Calcium in PDB 5xag: Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex, PDB code: 5xag was solved by H.Zhang, C.Luo, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.270, 156.117, 182.107, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.5

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex (pdb code 5xag). 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-Stathmin-Ttl-Compound Z2 Complex, PDB code: 5xag:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex


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-Stathmin-Ttl-Compound Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:97.0 occ:1.00 OE2 A:GLU55 2.4 90.9 1.0 O A:GLY44 2.4 85.5 1.0 O A:THR41 2.6 90.2 1.0 OD1 A:ASP39 2.6 90.3 1.0 OG1 A:THR41 2.8 0.9 1.0 OE1 A:GLU55 2.8 93.0 1.0 OD2 A:ASP39 2.9 94.8 1.0 CD A:GLU55 3.0 89.5 1.0 CG A:ASP39 3.1 91.0 1.0 C A:GLY44 3.5 88.5 1.0 CB A:THR41 3.6 99.9 1.0 C A:THR41 3.7 96.5 1.0 OD2 A:ASP47 4.1 85.5 1.0 CA A:THR41 4.1 0.3 1.0 CZ A:PHE49 4.1 77.7 1.0 OD1 A:ASN50 4.1 93.5 1.0 CA A:GLY45 4.2 0.9 1.0 N A:GLY45 4.2 99.6 1.0 ND2 A:ASN50 4.4 91.7 1.0 N A:THR41 4.4 0.2 1.0 N A:GLY44 4.5 97.1 1.0 CG A:GLU55 4.5 82.0 1.0 NE2 A:HIS61 4.5 83.1 1.0 CB A:ASP39 4.5 87.0 1.0 CA A:GLY44 4.6 90.8 1.0 CG A:ASN50 4.7 91.7 1.0 CE1 A:PHE49 4.8 83.0 1.0 N A:ILE42 4.8 97.9 1.0 CE2 A:PHE49 4.9 78.6 1.0 CG2 A:THR41 5.0 90.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex


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-Stathmin-Ttl-Compound Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.8 occ:1.00 OE1 B:GLU113 2.7 86.4 1.0 OE1 B:GLU110 3.3 55.5 1.0 CD B:GLU113 3.7 81.3 1.0 OE2 B:GLU113 4.0 82.0 1.0 CD B:GLU110 4.1 57.3 1.0 OE2 B:GLU110 4.1 64.1 1.0 OG B:SER97 4.8 0.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex


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-Stathmin-Ttl-Compound Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:0.5 occ:1.00 O C:TYR282 3.4 74.0 1.0 O C:GLU279 4.1 73.8 1.0 O C:LYS280 4.4 80.7 1.0 C C:TYR282 4.6 67.3 1.0 CB C:HIS283 4.7 83.8 1.0 CA C:LYS280 4.8 71.9 1.0 C C:LYS280 4.9 73.0 1.0 O C:HIS283 4.9 88.4 1.0

P.Zhou, Y.Liang, H.Zhang, H.Jiang, K.Feng, P.Xu, J.Wang, X.Wang, K.Ding, C.Luo, M.Liu, Y.Wang. Design, Synthesis, Biological Evaluation and Cocrystal Structures with Tubulin of Chiral Beta-Lactam Bridged Combretastatin A-4 Analogues As Potent Antitumor Agents Eur J Med Chem V. 144 817 2017.
ISSN: ISSN 1768-3254
PubMed: 29306206
DOI: 10.1016/J.EJMECH.2017.12.004