 4.0 40.7 1.0 CB A:GLN11 4.1 26.3 1.0 HB3 A:GLN11 4.1 31.6 1.0 HZ3 B:LYS252 4.1 40.6 1.0 HD21 B:ASN247 4.1 96.1 1.0 OD2 A:ASP69 4.1 27.9 1.0 HZ2 B:LYS252 4.1 40.6 1.0 CD A:GLU71 4.2 38.2 1.0 HD22 B:ASN247 4.2 96.1 1.0 ND2 B:ASN247 4.3 80.1 1.0 CB A:ASP98 4.3 30.2 1.0 OE1 A:GLN11 4.4 38.6 1.0 N A:GLN11 4.5 25.1 1.0 CG A:ASP69 4.5 28.8 1.0 OD2 A:ASP98 4.6 30.2 1.0 HG21 A:VAL74 4.7 49.9 1.0 O3G A:GTP501 4.7 24.1 1.0 HG1 A:THR145 4.8 29.0 1.0 CA A:GLN11 4.8 25.9 1.0 O2B A:GTP501 4.9 27.9 1.0 CG A:ASP98 4.9 30.0 1.0 O1A A:GTP501 4.9 28.7 1.0 HA2 A:GLY10 4.9 31.2 1.0 CB A:GLU71 4.9 34.0 1.0 OE2 A:GLU71 4.9 53.8 1.0 HG23 A:VAL74 4.9 49.9 1.0 PA A:GTP501 4.9 22.9 1.0 HB A:THR145 5.0 33.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:27.5 occ:1.00 O B:HOH665 1.9 34.4 1.0 O B:HOH664 1.9 24.4 1.0 OE1 B:GLN11 2.0 40.7 1.0 O B:HOH617 2.1 36.9 1.0 O1A B:GDP501 2.1 28.6 1.0 CD B:GLN11 3.3 42.4 1.0 OD2 B:ASP177 3.4 32.8 1.0 HB3 B:GLN11 3.6 38.4 1.0 HD21 B:ASN99 3.6 26.4 1.0 PA B:GDP501 3.6 22.0 1.0 H8 B:GDP501 3.7 36.7 1.0 HB2 B:GLN11 3.9 38.4 1.0 CB B:GLN11 4.1 31.9 1.0 HE22 B:GLN11 4.1 57.8 1.0 NE2 B:GLN11 4.2 48.1 1.0 O3A B:GDP501 4.2 23.6 1.0 OE1 C:GLU254 4.2 46.1 1.0 CG B:GLN11 4.2 38.1 1.0 C5' B:GDP501 4.3 24.8 1.0 ND2 B:ASN99 4.4 22.0 1.0 O5' B:GDP501 4.4 21.6 1.0 O1B B:GDP501 4.5 23.9 1.0 O2A B:GDP501 4.5 21.9 1.0 HG2 B:GLN11 4.6 45.7 1.0 CG B:ASP177 4.6 31.8 1.0 C8 B:GDP501 4.7 30.6 1.0 O C:HOH777 4.7 36.0 1.0 HD22 B:ASN99 4.8 26.4 1.0 HB3 B:ASP177 4.9 40.8 1.0 PB B:GDP501 4.9 24.4 1.0 HE21 B:GLN11 5.0 57.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:22.3 occ:1.00 O C:HOH681 2.1 23.9 1.0 O C:HOH666 2.1 17.3 1.0 O C:HOH726 2.1 20.5 1.0 O1B C:GTP501 2.2 19.8 1.0 O1G C:GTP501 2.2 20.5 1.0 O C:HOH621 2.4 19.1 1.0 HB2 C:GLN11 3.2 28.8 1.0 HZ1 D:LYS252 3.3 36.8 1.0 PB C:GTP501 3.4 14.7 1.0 PG C:GTP501 3.5 18.1 1.0 OE2 C:GLU71 3.6 32.6 1.0 H C:GLN11 3.7 22.7 1.0 O3A C:GTP501 3.8 23.4 1.0 O3B C:GTP501 3.8 21.6 1.0 OD2 C:ASP69 3.9 21.6 1.0 OD1 C:ASP69 4.0 22.9 1.0 NZ D:LYS252 4.0 30.6 1.0 HB2 C:ASP98 4.0 36.6 1.0 O2G C:GTP501 4.1 20.6 1.0 CB C:GLN11 4.1 24.0 1.0 HZ3 D:LYS252 4.1 36.8 1.0 HB3 C:GLN11 4.1 28.8 1.0 HB3 C:GLU71 4.1 37.7 1.0 HZ2 D:LYS252 4.2 36.8 1.0 OE1 C:GLN11 4.3 38.1 1.0 HB3 C:ASP98 4.3 36.6 1.0 N C:GLN11 4.4 18.9 1.0 CG C:ASP69 4.4 21.4 1.0 HG21 C:VAL74 4.5 35.2 1.0 HD21 D:ASN247 4.5 63.0 1.0 ND2 D:ASN247 4.5 52.5 1.0 CB C:ASP98 4.6 30.5 1.0 O2B C:GTP501 4.6 20.8 1.0 HD22 D:ASN247 4.6 63.0 1.0 O3G C:GTP501 4.6 19.4 1.0 HB3 D:ASN247 4.7 81.7 1.0 OD2 C:ASP98 4.7 32.8 1.0 CD C:GLU71 4.7 33.1 1.0 O1A C:GTP501 4.7 22.2 1.0 HA2 C:GLY10 4.8 25.4 1.0 CA C:GLN11 4.8 23.1 1.0 PA C:GTP501 4.8 18.3 1.0 CG D:ASN247 4.8 65.0 1.0 HG1 C:THR145 4.8 25.2 1.0 HG23 C:VAL74 4.9 35.2 1.0 HA C:GLN11 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-28 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-28 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:57.1 occ:1.00 O D:HOH630 2.0 38.3 1.0 O3G D:GTP501 2.1 52.8 1.0 O D:HOH647 2.1 43.1 1.0 O1B D:GTP501 2.7 58.2 1.0 PG D:GTP501 3.0 65.9 1.0 O1G D:GTP501 3.1 57.9 1.0 HB2 D:GLN11 3.3 76.3 1.0 PB D:GTP501 3.6 47.8 1.0 O3A D:GTP501 3.7 55.3 1.0 O3B D:GTP501 3.8 61.8 1.0 H D:GLN11 3.9 65.7 1.0 O D:HOH638 3.9 42.2 1.0 HB3 D:GLU69 4.1 88.9 1.0 HB3 D:GLN11 4.2 76.3 1.0 CB D:GLN11 4.2 63.6 1.0 HG2 D:GLU69 4.3 0.8 1.0 OE1 D:GLN11 4.3 79.5 1.0 O2G D:GTP501 4.3 57.7 1.0 HB2 D:GLU69 4.4 88.9 1.0 N D:GLN11 4.6 54.8 1.0 HG21 D:THR72 4.6 0.6 1.0 CB D:GLU69 4.7 74.1 1.0 OD1 D:ASP67 4.7 55.3 1.0 OD2 D:ASP67 4.7 53.9 1.0 HG1 D:THR143 4.8 79.1 1.0 O1A D:GTP501 4.8 49.9 1.0 PA D:GTP501 4.9 44.2 1.0 CA D:GLN11 4.9 57.4 1.0 HG23 D:THR72 5.0 0.6 1.0 CG D:GLU69 5.0 87.4 1.0 O2B D:GTP501 5.0 61.0 1.0

N.Ning, Y.Yu, M.Wu, R.Zhang, T.Zhang, C.Zhu, L.Huang, C.H.Yun, C.H.Benes, J.Zhang, X.Deng, Q.Chen, R.Ren. A Novel Microtubule Inhibitor Overcomes Multidrug Resistance in Tumors. Cancer Res. V. 78 5949 2018.
ISSN: ESSN 1538-7445
PubMed: 30135190
DOI: 10.1158/0008-5472.CAN-18-0455