Calcium in PDB 5jqg: An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison

The structure of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison, PDB code: 5jqg was solved by Y.X.Wang, J.H.Naismith, X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.22 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.050, 158.120, 180.630, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.2

The structure of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison (pdb code 5jqg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison, PDB code: 5jqg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.2 occ:1.00 O A:GLY44 2.3 66.7 1.0 OD2 A:ASP39 2.3 66.8 1.0 O A:THR41 2.3 75.7 1.0 OD1 A:ASP39 2.3 67.0 1.0 OE1 A:GLU55 2.4 62.7 1.0 OG1 A:THR41 2.4 67.2 1.0 OE2 A:GLU55 2.4 56.4 1.0 O A:HOH603 2.4 49.9 1.0 CG A:ASP39 2.7 62.6 1.0 CD A:GLU55 2.7 56.5 1.0 C A:THR41 3.4 73.1 1.0 C A:GLY44 3.4 70.0 1.0 CB A:THR41 3.4 70.8 1.0 CA A:THR41 3.8 75.1 1.0 N A:THR41 4.1 75.9 1.0 N A:GLY45 4.2 68.6 1.0 CB A:ASP39 4.3 62.8 1.0 CG A:GLU55 4.3 57.7 1.0 CA A:GLY45 4.3 66.2 1.0 O A:HOH622 4.4 45.7 1.0 N A:GLY44 4.4 73.2 1.0 CA A:GLY44 4.4 72.0 1.0 N A:ILE42 4.6 73.8 1.0 OD2 A:ASP47 4.6 58.8 1.0 CZ A:PHE49 4.6 55.5 1.0 OD1 A:ASN50 4.7 56.0 1.0 NE2 A:HIS61 4.7 61.3 1.0 CE1 A:PHE49 4.8 55.1 1.0 CG2 A:THR41 4.9 69.3 1.0

Calcium binding site 2 out of 3 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:81.7 occ:1.00 OE1 B:GLU111 2.3 60.7 1.0 OE2 B:GLU111 3.0 61.3 1.0 CD B:GLU111 3.0 57.5 1.0 CG B:GLU111 4.5 55.5 1.0 OE1 B:GLU108 4.6 45.4 1.0

Calcium binding site 3 out of 3 in the An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of An Apo Tubulin-Rb-Ttl Complex Structure Used For Side-By-Side Comparison within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:39.8 occ:1.00 O C:GLY44 2.3 55.0 1.0 OE1 C:GLU55 2.3 42.5 1.0 OD2 C:ASP39 2.3 49.2 1.0 O C:THR41 2.4 49.4 1.0 O C:HOH615 2.4 32.1 1.0 OD1 C:ASP39 2.4 49.0 1.0 OG1 C:THR41 2.4 47.5 1.0 OE2 C:GLU55 2.4 45.2 1.0 CD C:GLU55 2.7 44.8 1.0 CG C:ASP39 2.7 48.0 1.0 C C:THR41 3.4 48.4 1.0 CB C:THR41 3.4 47.7 1.0 C C:GLY44 3.5 60.2 1.0 CA C:THR41 3.8 49.3 1.0 N C:THR41 4.1 50.5 1.0 CG C:GLU55 4.2 39.5 1.0 N C:GLY45 4.3 60.5 1.0 CB C:ASP39 4.3 48.7 1.0 CA C:GLY45 4.3 58.6 1.0 O C:HOH608 4.4 39.6 1.0 N C:GLY44 4.4 56.1 1.0 CA C:GLY44 4.5 60.9 1.0 OD2 C:ASP47 4.5 51.4 1.0 N C:ILE42 4.6 50.8 1.0 NE2 C:HIS61 4.6 33.2 1.0 CZ C:PHE49 4.6 43.1 1.0 OD1 C:ASN50 4.6 36.3 1.0 CE1 C:PHE49 4.8 40.5 1.0 CG2 C:THR41 4.9 47.4 1.0 O C:HOH714 4.9 42.3 1.0

J.Yang, Y.X.Wang, T.Wang, J.Jiang, C.H.Botting, H.Liu, Q.Chen, J.Yang, J.H.Naismith, X.Zhu, L.Chen. Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule Nat Commun V. 7 12103 2016.
ISSN: ESSN 2041-1723
PubMed: 27357539
DOI: 10.1038/NCOMMS12103