Magnesium in PDB 7exc: Crystal Structure of T2R-Ttl-1129A2 Complex

The structure of Crystal Structure of T2R-Ttl-1129A2 Complex, PDB code: 7exc was solved by J.H.Yang, W.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.248, 157.375, 181.974, 90, 90, 90
R / Rfree (%)	21.8 / 26.4

The structure of Crystal Structure of T2R-Ttl-1129A2 Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-1129A2 Complex (pdb code 7exc). 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-1129A2 Complex, PDB code: 7exc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.4 occ:0.00 O2G A:GTP501 2.1 33.1 0.0 O1B A:GTP501 2.2 32.4 0.0 HB2 A:GLN11 3.1 27.6 1.0 HZ1 B:LYS252 3.4 37.7 1.0 PB A:GTP501 3.4 31.2 0.0 PG A:GTP501 3.5 31.1 0.0 OE1 A:GLU71 3.5 51.1 1.0 H A:GLN11 3.7 30.6 1.0 O3B A:GTP501 3.8 30.7 0.0 O3A A:GTP501 3.8 31.8 0.0 CB A:GLN11 4.0 22.9 1.0 HE21 A:GLN11 4.0 45.6 1.0 HB2 A:ASP98 4.0 31.0 1.0 OD1 A:ASP69 4.1 31.3 1.0 OD2 A:ASP69 4.1 36.9 1.0 NZ B:LYS252 4.1 31.4 1.0 HB3 A:GLU71 4.1 58.4 1.0 HB3 A:GLN11 4.1 27.6 1.0 HZ2 B:LYS252 4.1 37.7 1.0 O1G A:GTP501 4.2 30.8 0.0 HB3 A:ASP98 4.3 31.0 1.0 OD2 A:ASP98 4.3 36.0 1.0 N A:GLN11 4.3 25.4 1.0 HZ3 B:LYS252 4.3 37.7 1.0 NE2 A:GLN11 4.4 37.9 1.0 CB A:ASP98 4.5 25.7 1.0 CG A:ASP69 4.5 36.5 1.0 O3G A:GTP501 4.6 29.9 0.0 O2B A:GTP501 4.6 30.9 0.0 HG21 A:VAL74 4.7 64.1 1.0 CD A:GLU71 4.7 39.7 1.0 HE22 A:GLN11 4.7 45.6 1.0 CA A:GLN11 4.7 35.7 1.0 CG A:ASP98 4.7 38.0 1.0 HA2 A:GLY10 4.8 30.3 1.0 HG1 A:THR145 4.8 35.5 1.0 O1A A:GTP501 4.8 32.8 0.0 HA A:GLN11 4.9 43.0 1.0 PA A:GTP501 4.9 31.6 0.0 CB A:GLU71 5.0 48.6 1.0 HB A:THR145 5.0 36.0 1.0 CD A:GLN11 5.0 32.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:33.2 occ:0.00 OE1 B:GLN11 2.3 25.6 1.0 O1A B:GDP504 2.5 28.7 0.0 OD2 B:ASP177 2.9 39.5 1.0 OD1 B:ASN99 3.1 32.4 1.0 HD21 B:ASN99 3.2 27.9 1.0 CD B:GLN11 3.4 52.7 1.0 O B:HOH616 3.5 29.4 1.0 HE22 B:GLN11 3.6 62.6 1.0 HB3 B:ASP177 3.7 36.5 1.0 C5' B:GDP504 3.8 28.4 0.0 CG B:ASP177 3.8 33.6 1.0 OE2 C:GLU254 3.8 38.4 1.0 ND2 B:ASN99 3.8 23.1 1.0 PA B:GDP504 3.8 27.1 0.0 CG B:ASN99 3.8 32.7 1.0 H8 B:GDP504 3.9 39.3 0.0 HB2 B:ASP177 3.9 36.5 1.0 NE2 B:GLN11 3.9 52.0 1.0 CB B:ASP177 4.0 30.3 1.0 O5' B:GDP504 4.3 26.9 0.0 O C:HOH645 4.3 45.3 1.0 CD C:GLU254 4.4 39.9 1.0 OE1 C:GLU254 4.5 36.5 1.0 O2A B:GDP504 4.5 28.3 0.0 HB3 B:GLN11 4.5 25.6 1.0 HD22 B:ASN99 4.6 27.9 1.0 CG B:GLN11 4.7 38.4 1.0 HE21 B:GLN11 4.8 62.6 1.0 H3' B:GDP504 4.9 36.8 0.0 HB2 B:GLN11 4.9 25.6 1.0 OD1 B:ASP177 4.9 43.9 1.0 HG2 B:GLN11 4.9 46.2 1.0 HG23 B:THR178 5.0 32.7 1.0 C8 B:GDP504 5.0 32.7 0.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.4 occ:0.00 O1B C:GTP501 2.2 27.4 0.0 O1G C:GTP501 2.5 31.1 0.0 HB2 C:GLN11 3.3 21.1 1.0 HZ1 D:LYS252 3.5 43.6 1.0 OD2 C:ASP69 3.5 30.8 1.0 PB C:GTP501 3.5 26.7 0.0 OE1 C:GLU71 3.6 32.1 1.0 PG C:GTP501 3.7 29.3 0.0 OD1 C:ASP69 3.7 29.5 1.0 HB3 C:GLU71 3.7 45.0 1.0 H C:GLN11 3.7 24.3 1.0 HD22 D:ASN247 3.8 65.9 1.0 HB2 C:ASP98 3.9 35.5 1.0 O3B C:GTP501 3.9 27.8 0.0 CG C:ASP69 4.0 27.5 1.0 O2G C:GTP501 4.2 30.3 0.0 CB C:GLN11 4.2 17.5 1.0 O3A C:GTP501 4.2 28.0 0.0 HB3 C:ASP98 4.3 35.5 1.0 NZ D:LYS252 4.3 36.3 1.0 OD2 C:ASP98 4.3 36.1 1.0 HZ2 D:LYS252 4.3 43.6 1.0 N C:GLN11 4.4 20.1 1.0 CB C:ASP98 4.5 29.5 1.0 HB2 C:GLU71 4.5 45.0 1.0 HB3 C:GLN11 4.5 21.1 1.0 CB C:GLU71 4.5 37.5 1.0 HG21 C:VAL74 4.5 28.4 1.0 HZ3 D:LYS252 4.6 43.6 1.0 HA2 C:GLY10 4.6 27.2 1.0 O2B C:GTP501 4.6 25.5 0.0 ND2 D:ASN247 4.7 54.8 1.0 CD C:GLU71 4.7 45.7 1.0 OE1 C:GLN11 4.8 43.7 1.0 HG1 C:THR145 4.8 37.1 1.0 HG23 C:VAL74 4.8 28.4 1.0 CA C:GLN11 4.8 21.2 1.0 CG C:ASP98 4.8 30.6 1.0 HG3 C:GLU71 4.9 52.3 1.0 HA C:GLN11 4.9 25.6 1.0 O3G C:GTP501 4.9 29.9 0.0 CG C:GLU71 5.0 43.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-1129A2 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-1129A2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:75.5 occ:0.00 HG2 D:GLN11 1.9 87.7 1.0 HG3 D:GLN11 2.2 87.7 1.0 O3G D:GTP501 2.5 71.2 0.0 CG D:GLN11 2.5 73.0 1.0 HG1 D:THR72 2.8 108.7 1.0 OE1 D:GLU69 3.2 98.3 1.0 CD D:GLU69 3.2 96.1 1.0 OG1 D:THR72 3.4 90.5 1.0 HG2 D:GLU69 3.4 102.3 1.0 H D:GLN11 3.4 92.3 1.0 O1G D:GTP501 3.4 70.7 0.0 PG D:GTP501 3.5 69.7 0.0 HE21 D:GLN11 3.5 80.7 1.0 HA D:GLN11 3.5 94.7 1.0 CB D:GLN11 3.5 83.4 1.0 CD D:GLN11 3.6 79.0 1.0 OE2 D:GLU69 3.6 92.3 1.0 CG D:GLU69 3.7 85.2 1.0 HG3 D:GLU69 3.8 102.3 1.0 CA D:GLN11 3.8 78.8 1.0 N D:GLN11 3.8 76.8 1.0 NE2 D:GLN11 3.9 67.1 1.0 OD2 D:ASP67 4.0 65.5 1.0 HB2 D:GLN11 4.1 100.2 1.0 O1B D:GTP501 4.1 69.8 0.0 HB3 D:GLN11 4.2 100.2 1.0 O3B D:GTP501 4.4 68.2 0.0 OD1 D:ASP67 4.4 60.1 1.0 HG21 D:THR72 4.5 88.9 1.0 OE1 D:GLN11 4.6 77.7 1.0 O2G D:GTP501 4.6 68.8 0.0 CG D:ASP67 4.6 67.4 1.0 CB D:THR72 4.6 88.7 1.0 HE22 D:GLN11 4.7 80.7 1.0 PB D:GTP501 4.8 69.3 0.0 HB D:THR72 4.9 106.5 1.0 C D:GLY10 4.9 66.3 1.0 HA2 D:GLY10 5.0 81.6 1.0 CG2 D:THR72 5.0 74.0 1.0

Y.Li, Y.Liu, Z.Zhu, W.Yan, C.Zhang, Z.Yang, P.Bai, M.Tang, M.Shi, W.He, S.Fu, J.Liu, K.Han, J.Li, L.Xie, H.Ye, J.Yang, L.Chen. Structure-Based Design and Synthesis of N-Substituted 3-Amino-Beta-Carboline Derivatives As Potent Alpha Beta-Tubulin Degradation Agents J.Med.Chem. V. 65 2675 2022.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C02159