Calcium in PDB 5lxt: Tubulin-Discodermolide Complex

The structure of Tubulin-Discodermolide Complex, PDB code: 5lxt 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)	52.25 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.500, 157.790, 180.230, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.8

The structure of Tubulin-Discodermolide Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Discodermolide Complex (pdb code 5lxt). 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-Discodermolide Complex, PDB code: 5lxt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:51.6 occ:1.00 O A:GLY44 2.3 69.5 1.0 O A:THR41 2.4 66.2 1.0 O A:HOH622 2.4 49.7 1.0 OE1 A:GLU55 2.5 55.0 1.0 OG1 A:THR41 2.5 58.5 1.0 OD1 A:ASP39 2.5 62.2 1.0 OD2 A:ASP39 2.6 56.9 1.0 OE2 A:GLU55 2.6 51.2 1.0 CD A:GLU55 2.9 52.5 1.0 CG A:ASP39 2.9 59.3 1.0 CB A:THR41 3.4 67.8 1.0 C A:GLY44 3.4 68.9 1.0 C A:THR41 3.4 68.1 1.0 CA A:THR41 3.8 69.6 1.0 N A:THR41 4.1 72.2 1.0 CA A:GLY45 4.1 63.3 1.0 N A:GLY45 4.2 68.3 1.0 N A:GLY44 4.3 67.6 1.0 CA A:GLY44 4.4 65.4 1.0 CG A:GLU55 4.4 53.6 1.0 CB A:ASP39 4.4 58.8 1.0 O A:HOH779 4.5 48.6 1.0 O A:HOH710 4.5 64.2 1.0 CZ A:PHE49 4.5 55.2 1.0 N A:ILE42 4.6 64.9 1.0 OD1 A:ASN50 4.6 59.5 1.0 O A:HOH842 4.7 61.4 1.0 OD2 A:ASP47 4.7 61.6 1.0 CG2 A:THR41 4.8 63.3 1.0 NE2 A:HIS61 4.8 56.4 1.0 CE1 A:PHE49 4.9 56.8 1.0 ND2 A:ASN50 4.9 47.8 1.0

Calcium binding site 2 out of 4 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:80.7 occ:1.00 O A:HOH850 2.4 63.5 1.0 O E:HOH211 2.4 62.4 1.0 O A:HOH813 2.8 50.2 1.0 O A:HOH681 3.0 42.3 1.0 O E:HOH301 3.1 71.8 1.0 O A:HOH643 3.7 70.2 1.0 OG A:SER158 4.2 44.6 1.0 OD2 E:ASP44 4.2 76.0 1.0 NZ A:LYS166 4.2 35.8 1.0 O A:GLU196 4.4 42.8 1.0 OD1 A:ASP199 4.4 43.9 1.0 O A:GLY162 4.5 56.5 1.0 O A:HOH663 4.7 50.4 1.0 O A:HIS197 4.7 41.1 1.0 CB A:SER158 4.8 40.3 1.0 CA A:HIS197 4.9 37.9 1.0 OD2 A:ASP199 5.0 43.1 1.0

Calcium binding site 3 out of 4 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:75.6 occ:1.00 O B:HOH667 2.3 46.9 1.0 O B:HOH822 2.3 49.9 1.0 OE2 B:GLU113 2.4 54.5 1.0 CD B:GLU113 3.5 51.5 1.0 OE1 B:GLU110 3.7 39.1 1.0 OE1 B:GLU113 3.9 60.3 1.0 O B:HOH758 4.0 37.6 1.0 CD B:GLU110 4.5 40.4 1.0 OE2 B:GLU110 4.6 51.5 1.0 O B:HOH793 4.7 50.2 1.0 CG B:GLU113 4.8 40.6 1.0 CB B:GLU113 4.9 35.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Discodermolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Discodermolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:42.0 occ:1.00 O C:THR41 2.3 47.6 1.0 O C:HOH621 2.4 34.7 1.0 OE2 C:GLU55 2.4 39.5 1.0 OE1 C:GLU55 2.4 43.4 1.0 OD2 C:ASP39 2.5 44.1 1.0 O C:GLY44 2.5 52.2 1.0 OG1 C:THR41 2.5 47.6 1.0 OD1 C:ASP39 2.5 47.2 1.0 CD C:GLU55 2.7 40.1 1.0 CG C:ASP39 2.8 45.9 1.0 C C:THR41 3.4 53.3 1.0 CB C:THR41 3.5 52.5 1.0 C C:GLY44 3.6 57.8 1.0 CA C:THR41 3.8 52.0 1.0 N C:THR41 4.1 51.8 1.0 CG C:GLU55 4.2 34.7 1.0 O C:HOH637 4.3 54.9 1.0 CA C:GLY45 4.3 52.9 1.0 CB C:ASP39 4.4 43.2 1.0 N C:GLY45 4.4 52.4 1.0 OD2 C:ASP47 4.4 52.6 1.0 O C:HOH687 4.4 38.0 1.0 N C:GLY44 4.4 59.9 1.0 OD1 C:ASN50 4.5 40.5 1.0 N C:ILE42 4.6 52.7 1.0 CA C:GLY44 4.6 58.8 1.0 CZ C:PHE49 4.6 42.6 1.0 NE2 C:HIS61 4.6 33.3 1.0 CG2 C:THR41 4.8 51.3 1.0 ND2 C:ASN50 4.8 32.5 1.0 CE1 C:PHE49 4.9 40.9 1.0 CA C:ILE42 5.0 51.2 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