Calcium in PDB 4yj2: Crystal Structure of Tubulin Bound to Mi-181

The structure of Crystal Structure of Tubulin Bound to Mi-181, PDB code: 4yj2 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)	90.72 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.830, 157.650, 181.030, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.1

The structure of Crystal Structure of Tubulin Bound to Mi-181 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin Bound to Mi-181 (pdb code 4yj2). 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 Mi-181, PDB code: 4yj2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Tubulin Bound to Mi-181


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 Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:95.1 occ:1.00 O A:GLY44 2.3 91.7 1.0 OE2 A:GLU55 2.3 89.2 1.0 OD1 A:ASP39 2.4 99.1 1.0 OD2 A:ASP39 2.4 99.2 1.0 OG1 A:THR41 2.4 0.2 1.0 O A:THR41 2.4 0.9 1.0 O A:HOH601 2.4 0.3 1.0 OE1 A:GLU55 2.4 0.9 1.0 CG A:ASP39 2.6 97.3 1.0 CD A:GLU55 2.7 95.0 1.0 C A:THR41 3.4 0.9 1.0 CB A:THR41 3.4 0.8 1.0 C A:GLY44 3.6 98.5 1.0 CA A:THR41 3.8 0.9 1.0 CB A:ASP39 4.1 94.5 1.0 N A:THR41 4.2 0.8 1.0 CG A:GLU55 4.2 93.2 1.0 N A:GLY44 4.3 0.7 1.0 N A:GLY45 4.4 0.4 1.0 CZ A:PHE49 4.4 77.7 1.0 CA A:GLY45 4.4 0.1 1.0 OD2 A:ASP47 4.4 96.3 1.0 OD1 A:ASN50 4.5 91.4 1.0 CA A:GLY44 4.5 99.0 1.0 N A:ILE42 4.5 0.8 1.0 ND2 A:ASN50 4.6 79.8 1.0 NE2 A:HIS61 4.6 83.0 1.0 CG2 A:THR41 4.7 0.2 1.0 O A:GLY45 4.8 84.5 1.0 C A:GLY45 4.9 97.5 1.0 CA A:ILE42 5.0 0.6 1.0 N A:GLY43 5.0 0.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin Bound to Mi-181


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 Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.5 occ:1.00 O B:HOH613 2.4 60.8 1.0 OE2 B:GLU113 2.4 87.6 1.0 OE1 B:GLU113 3.1 91.5 1.0 CD B:GLU113 3.1 82.1 1.0 OE1 B:GLU110 4.4 54.9 1.0 CG B:GLU113 4.6 66.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Tubulin Bound to Mi-181


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 Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:86.0 occ:1.00 OD2 C:ASP39 2.3 85.1 1.0 OE2 C:GLU55 2.4 82.4 1.0 O C:THR41 2.4 83.7 1.0 O C:GLY44 2.4 93.4 1.0 OG1 C:THR41 2.4 83.1 1.0 OE1 C:GLU55 2.4 76.3 1.0 O C:HOH609 2.4 55.3 1.0 OD1 C:ASP39 2.4 86.5 1.0 CG C:ASP39 2.7 85.3 1.0 CD C:GLU55 2.7 77.4 1.0 C C:THR41 3.4 86.3 1.0 CB C:THR41 3.5 83.3 1.0 C C:GLY44 3.5 93.9 1.0 CA C:THR41 3.9 83.0 1.0 N C:THR41 4.2 84.2 1.0 CB C:ASP39 4.2 86.3 1.0 CG C:GLU55 4.2 69.1 1.0 CA C:GLY45 4.3 84.4 1.0 N C:GLY45 4.4 90.2 1.0 CA C:GLY44 4.5 96.4 1.0 NE2 C:HIS61 4.5 65.9 1.0 OD2 C:ASP47 4.5 87.6 1.0 N C:GLY44 4.5 100.0 1.0 N C:ILE42 4.6 97.1 1.0 CZ C:PHE49 4.7 63.6 1.0 OD1 C:ASN50 4.7 64.1 1.0 CG2 C:THR41 4.8 86.5 1.0 ND2 C:ASN50 4.9 56.8 1.0 CE1 C:PHE49 4.9 65.6 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