Calcium in PDB 4o4i: Tubulin-Laulimalide-Epothilone A Complex

The structure of Tubulin-Laulimalide-Epothilone A Complex, PDB code: 4o4i was solved by A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.21 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.200, 158.030, 180.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.4

The structure of Tubulin-Laulimalide-Epothilone A Complex also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Calcium atom in the Tubulin-Laulimalide-Epothilone A Complex (pdb code 4o4i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tubulin-Laulimalide-Epothilone A Complex, PDB code: 4o4i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Laulimalide-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:64.1 occ:1.00 OE1 A:GLU55 2.7 69.8 1.0 O A:THR41 2.8 68.1 1.0 O A:GLY44 2.8 61.6 1.0 OD1 A:ASP39 2.8 51.5 1.0 OE2 A:GLU55 2.8 64.2 1.0 OD2 A:ASP39 2.8 42.1 1.0 OG1 A:THR41 2.9 66.0 1.0 CD A:GLU55 3.2 63.9 1.0 CG A:ASP39 3.2 51.8 1.0 CA A:GLY45 3.3 65.2 1.0 C A:GLY44 3.4 58.8 1.0 CB A:THR41 3.4 65.5 1.0 N A:GLY45 3.6 61.4 1.0 C A:THR41 3.7 67.1 1.0 OD1 A:ASN50 4.0 49.6 1.0 CA A:THR41 4.0 65.9 1.0 CZ A:PHE49 4.2 42.0 1.0 N A:THR41 4.4 62.8 1.0 OD2 A:ASP47 4.4 62.0 1.0 C A:GLY45 4.5 67.0 1.0 CA A:GLY44 4.5 57.0 1.0 ND2 A:ASN50 4.6 43.0 1.0 CE1 A:PHE49 4.6 40.8 1.0 CG A:GLU55 4.7 55.3 1.0 N A:GLY44 4.7 56.0 1.0 CB A:ASP39 4.7 47.8 1.0 CG A:ASN50 4.7 46.6 1.0 CG2 A:THR41 4.7 67.1 1.0 O A:HOH698 4.8 49.9 1.0 N A:ILE42 5.0 66.6 1.0

Calcium binding site 2 out of 3 in the Tubulin-Laulimalide-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:80.7 occ:1.00 OE2 B:GLU113 2.8 73.9 1.0 OE1 B:GLU113 3.5 75.7 1.0 CD B:GLU113 3.5 69.4 1.0 OE1 B:GLU110 4.4 49.2 1.0

Calcium binding site 3 out of 3 in the Tubulin-Laulimalide-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Laulimalide-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:68.4 occ:1.00 O C:GLY44 2.4 48.6 1.0 O C:THR41 2.8 58.9 1.0 OD1 C:ASP39 2.8 52.2 1.0 OE1 C:GLU55 2.8 45.2 1.0 OG1 C:THR41 2.9 58.4 1.0 OD2 C:ASP39 2.9 43.0 1.0 OE2 C:GLU55 2.9 46.5 1.0 CG C:ASP39 3.2 47.3 1.0 CD C:GLU55 3.2 44.2 1.0 CB C:THR41 3.3 59.9 1.0 C C:GLY44 3.4 52.4 1.0 CA C:GLY45 3.5 57.3 1.0 C C:THR41 3.6 58.7 1.0 OD2 C:ASP47 3.8 56.6 1.0 N C:GLY45 3.8 56.7 1.0 CA C:THR41 3.9 59.4 1.0 OD1 C:ASN50 3.9 36.5 1.0 N C:THR41 4.2 57.3 1.0 CZ C:PHE49 4.5 42.7 1.0 O C:HOH614 4.6 35.1 1.0 CA C:GLY44 4.6 54.3 1.0 CG2 C:THR41 4.7 62.3 1.0 CB C:ASP39 4.7 46.8 1.0 CG C:GLU55 4.7 37.2 1.0 C C:GLY45 4.8 58.5 1.0 N C:GLY44 4.8 56.8 1.0 N C:ILE42 4.8 56.9 1.0 CG C:ASN50 4.8 29.8 1.0 ND2 C:ASN50 4.8 28.8 1.0 CE1 C:PHE49 4.9 38.2 1.0 CG C:ASP47 4.9 50.1 1.0 O C:HOH754 5.0 50.3 1.0

A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Laulimalide and Peloruside A. Angew.Chem.Int.Ed.Engl. V. 53 1621 2014.
ISSN: ISSN 1433-7851
PubMed: 24470331
DOI: 10.1002/ANIE.201307749