Magnesium in PDB 8jjb: Crystal Structure of T2R-Ttl-Y61 Complex

The structure of Crystal Structure of T2R-Ttl-Y61 Complex, PDB code: 8jjb was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.06 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.287, 157.915, 181.748, 90, 90, 90
R / Rfree (%)	22.7 / 26

The structure of Crystal Structure of T2R-Ttl-Y61 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	6 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Y61 Complex (pdb code 8jjb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Y61 Complex, PDB code: 8jjb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:54.9 occ:0.00 O1B A:GTP501 1.8 51.6 0.0 O3B A:GTP501 2.4 50.4 0.0 PB A:GTP501 2.6 49.7 0.0 HZ1 B:LYS252 3.0 77.8 1.0 PG A:GTP501 3.1 49.9 0.0 O3G A:GTP501 3.2 52.5 0.0 O2G A:GTP501 3.3 50.0 0.0 HG3 A:GLU71 3.4 68.2 1.0 HG2 A:GLU71 3.4 68.2 1.0 HD21 B:ASN247 3.4 92.2 1.0 HB2 A:ASP98 3.5 68.7 1.0 O3A A:GTP501 3.7 50.5 0.0 O2B A:GTP501 3.7 48.8 0.0 OE2 A:GLU71 3.7 84.3 1.0 HD22 B:ASN247 3.7 92.2 1.0 HB2 A:GLN11 3.7 42.7 1.0 NZ B:LYS252 3.8 64.7 1.0 HZ2 B:LYS252 3.8 77.8 1.0 HB3 A:ASP98 3.8 68.7 1.0 ND2 B:ASN247 3.8 76.8 1.0 CG A:GLU71 3.8 56.8 1.0 OD2 A:ASP98 3.9 57.6 1.0 OD1 A:ASP69 4.0 56.2 1.0 CB A:ASP98 4.0 57.2 1.0 O1A A:GTP501 4.0 52.8 0.0 OD2 A:ASP69 4.1 52.2 1.0 HZ3 B:LYS252 4.1 77.8 1.0 H A:GLN11 4.2 43.4 1.0 CD A:GLU71 4.2 58.0 1.0 CG A:ASP98 4.4 49.3 1.0 CG A:ASP69 4.5 51.0 1.0 PA A:GTP501 4.5 51.2 0.0 O1G A:GTP501 4.5 47.9 0.0 HG1 A:THR145 4.6 57.7 1.0 CB A:GLN11 4.6 35.5 1.0 HB3 A:GLN11 4.7 42.7 1.0 HB A:THR145 4.8 51.2 1.0 CG B:ASN247 4.9 98.8 1.0 N A:GLN11 4.9 36.1 1.0 CE B:LYS252 5.0 49.4 1.0 OG1 A:THR145 5.0 48.0 1.0 HE21 A:GLN11 5.0 82.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:58.6 occ:0.00 OE1 B:GLN11 2.1 69.1 1.0 O1A B:GDP506 2.1 54.2 0.0 CD B:GLN11 3.3 82.4 1.0 PA B:GDP506 3.5 53.6 0.0 HD21 B:ASN99 3.9 52.9 1.0 HB3 B:GLN11 3.9 67.3 1.0 HE22 B:GLN11 3.9 102.3 1.0 O2A B:GDP506 3.9 54.9 0.0 HB2 B:GLN11 4.0 67.3 1.0 OD1 B:ASN99 4.0 42.1 1.0 NE2 B:GLN11 4.1 85.2 1.0 OD2 B:ASP177 4.3 48.2 1.0 CB B:GLN11 4.3 56.0 1.0 OE1 C:GLU254 4.3 62.4 1.0 O1B B:GDP506 4.3 47.4 0.0 O3B B:GDP506 4.4 52.1 0.0 CG B:GLN11 4.4 61.0 1.0 H8 B:GDP506 4.5 64.6 0.0 O5' B:GDP506 4.5 51.6 0.0 ND2 B:ASN99 4.6 44.0 1.0 O3A B:GDP506 4.6 50.1 0.0 C5' B:GDP506 4.6 52.5 0.0 PB B:GDP506 4.7 48.8 0.0 CG B:ASN99 4.7 43.8 1.0 HG3 B:GLN11 4.9 73.3 1.0 HE21 B:GLN11 4.9 102.3 1.0 CD C:GLU254 5.0 47.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.6 occ:0.00 O1B C:GTP501 2.4 40.1 0.0 O1G C:GTP501 2.7 43.1 0.0 O3B C:GTP501 3.3 40.7 0.0 HZ1 D:LYS252 3.3 58.1 1.0 PG C:GTP501 3.4 41.8 0.0 PB C:GTP501 3.4 40.0 0.0 HB2 C:GLN11 3.4 42.2 1.0 O2G C:GTP501 3.5 42.9 0.0 HG3 C:GLU71 3.6 51.7 1.0 HG2 C:GLU71 3.7 51.7 1.0 H C:GLN11 3.7 28.1 1.0 OE2 C:GLU71 3.9 73.2 1.0 HB2 C:ASP98 3.9 51.9 1.0 OD1 C:ASP69 3.9 45.5 1.0 OD2 C:ASP69 3.9 37.2 1.0 O1A C:GTP501 4.0 44.6 0.0 HZ3 D:LYS252 4.1 58.1 1.0 NZ D:LYS252 4.1 48.4 1.0 CG C:GLU71 4.1 43.0 1.0 O3A C:GTP501 4.1 42.0 0.0 CB C:GLN11 4.3 35.1 1.0 HB3 C:ASP98 4.3 51.9 1.0 CG C:ASP69 4.3 38.3 1.0 HZ2 D:LYS252 4.3 58.1 1.0 HB3 C:GLN11 4.3 42.2 1.0 HD22 D:ASN247 4.4 77.9 1.0 N C:GLN11 4.5 23.3 1.0 ND2 D:ASN247 4.5 64.9 1.0 CD C:GLU71 4.5 49.3 1.0 HD21 D:ASN247 4.5 77.9 1.0 CB C:ASP98 4.5 43.2 1.0 HG1 C:THR145 4.6 52.1 1.0 OD2 C:ASP98 4.6 46.0 1.0 OE1 C:GLN11 4.6 47.9 1.0 O2B C:GTP501 4.7 39.7 0.0 PA C:GTP501 4.7 43.4 0.0 HB C:THR145 4.7 41.9 1.0 HA2 C:GLY10 4.7 40.5 1.0 HB3 D:ASN247 4.8 74.4 1.0 O3G C:GTP501 4.8 41.8 0.0 HG21 C:VAL74 4.8 53.6 1.0 OG1 C:THR145 4.9 43.3 1.0 CA C:GLN11 4.9 37.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-Y61 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-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:95.0 occ:0.00 O3G D:GTP503 1.9 86.8 0.0 OE2 D:GLU69 2.0 103.6 1.0 CD D:GLU69 2.6 131.2 1.0 PG D:GTP503 3.0 85.7 0.0 O2G D:GTP503 3.0 86.2 0.0 HB2 D:GLN11 3.0 119.9 1.0 OE1 D:GLU69 3.1 133.6 1.0 HG2 D:GLU69 3.3 141.8 1.0 CG D:GLU69 3.5 118.1 1.0 H D:GLN11 3.7 84.0 1.0 CB D:GLN11 3.9 99.8 1.0 O1G D:GTP503 3.9 85.5 0.0 HB3 D:GLU69 3.9 116.2 1.0 O2B D:GTP503 4.0 80.7 0.0 OD1 D:ASP67 4.1 67.7 1.0 HB3 D:GLN11 4.1 119.9 1.0 O3B D:GTP503 4.1 83.8 0.0 HG1 D:THR143 4.1 102.6 1.0 OD2 D:ASP67 4.2 61.6 1.0 N D:GLN11 4.3 70.0 1.0 HG3 D:GLU69 4.3 141.8 1.0 CB D:GLU69 4.3 96.7 1.0 OE1 D:GLN11 4.4 106.2 1.0 O2A D:GTP503 4.5 84.8 0.0 PB D:GTP503 4.5 82.7 0.0 CG D:ASP67 4.6 73.9 1.0 CA D:GLN11 4.6 86.6 1.0 HG21 D:THR72 4.7 122.3 1.0 HA D:GLN11 4.7 104.0 1.0 OG1 D:THR143 4.7 85.4 1.0 O3A D:GTP503 4.7 84.4 0.0 HA2 D:GLY10 4.7 76.3 1.0 HB2 D:GLU69 4.8 116.2 1.0 HB D:THR143 4.9 101.5 1.0 CG D:GLN11 4.9 100.2 1.0 HG3 D:GLN11 4.9 120.3 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:112.9 occ:0.00 O1G F:ACP402 2.0 101.8 0.0 HZ3 F:LYS74 3.2 132.2 1.0 OG F:SER152 3.2 123.6 1.0 HG F:SER152 3.3 148.4 1.0 PG F:ACP402 3.4 100.5 0.0 O2B F:ACP402 3.5 107.5 0.0 HA F:SER152 3.6 175.1 1.0 NZ F:LYS74 4.0 110.0 1.0 O F:SER152 4.1 141.6 1.0 HZ1 F:LYS74 4.2 132.2 1.0 CB F:SER152 4.2 134.0 1.0 CA F:SER152 4.3 145.9 1.0 O3G F:ACP402 4.3 99.5 0.0 HZ2 F:LYS74 4.3 132.2 1.0 C3B F:ACP402 4.3 102.7 0.0 PB F:ACP402 4.3 106.3 0.0 O2G F:ACP402 4.3 96.6 0.0 H3B1 F:ACP402 4.3 123.3 0.0 HB2 F:SER152 4.4 160.9 1.0 O1B F:ACP402 4.5 108.2 0.0 C F:SER152 4.7 152.4 1.0 HD2 F:LYS74 4.9 114.7 1.0

C.Zhang, W.Yan, Y.Liu, M.Tang, Y.Teng, F.Wang, X.Hu, M.Zhao, J.Yang, Y.Li. Structure-Based Design and Synthesis of BML284 Derivatives: A Novel Class of Colchicine-Site Noncovalent Tubulin Degradation Agents. Eur.J.Med.Chem. V. 268 16265 2024.
ISSN: ISSN 0223-5234
PubMed: 38430854
DOI: 10.1016/J.EJMECH.2024.116265