Calcium in PDB 5xaf: Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex, PDB code: 5xaf 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)	49.77 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.568, 156.509, 182.078, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.7

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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 Z1 Complex (pdb code 5xaf). 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 Z1 Complex, PDB code: 5xaf:
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 Z1 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 Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:0.9 occ:1.00 O A:GLY44 2.3 94.3 1.0 OE2 A:GLU55 2.4 94.9 1.0 O A:THR41 2.5 0.8 1.0 OD1 A:ASP39 2.6 85.4 1.0 OD2 A:ASP39 2.8 0.1 1.0 OE1 A:GLU55 2.9 0.7 1.0 CD A:GLU55 3.0 0.2 1.0 CG A:ASP39 3.0 94.6 1.0 CB A:THR41 3.2 1.0 1.0 C A:GLY44 3.3 1.0 1.0 C A:THR41 3.5 0.9 1.0 OG1 A:THR41 3.6 0.9 1.0 CA A:THR41 3.8 0.8 1.0 OD1 A:ASN50 3.9 89.8 1.0 CA A:GLY45 3.9 0.5 1.0 N A:GLY45 4.0 0.9 1.0 OD2 A:ASP47 4.1 89.8 1.0 CZ A:PHE49 4.1 81.0 1.0 N A:THR41 4.2 0.2 1.0 N A:GLY44 4.3 1.0 1.0 CG2 A:THR41 4.4 0.3 1.0 CG A:GLU55 4.5 94.6 1.0 CA A:GLY44 4.5 96.6 1.0 ND2 A:ASN50 4.5 0.6 1.0 CB A:ASP39 4.5 92.3 1.0 CG A:ASN50 4.6 94.2 1.0 N A:ILE42 4.7 0.8 1.0 NE2 A:HIS61 4.8 89.9 1.0 CE2 A:PHE49 4.9 84.2 1.0 CE1 A:PHE49 5.0 82.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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 Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.1 occ:1.00 OE1 B:GLU113 2.4 87.7 1.0 O B:HOH708 2.7 40.5 1.0 CD B:GLU113 3.2 84.4 1.0 OE2 B:GLU113 3.4 92.9 1.0 OE1 B:GLU110 3.6 53.7 1.0 O B:HOH679 4.1 40.5 1.0 CD B:GLU110 4.5 61.8 1.0 CG B:GLU113 4.6 68.2 1.0 OG B:SER97 4.7 0.5 1.0 OE2 B:GLU110 4.7 73.3 1.0 CB B:GLU113 5.0 59.0 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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 Z1 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 82.2 1.0 O C:HOH742 3.5 40.5 1.0 O C:GLU279 3.8 71.5 1.0 O C:LYS280 4.4 86.1 1.0 C C:TYR282 4.6 71.9 1.0 CA C:LYS280 4.6 69.9 1.0 C C:LYS280 4.6 73.3 1.0 CG C:GLU284 4.8 0.2 1.0 C C:GLU279 4.9 69.6 1.0 CB C:HIS283 4.9 82.8 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