Calcium in PDB 5lxs: Tubulin-Ks-1-199-32 Complex

The structure of Tubulin-Ks-1-199-32 Complex, PDB code: 5lxs was solved by A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.23 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.580, 157.800, 179.440, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

The structure of Tubulin-Ks-1-199-32 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Ks-1-199-32 Complex (pdb code 5lxs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-Ks-1-199-32 Complex, PDB code: 5lxs:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:59.2 occ:1.00 O A:THR41 2.4 72.4 1.0 OD2 A:ASP39 2.5 57.9 1.0 OD1 A:ASP39 2.5 65.5 1.0 OE1 A:GLU55 2.6 62.8 1.0 O A:GLY44 2.6 71.8 1.0 OE2 A:GLU55 2.6 55.0 1.0 OG1 A:THR41 2.7 62.8 1.0 O A:HOH631 2.8 62.4 1.0 CG A:ASP39 2.8 64.7 1.0 CD A:GLU55 2.9 60.1 1.0 CB A:THR41 3.4 61.0 1.0 C A:THR41 3.4 73.5 1.0 C A:GLY44 3.5 70.2 1.0 CA A:THR41 3.8 68.1 1.0 N A:THR41 4.1 70.3 1.0 N A:GLY45 4.3 64.6 1.0 N A:GLY44 4.3 73.9 1.0 CA A:GLY45 4.3 64.3 1.0 CB A:ASP39 4.4 64.6 1.0 CA A:GLY44 4.4 78.4 1.0 CG A:GLU55 4.4 60.6 1.0 O A:HOH672 4.5 58.1 1.0 N A:ILE42 4.6 81.7 1.0 OD1 A:ASN50 4.6 50.5 1.0 CZ A:PHE49 4.6 52.9 1.0 CG2 A:THR41 4.8 60.8 1.0 NE2 A:HIS61 4.8 53.9 1.0 CE1 A:PHE49 5.0 54.5 1.0 OD2 A:ASP47 5.0 73.4 1.0

Calcium binding site 2 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:85.0 occ:1.00 O B:HOH705 2.4 54.0 1.0 OE1 B:GLU113 2.7 85.2 1.0 CD B:GLU113 3.5 78.4 1.0 OE2 B:GLU113 3.6 89.1 1.0 OE1 B:GLU110 4.1 45.2 1.0 OG B:SER97 4.5 86.8 1.0 CG B:GLU113 4.9 55.7 1.0

Calcium binding site 3 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:52.9 occ:1.00 O C:GLY44 2.4 55.1 1.0 OD2 C:ASP39 2.4 48.8 1.0 OG1 C:THR41 2.5 54.5 1.0 OE2 C:GLU55 2.5 41.4 1.0 O C:HOH605 2.5 51.9 1.0 OE1 C:GLU55 2.5 47.8 1.0 O C:THR41 2.6 53.2 1.0 OD1 C:ASP39 2.6 56.0 1.0 CD C:GLU55 2.9 47.9 1.0 CG C:ASP39 2.9 54.2 1.0 C C:GLY44 3.6 62.2 1.0 C C:THR41 3.6 60.9 1.0 CB C:THR41 3.6 59.4 1.0 CA C:THR41 4.0 61.8 1.0 CA C:GLY45 4.3 64.9 1.0 N C:THR41 4.3 59.0 1.0 OD1 C:ASN50 4.3 37.8 1.0 N C:GLY45 4.3 62.7 1.0 OD2 C:ASP47 4.4 71.4 1.0 CG C:GLU55 4.4 40.6 1.0 CB C:ASP39 4.4 57.1 1.0 CZ C:PHE49 4.5 49.1 1.0 N C:GLY44 4.6 72.2 1.0 CA C:GLY44 4.6 69.1 1.0 NE2 C:HIS61 4.7 37.9 1.0 O C:HOH683 4.7 49.3 1.0 N C:ILE42 4.8 63.7 1.0 ND2 C:ASN50 4.8 37.0 1.0 CG2 C:THR41 4.9 50.7 1.0 CE1 C:PHE49 4.9 47.6 1.0

Calcium binding site 4 out of 4 in the Tubulin-Ks-1-199-32 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Ks-1-199-32 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:82.2 occ:1.00 O A:HOH683 3.5 45.4 1.0 OD2 E:ASP44 3.5 90.0 1.0 OG A:SER158 4.1 48.8 1.0 O A:GLU196 4.4 45.2 1.0 NZ A:LYS166 4.4 36.4 1.0 CB A:SER158 4.5 40.8 1.0 O A:GLY162 4.6 54.7 1.0 CG E:ASP44 4.6 89.6 1.0 O A:HOH622 4.8 52.2 1.0 OD1 A:ASP199 4.9 45.0 1.0 CA A:HIS197 4.9 37.7 1.0 O A:HIS197 4.9 48.1 1.0

A.E.Prota, K.Bargsten, M.Redondo-Horcajo, A.B.Smith, C.H.Yang, H.M.Mcdaid, I.Paterson, S.B.Horwitz, J.Fernando Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Discodermolide. Chembiochem V. 18 905 2017.
ISSN: ESSN 1439-7633
PubMed: 28207984
DOI: 10.1002/CBIC.201600696