Calcium in PDB 4yj3: Crystal Structure of Tubulin Bound to Compound 2

The structure of Crystal Structure of Tubulin Bound to Compound 2, PDB code: 4yj3 was solved by D.E.Mcnamara, J.Z.Torres, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.07 / 3.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.200, 157.690, 181.920, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.9

The structure of Crystal Structure of Tubulin Bound to Compound 2 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin Bound to Compound 2 (pdb code 4yj3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Tubulin Bound to Compound 2, PDB code: 4yj3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Tubulin Bound to Compound 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tubulin Bound to Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.1 occ:1.00 OG1 A:THR41 2.4 0.3 1.0 OE2 A:GLU55 2.4 1.0 1.0 OD1 A:ASP39 2.5 0.5 1.0 O A:GLY44 2.6 0.4 1.0 O A:THR41 3.1 0.5 1.0 CG A:ASP39 3.2 0.9 1.0 CD A:GLU55 3.2 0.3 1.0 OD2 A:ASP39 3.2 0.9 1.0 OE1 A:GLU55 3.3 0.6 1.0 CB A:THR41 3.6 0.6 1.0 C A:GLY44 3.6 0.1 1.0 CA A:GLY45 3.7 0.8 1.0 CZ A:PHE49 3.7 0.3 1.0 OD1 A:ASN50 3.8 0.1 1.0 ND2 A:ASN50 4.1 0.7 1.0 OD2 A:ASP47 4.1 0.9 1.0 C A:THR41 4.1 0.1 1.0 N A:GLY45 4.1 1.0 1.0 CA A:THR41 4.3 0.5 1.0 CE2 A:PHE49 4.4 0.7 1.0 CG A:ASN50 4.4 0.2 1.0 C A:GLY45 4.4 0.2 1.0 CB A:ASP39 4.6 0.5 1.0 CG A:GLU55 4.6 0.6 1.0 CE1 A:PHE49 4.6 0.4 1.0 N A:THR41 4.6 0.7 1.0 CG2 A:THR41 4.7 0.3 1.0 O A:GLY45 4.8 0.5 1.0 CG A:ASP47 4.8 0.9 1.0 CA A:GLY44 4.9 0.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin Bound to Compound 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tubulin Bound to Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:71.2 occ:1.00 OE2 B:GLU113 3.1 82.3 1.0 OE1 B:GLU110 3.7 79.6 1.0 CD B:GLU113 3.9 84.0 1.0 OE1 B:GLU113 4.0 86.8 1.0 OE2 B:GLU110 4.0 77.3 1.0 CD B:GLU110 4.2 77.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Tubulin Bound to Compound 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin Bound to Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:0.3 occ:1.00 O C:THR41 2.3 99.7 1.0 OG1 C:THR41 2.3 99.2 1.0 OD1 C:ASP39 2.3 96.4 1.0 OE2 C:GLU55 2.4 94.6 1.0 OD2 C:ASP39 2.4 95.8 1.0 OE1 C:GLU55 2.4 96.3 1.0 O C:HOH601 2.4 90.4 1.0 O C:GLY44 2.5 0.8 1.0 CG C:ASP39 2.7 96.1 1.0 CD C:GLU55 2.7 95.0 1.0 C C:THR41 3.3 0.1 1.0 CB C:THR41 3.4 0.7 1.0 C C:GLY44 3.6 0.1 1.0 CA C:THR41 3.7 0.7 1.0 N C:THR41 4.1 0.9 1.0 CB C:ASP39 4.2 96.2 1.0 CG C:GLU55 4.2 94.0 1.0 CA C:GLY44 4.4 99.9 1.0 N C:ILE42 4.4 0.2 1.0 N C:GLY44 4.5 0.2 1.0 NE2 C:HIS61 4.5 92.2 1.0 N C:GLY45 4.5 99.3 1.0 OD2 C:ASP47 4.6 92.9 1.0 CG2 C:THR41 4.6 0.8 1.0 CA C:GLY45 4.7 99.6 1.0 CZ C:PHE49 4.7 88.1 1.0 CE1 C:PHE49 4.7 87.2 1.0 ND2 C:ASN50 4.8 87.1 1.0 CA C:ILE42 4.9 0.9 1.0

D.E.Mcnamara, S.Senese, T.O.Yeates, J.Z.Torres. Structures of Potent Anticancer Compounds Bound to Tubulin. Protein Sci. 2015.
ISSN: ESSN 1469-896X
PubMed: 25970265
DOI: 10.1002/PRO.2704