Magnesium in PDB 7dba: Ryx in Complex with Tubulin

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

Resolution Low / High (Å)	31.30 / 2.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.449, 158.876, 181.608, 90, 90, 90
R / Rfree (%)	18.8 / 22.8

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

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

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

Magnesium binding site 1 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.4 occ:1.00 O1G A:GTP501 2.0 26.4 1.0 O A:HOH623 2.1 28.8 1.0 O A:HOH641 2.1 35.3 1.0 O1B A:GTP501 2.2 25.0 1.0 O A:HOH612 2.2 44.2 1.0 O A:HOH616 2.3 29.4 1.0 PG A:GTP501 3.0 36.2 1.0 PB A:GTP501 3.3 28.4 1.0 O2G A:GTP501 3.4 36.4 1.0 O3B A:GTP501 3.4 48.7 1.0 OD1 A:ASP69 3.9 36.7 1.0 O3A A:GTP501 4.0 42.8 1.0 NZ B:LYS252 4.0 36.4 1.0 OD2 A:ASP69 4.0 37.0 1.0 CG A:GLU71 4.1 62.5 1.0 OE1 A:GLU71 4.2 52.3 1.0 CB A:ASP98 4.2 32.1 1.0 OD2 A:ASP98 4.4 42.3 1.0 CG A:ASP69 4.4 41.6 1.0 O3G A:GTP501 4.4 31.5 1.0 CB A:GLN11 4.4 30.5 1.0 N A:GLN11 4.5 34.9 1.0 CG A:ASP98 4.5 39.4 1.0 O2B A:GTP501 4.5 43.0 1.0 CD A:GLU71 4.6 60.4 1.0 OG1 A:THR145 4.7 32.4 1.0 O1A A:GTP501 4.9 39.9 1.0 PA A:GTP501 5.0 40.4 1.0 NE2 A:GLN11 5.0 48.0 1.0

Magnesium binding site 2 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:23.1 occ:1.00 OE1 B:GLN11 2.1 34.8 1.0 O B:HOH655 2.1 38.0 1.0 O1A B:GDP501 2.2 33.3 1.0 O C:HOH694 2.2 38.4 1.0 O B:HOH677 2.5 35.3 1.0 O B:HOH624 2.7 42.5 1.0 CD B:GLN11 3.2 43.9 1.0 PA B:GDP501 3.5 27.6 1.0 OD2 B:ASP177 3.7 49.6 1.0 O3A B:GDP501 3.9 31.9 1.0 CB B:GLN11 4.0 26.0 1.0 CG B:GLN11 4.0 34.7 1.0 C5' B:GDP501 4.3 27.5 1.0 NE2 B:GLN11 4.3 33.0 1.0 O5' B:GDP501 4.4 20.9 1.0 OD1 B:ASN99 4.4 34.4 1.0 O2A B:GDP501 4.5 31.4 1.0 O1B B:GDP501 4.6 27.8 1.0 C8 B:GDP501 4.7 27.8 1.0 CG B:ASP177 4.7 36.9 1.0 OE1 C:GLU254 4.7 45.1 1.0 PB B:GDP501 4.9 26.7 1.0

Magnesium binding site 3 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.3 occ:1.00 O1G C:GTP501 2.0 26.0 1.0 O C:HOH656 2.0 28.8 1.0 O1B C:GTP501 2.1 28.2 1.0 O C:HOH630 2.1 28.8 1.0 O C:HOH704 2.1 29.6 1.0 O C:HOH648 2.2 29.4 1.0 PG C:GTP501 3.1 29.6 1.0 PB C:GTP501 3.1 22.3 1.0 O3B C:GTP501 3.4 36.8 1.0 O2G C:GTP501 3.6 29.1 1.0 O3A C:GTP501 3.8 41.0 1.0 OD1 C:ASP69 3.9 28.1 1.0 NZ D:LYS252 3.9 30.2 1.0 OE1 C:GLU71 4.1 55.8 1.0 OD2 C:ASP69 4.2 29.7 1.0 CG C:GLU71 4.2 32.8 1.0 CB C:GLN11 4.2 22.7 1.0 OD2 C:ASP98 4.4 36.1 1.0 N C:GLN11 4.4 26.1 1.0 CB C:ASP98 4.4 30.0 1.0 O3G C:GTP501 4.4 24.1 1.0 O2B C:GTP501 4.4 32.8 1.0 CG C:ASP69 4.5 31.1 1.0 O1A C:GTP501 4.6 33.0 1.0 CD C:GLU71 4.7 47.7 1.0 PA C:GTP501 4.7 26.7 1.0 CG C:ASP98 4.8 40.7 1.0 OE1 C:GLN11 4.8 45.1 1.0 OG1 C:THR145 4.9 29.0 1.0 CA C:GLN11 4.9 29.9 1.0

Magnesium binding site 4 out of 4 in the Ryx 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 Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:57.7 occ:1.00 O1A D:GDP501 2.1 80.8 1.0 NE2 D:GLN11 2.4 54.0 1.0 O D:HOH621 3.0 48.9 1.0 OD1 D:ASN99 3.6 63.8 1.0 PA D:GDP501 3.6 51.3 1.0 CD D:GLN11 3.7 76.3 1.0 C5' D:GDP501 4.2 53.0 1.0 O3A D:GDP501 4.2 51.4 1.0 O5' D:GDP501 4.4 55.3 1.0 CG D:ASN99 4.5 63.5 1.0 OE1 D:GLN11 4.5 82.5 1.0 O1B D:GDP501 4.5 58.3 1.0 CB D:GLN11 4.6 62.5 1.0 O2A D:GDP501 4.6 49.7 1.0 ND2 D:ASN99 4.6 76.2 1.0 CG D:GLN11 4.7 63.1 1.0 O D:HOH605 4.9 46.5 1.0 PB D:GDP501 4.9 54.0 1.0

C.Y.Wu, Y.X.Wang. Ryx in Complex with Tubulin To Be Published.