Magnesium in PDB 5zxh: The Structure of MT189-Tubulin Complex

The structure of The Structure of MT189-Tubulin Complex, PDB code: 5zxh was solved by Z.P.Li, Y.X.Wang, T.Meng, J.L.Yang, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.910, 157.060, 182.838, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.9

The structure of The Structure of MT189-Tubulin Complex also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Calcium	(Ca)	3 atoms

The binding sites of Magnesium atom in the The Structure of MT189-Tubulin Complex (pdb code 5zxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of MT189-Tubulin Complex, PDB code: 5zxh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Structure of MT189-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of MT189-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.4 occ:1.00 O A:HOH604 1.8 41.6 1.0 O A:HOH606 1.9 18.3 1.0 O2G A:GTP501 2.2 23.6 1.0 O A:HOH602 2.3 26.8 1.0 O1B A:GTP501 2.4 20.1 1.0 O B:HOH601 2.5 40.1 1.0 PG A:GTP501 3.3 24.0 1.0 PB A:GTP501 3.5 21.6 1.0 O1G A:GTP501 3.7 23.9 1.0 O3B A:GTP501 3.7 24.0 1.0 OE2 A:GLU71 4.0 54.3 1.0 NZ B:LYS252 4.0 45.6 1.0 CG A:GLU71 4.1 51.6 1.0 O3A A:GTP501 4.1 23.1 1.0 OD1 A:ASP69 4.2 39.9 1.0 CB A:GLN11 4.4 28.4 1.0 CB A:ASP98 4.4 44.8 1.0 OE1 A:GLN11 4.5 26.7 1.0 O B:HOH604 4.5 45.2 1.0 OD2 A:ASP69 4.6 48.0 1.0 CD A:GLU71 4.6 53.9 1.0 O1A A:GTP501 4.6 25.0 1.0 N A:GLN11 4.7 26.2 1.0 O3G A:GTP501 4.7 22.3 1.0 O2B A:GTP501 4.8 20.4 1.0 CG A:ASP69 4.8 43.0 1.0 PA A:GTP501 5.0 24.5 1.0 ND2 B:ASN247 5.0 67.6 1.0 CG A:ASP98 5.0 48.9 1.0

Magnesium binding site 2 out of 4 in the The Structure of MT189-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of MT189-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.1 occ:1.00 OE1 B:GLN11 2.3 45.9 1.0 O1A B:GDP501 2.5 18.4 1.0 OD2 B:ASP177 2.8 58.5 1.0 CD B:GLN11 3.5 40.3 1.0 PA B:GDP501 3.9 17.5 1.0 CG B:ASP177 4.0 51.2 1.0 NE2 B:GLN11 4.2 40.9 1.0 OD1 B:ASN99 4.2 22.3 1.0 O3A B:GDP501 4.3 17.9 1.0 C5' B:GDP501 4.4 20.6 1.0 CB B:GLN11 4.5 32.5 1.0 CG B:GLN11 4.6 36.5 1.0 O5' B:GDP501 4.6 17.7 1.0 CB B:ASP177 4.7 47.4 1.0 OE1 C:GLU254 4.7 50.7 1.0 OE2 C:GLU254 4.8 47.5 1.0 OD1 B:ASP177 5.0 54.0 1.0

Magnesium binding site 3 out of 4 in the The Structure of MT189-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of MT189-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:17.4 occ:1.00 O C:HOH603 2.0 25.3 1.0 O1G C:GTP501 2.0 19.7 1.0 O1B C:GTP501 2.1 20.4 1.0 O C:HOH604 2.1 27.6 1.0 O C:HOH601 2.1 25.7 1.0 O C:HOH602 2.2 13.8 1.0 PG C:GTP501 3.2 21.5 1.0 PB C:GTP501 3.2 20.6 1.0 O3B C:GTP501 3.6 20.7 1.0 O2G C:GTP501 3.7 21.1 1.0 O3A C:GTP501 3.8 21.5 1.0 OE2 C:GLU71 3.9 41.1 1.0 NZ D:LYS252 4.0 50.6 1.0 OD1 C:ASP69 4.1 23.8 1.0 CB C:GLN11 4.2 25.5 1.0 OD2 C:ASP69 4.3 24.6 1.0 CG C:GLU71 4.3 37.7 1.0 N C:GLN11 4.4 22.6 1.0 OD2 C:ASP98 4.4 38.0 1.0 O1A C:GTP501 4.4 21.6 1.0 OE1 C:GLN11 4.5 30.7 1.0 O3G C:GTP501 4.5 18.8 1.0 O2B C:GTP501 4.6 20.4 1.0 CD C:GLU71 4.6 39.4 1.0 CG C:ASP69 4.6 26.0 1.0 CB C:ASP98 4.7 34.7 1.0 PA C:GTP501 4.7 22.0 1.0 CG C:ASP98 4.9 37.7 1.0 CA C:GLN11 4.9 24.0 1.0 OG1 C:THR145 5.0 21.4 1.0

Magnesium binding site 4 out of 4 in the The Structure of MT189-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of MT189-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:42.9 occ:1.00 O1G D:GTP501 2.4 44.7 1.0 O2G D:GTP501 3.0 46.2 1.0 O1B D:GTP501 3.1 47.1 1.0 PG D:GTP501 3.2 54.4 1.0 OD2 D:ASP67 3.7 63.4 1.0 OD1 D:ASP67 3.8 56.3 1.0 CB D:GLU69 4.0 75.8 1.0 CB D:GLN11 4.0 66.0 1.0 PB D:GTP501 4.0 50.2 1.0 O3B D:GTP501 4.0 49.1 1.0 CG D:ASP67 4.2 60.8 1.0 O3A D:GTP501 4.4 48.1 1.0 N D:GLN11 4.4 54.1 1.0 CG D:GLU69 4.5 79.7 1.0 O3G D:GTP501 4.6 41.2 1.0 OE2 D:GLU69 4.7 79.8 1.0 OE1 D:GLN11 4.7 72.2 1.0 CA D:GLN11 4.7 59.5 1.0 CG D:GLN11 4.9 70.2 1.0 OG1 D:THR143 5.0 58.3 1.0

Z.P.Li, L.L.Ma, C.Y.Wu, T.Meng, L.P.Ma, W.Zheng, Y.Yu, Q.Chen, J.L.Yang, J.G.Shen. The Structure of MT189-Tubulin Complex Provides Insights Into Drug Design Lett.Drug Des.Discovery 2019.
ISSN: ISSN 1570-1808
DOI: 10.2174/1570180816666181122122655