Magnesium in PDB 7daf: Ixa in Complex with Tubulin

The structure of Ixa in Complex with Tubulin, PDB code: 7daf was solved by C.Wu, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.162, 158.179, 181.875, 90, 90, 90
R / Rfree (%)	17.4 / 22.2

The structure of Ixa in Complex with Tubulin also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Magnesium atom in the Ixa in Complex with Tubulin (pdb code 7daf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ixa in Complex with Tubulin, PDB code: 7daf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.4 occ:1.00 O A:HOH622 2.0 28.2 1.0 O A:HOH677 2.1 26.0 1.0 O1G A:GTP501 2.1 21.7 1.0 O A:HOH710 2.1 24.4 1.0 O A:HOH671 2.1 24.5 1.0 O1B A:GTP501 2.3 21.4 1.0 PG A:GTP501 3.2 29.5 1.0 PB A:GTP501 3.4 24.5 1.0 O2G A:GTP501 3.6 25.2 1.0 O3B A:GTP501 3.7 36.6 1.0 NZ B:LYS252 3.8 35.1 1.0 OE1 A:GLU71 3.9 54.9 1.0 O3A A:GTP501 4.0 34.3 1.0 OD2 A:ASP69 4.1 31.5 1.0 CG A:GLU71 4.1 46.2 1.0 OD2 A:ASP98 4.2 41.9 1.0 OD1 A:ASP69 4.2 28.8 1.0 CB A:GLN11 4.3 27.2 1.0 O A:HOH617 4.3 41.6 1.0 CB A:ASP98 4.4 27.7 1.0 N A:GLN11 4.5 24.5 1.0 CD A:GLU71 4.6 50.8 1.0 O3G A:GTP501 4.6 22.1 1.0 O1A A:GTP501 4.6 28.0 1.0 CG A:ASP98 4.6 38.5 1.0 CG A:ASP69 4.6 36.5 1.0 O2B A:GTP501 4.7 28.6 1.0 NE2 A:GLN11 4.8 33.6 1.0 O B:HOH627 4.8 39.0 1.0 PA A:GTP501 4.9 27.8 1.0 CE B:LYS252 5.0 37.6 1.0 CA A:GLN11 5.0 28.2 1.0

Magnesium binding site 2 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.4 occ:1.00 OE1 B:GLN11 1.9 38.9 1.0 O1A B:GDP501 1.9 39.2 1.0 O B:HOH626 2.1 50.5 1.0 O B:HOH680 2.5 51.2 1.0 O B:HOH609 2.7 39.5 1.0 O B:HOH654 3.0 35.6 1.0 CD B:GLN11 3.2 41.2 1.0 PA B:GDP501 3.4 20.4 1.0 OD2 B:ASP177 3.6 38.4 1.0 O3A B:GDP501 3.9 26.0 1.0 CG B:GLN11 4.1 33.6 1.0 NE2 B:GLN11 4.1 35.7 1.0 OD1 B:ASN99 4.1 35.9 1.0 CB B:GLN11 4.2 25.7 1.0 O5' B:GDP501 4.2 21.1 1.0 C5' B:GDP501 4.2 29.1 1.0 O C:HOH721 4.2 38.9 1.0 O2A B:GDP501 4.5 26.7 1.0 OE1 C:GLU254 4.6 43.5 1.0 O1B B:GDP501 4.6 20.5 1.0 CG B:ASP177 4.6 41.3 1.0 C8 B:GDP501 4.8 32.8 1.0 PB B:GDP501 4.9 23.7 1.0

Magnesium binding site 3 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:54.2 occ:1.00 OD2 B:ASP118 4.1 46.7 1.0 OD1 B:ASP118 4.3 44.2 1.0 CB B:ASP114 4.6 32.2 1.0 OD2 B:ASP114 4.6 70.6 1.0 CG B:ASP118 4.7 47.3 1.0 CG B:ASP114 4.9 44.9 1.0

Magnesium binding site 4 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:25.6 occ:1.00 O C:HOH633 2.0 25.4 1.0 O1G C:GTP501 2.1 25.8 1.0 O C:HOH638 2.1 21.6 1.0 O1B C:GTP501 2.1 23.5 1.0 O C:HOH738 2.1 25.7 1.0 O C:HOH697 2.2 30.2 1.0 PG C:GTP501 3.1 23.3 1.0 PB C:GTP501 3.2 19.8 1.0 O3B C:GTP501 3.5 30.0 1.0 O2G C:GTP501 3.5 27.6 1.0 O3A C:GTP501 3.8 29.6 1.0 NZ D:LYS252 3.9 28.9 1.0 OD1 C:ASP69 4.0 29.1 1.0 OE1 C:GLU71 4.1 46.0 1.0 OD2 C:ASP69 4.2 27.0 1.0 CB C:GLN11 4.2 18.5 1.0 O C:HOH690 4.3 40.8 1.0 CG C:GLU71 4.3 31.5 1.0 N C:GLN11 4.4 20.6 1.0 OD2 C:ASP98 4.4 39.0 1.0 CB C:ASP98 4.4 26.7 1.0 O1A C:GTP501 4.5 22.6 1.0 O3G C:GTP501 4.5 25.0 1.0 O2B C:GTP501 4.5 23.3 1.0 CG C:ASP69 4.5 30.5 1.0 PA C:GTP501 4.7 24.3 1.0 CD C:GLU71 4.7 51.7 1.0 CG C:ASP98 4.8 32.0 1.0 OG1 C:THR145 4.9 25.9 1.0 CA C:GLN11 4.9 22.6 1.0 OE1 C:GLN11 4.9 39.4 1.0

Magnesium binding site 5 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.3 occ:1.00 NE2 D:GLN11 2.4 62.0 1.0 O1A D:GDP501 2.4 53.2 1.0 O D:HOH612 3.0 42.8 1.0 PA D:GDP501 3.5 41.8 1.0 O3A D:GDP501 3.6 38.8 1.0 CD D:GLN11 3.7 74.1 1.0 OD1 D:ASN99 3.9 62.0 1.0 C5' D:GDP501 4.2 44.2 1.0 O5' D:GDP501 4.3 40.3 1.0 OE1 D:GLN11 4.4 77.6 1.0 O1B D:GDP501 4.5 39.8 1.0 CB D:GLN11 4.5 49.9 1.0 CG D:GLN11 4.6 56.1 1.0 PB D:GDP501 4.6 43.6 1.0 O2A D:GDP501 4.7 47.9 1.0 CG D:ASN99 4.9 62.1 1.0 ND2 D:ASN99 4.9 73.0 1.0

Magnesium binding site 6 out of 6 in the Ixa in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ixa in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:78.8 occ:1.00 O2B F:ACP402 2.4 94.8 1.0 O2G F:ACP402 2.4 83.2 1.0 OE2 F:GLU331 2.9 99.6 1.0 OE1 F:GLU331 3.1 74.0 1.0 OD1 F:ASN333 3.1 85.5 1.0 CD F:GLU331 3.3 85.6 1.0 PB F:ACP402 3.6 112.4 1.0 OE2 A:GLU450 3.6 103.6 1.0 PG F:ACP402 3.7 108.8 1.0 NZ F:LYS74 3.8 83.8 1.0 C3B F:ACP402 4.0 103.0 1.0 CG F:ASN333 4.2 77.0 1.0 O3A F:ACP402 4.3 93.4 1.0 O1G F:ACP402 4.5 95.7 1.0 CD A:GLU450 4.6 95.2 1.0 O1B F:ACP402 4.8 123.7 1.0 O3G F:ACP402 4.8 97.0 1.0 CG F:GLU331 4.8 57.8 1.0 ND2 F:ASN333 4.8 79.1 1.0 CB A:GLU450 5.0 99.5 1.0

Q.Xiao, T.Xue, W.Shuai, C.Wu, Z.Zhang, T.Zhang, S.Zeng, B.Sun, Y.Wang. High-Resolution X-Ray Structure of Three Microtubule-Stabilizing Agents in Complex with Tubulin Provide A Rationale For Drug Design. Biochem.Biophys.Res.Commun. V. 534 330 2021.
ISSN: ESSN 1090-2104
PubMed: 33272565
DOI: 10.1016/J.BBRC.2020.11.082