Calcium 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:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

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

Calcium binding site 1 out of 2 in the Ryx in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.3 occ:1.00 OD1 A:ASP39 2.3 62.7 1.0 O A:GLY44 2.3 57.5 1.0 OE2 A:GLU55 2.4 70.8 1.0 OD2 A:ASP39 2.4 56.1 1.0 OG1 A:THR41 2.6 71.5 1.0 O A:THR41 2.7 70.7 1.0 CG A:ASP39 2.7 57.4 1.0 CD A:GLU55 3.1 74.8 1.0 OE1 A:GLU55 3.2 68.4 1.0 C A:GLY44 3.5 68.6 1.0 CB A:THR41 3.5 60.3 1.0 C A:THR41 3.7 72.7 1.0 CA A:THR41 4.0 64.0 1.0 CA A:GLY45 4.0 76.2 1.0 N A:GLY45 4.2 60.5 1.0 CB A:ASP39 4.2 57.5 1.0 N A:THR41 4.2 58.9 1.0 CZ A:PHE49 4.2 58.5 1.0 OD1 A:ASN50 4.5 65.3 1.0 CA A:GLY44 4.6 69.3 1.0 N A:GLY44 4.6 76.9 1.0 CG A:GLU55 4.6 70.9 1.0 NE2 A:HIS61 4.7 67.5 1.0 CG2 A:THR41 4.8 53.0 1.0 N A:ILE42 4.9 77.7 1.0 CE1 A:PHE49 4.9 62.2 1.0 CA A:ASP39 4.9 74.0 1.0 ND2 A:ASN50 5.0 58.2 1.0

Calcium binding site 2 out of 2 in the Ryx in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ryx in Complex with Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:49.1 occ:1.00 OG1 C:THR41 2.3 61.6 1.0 OE2 C:GLU55 2.4 53.3 1.0 OD2 C:ASP39 2.4 51.7 1.0 O C:THR41 2.5 69.8 1.0 OE1 C:GLU55 2.5 46.8 1.0 O C:GLY44 2.5 45.7 1.0 O C:HOH613 2.6 37.6 1.0 OD1 C:ASP39 2.6 45.0 1.0 CD C:GLU55 2.7 50.6 1.0 CG C:ASP39 2.9 51.2 1.0 CB C:THR41 3.3 62.2 1.0 C C:THR41 3.4 55.0 1.0 C C:GLY44 3.5 57.4 1.0 CA C:THR41 3.8 51.7 1.0 O C:HOH604 4.0 52.1 1.0 CA C:GLY45 4.1 49.2 1.0 N C:THR41 4.2 52.0 1.0 N C:GLY45 4.2 43.9 1.0 CG C:GLU55 4.3 36.3 1.0 CB C:ASP39 4.4 48.6 1.0 N C:GLY44 4.4 46.4 1.0 N C:ILE42 4.5 58.2 1.0 CA C:GLY44 4.5 51.4 1.0 NE2 C:HIS61 4.6 47.4 1.0 CZ C:PHE49 4.6 36.2 1.0 CG2 C:THR41 4.6 52.2 1.0 OD1 C:ASN50 4.6 36.8 1.0 OD2 C:ASP47 4.6 60.0 1.0 CE1 C:PHE49 4.8 51.2 1.0 ND2 C:ASN50 4.9 33.4 1.0 O C:HOH675 4.9 47.4 1.0 CA C:ILE42 5.0 50.0 1.0

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