Magnesium in PDB 5ylj: Crystal Structure of T2R-Ttl-Millepachine Complex

The structure of Crystal Structure of T2R-Ttl-Millepachine Complex, PDB code: 5ylj was solved by J.H.Yang, L.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.90 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.231, 157.367, 182.684, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.5

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

Calcium

(Ca)

2 atoms

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

Magnesium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl-Millepachine 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-Millepachine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.2 occ:1.00 O A:HOH603 2.1 57.9 1.0 O2G A:GTP501 2.1 41.1 1.0 O A:HOH601 2.2 52.0 1.0 O1B A:GTP501 2.2 40.0 1.0 O A:HOH602 2.2 44.4 1.0 O B:HOH604 2.3 50.4 1.0 PG A:GTP501 3.3 42.2 1.0 PB A:GTP501 3.3 41.1 1.0 O3B A:GTP501 3.6 42.5 1.0 O1G A:GTP501 3.8 42.2 1.0 O3A A:GTP501 3.9 42.9 1.0 CB A:GLN11 4.3 49.8 1.0 OD1 A:ASP69 4.4 63.6 1.0 OD2 A:ASP69 4.4 64.7 1.0 NZ B:LYS252 4.4 55.4 1.0 OE2 A:GLU71 4.5 78.3 1.0 O1A A:GTP501 4.5 44.2 1.0 CB A:ASP98 4.5 62.1 1.0 O3G A:GTP501 4.6 41.0 1.0 N A:GLN11 4.6 50.0 1.0 OE1 A:GLN11 4.6 51.3 1.0 O2B A:GTP501 4.7 42.5 1.0 CD A:GLU71 4.7 77.5 1.0 PA A:GTP501 4.8 43.3 1.0 CG A:ASP98 4.8 64.3 1.0 CG A:ASP69 4.8 64.5 1.0 CB A:GLU71 5.0 70.2 1.0 OE1 A:GLU71 5.0 82.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl-Millepachine 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-Millepachine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:43.5 occ:1.00 O B:HOH609 2.0 62.6 1.0 O C:HOH607 2.1 67.7 1.0 OE1 B:GLN11 2.2 60.7 1.0 O1A B:GDP501 2.3 36.8 1.0 O B:HOH611 2.4 43.1 1.0 O B:HOH608 2.6 55.5 1.0 O B:HOH610 3.2 38.4 1.0 CD B:GLN11 3.4 58.5 1.0 PA B:GDP501 3.7 36.0 1.0 O3A B:GDP501 4.0 36.5 1.0 OD2 B:ASP177 4.1 65.5 1.0 CB B:GLN11 4.2 50.5 1.0 OD1 B:ASN99 4.2 48.2 1.0 CG B:GLN11 4.4 55.9 1.0 NE2 B:GLN11 4.4 58.2 1.0 C5' B:GDP501 4.5 37.9 1.0 O1B B:GDP501 4.5 38.5 1.0 O5' B:GDP501 4.5 36.0 1.0 OE1 C:GLU254 4.7 67.4 1.0 CG B:ASP177 4.7 63.3 1.0 O2A B:GDP501 4.8 36.1 1.0 PB B:GDP501 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl-Millepachine 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-Millepachine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.7 occ:1.00 O1B C:GTP501 2.0 39.5 1.0 O C:HOH602 2.0 38.9 1.0 O C:HOH606 2.1 61.8 1.0 O C:HOH605 2.1 56.4 1.0 O1G C:GTP501 2.1 36.3 1.0 O C:HOH603 2.2 33.6 1.0 PB C:GTP501 3.2 39.7 1.0 PG C:GTP501 3.3 36.6 1.0 O3B C:GTP501 3.6 37.5 1.0 O3A C:GTP501 3.8 40.2 1.0 O2G C:GTP501 3.8 36.2 1.0 OE1 C:GLU71 4.1 61.4 1.0 CB C:GLN11 4.2 38.9 1.0 OD1 C:ASP69 4.3 45.9 1.0 OD2 C:ASP69 4.3 44.9 1.0 O1A C:GTP501 4.4 40.5 1.0 N C:GLN11 4.5 37.9 1.0 O2B C:GTP501 4.5 39.2 1.0 NZ D:LYS252 4.6 57.5 1.0 O3G C:GTP501 4.6 35.9 1.0 PA C:GTP501 4.6 39.9 1.0 CB C:ASP98 4.6 55.6 1.0 ND2 D:ASN247 4.6 0.1 1.0 NE2 C:GLN11 4.6 42.2 1.0 CG C:ASP69 4.7 45.9 1.0 OD2 C:ASP98 4.8 59.0 1.0 CB C:GLU71 4.9 56.4 1.0 OD1 D:ASN247 4.9 0.2 1.0 CG C:ASP98 5.0 57.9 1.0 CA C:GLN11 5.0 38.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl-Millepachine 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-Millepachine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:83.9 occ:1.00 O D:HOH602 1.9 70.8 1.0 O1G D:GTP501 2.3 86.2 1.0 O D:HOH605 2.4 78.8 1.0 O D:HOH603 2.5 68.9 1.0 O1B D:GTP501 3.1 81.6 1.0 PG D:GTP501 3.5 90.8 1.0 CB D:GLN11 3.6 89.8 1.0 O3G D:GTP501 3.8 88.1 1.0 PB D:GTP501 4.1 87.0 1.0 O3A D:GTP501 4.2 84.2 1.0 O3B D:GTP501 4.3 87.7 1.0 N D:GLN11 4.3 81.9 1.0 CG D:GLN11 4.3 93.5 1.0 CD D:GLN11 4.3 95.1 1.0 CB D:GLU69 4.4 99.8 1.0 OD2 D:ASP67 4.5 86.9 1.0 CA D:GLN11 4.5 85.5 1.0 NE2 D:GLN11 4.5 94.9 1.0 OE1 D:GLU69 4.5 0.4 1.0 O1A D:GTP501 4.6 84.8 1.0 O D:HOH601 4.6 49.6 1.0 CG D:GLU69 4.7 0.8 1.0 OD1 D:ASP67 4.7 82.8 1.0 OE1 D:GLN11 4.8 95.6 1.0 O2G D:GTP501 4.8 88.2 1.0 PA D:GTP501 4.9 81.3 1.0

J.H.Yang, W.Yan, Y.M.Yu, Y.X.Wang, T.Yang, L.L.Xue, X.Yuan, C.F.Long, Z.W.Liu, X.X.Chen, M.S.Hu, L.Zheng, Q.Qiu, H.Y.Pei, D.Li, F.Wang, P.Bai, J.L.Wen, H.Y.Ye, L.J.Chen. The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. V. 293 9461 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658