Calcium in PDB 4i4t: Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t was solved by A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.32 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.770, 158.640, 179.240, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.4

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex (pdb code 4i4t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:45.0 occ:1.00 O A:GLY44 2.4 49.1 1.0 O A:THR41 2.5 50.7 1.0 OG1 A:THR41 2.5 41.7 1.0 OE1 A:GLU55 2.5 41.9 1.0 OD2 A:ASP39 2.6 48.0 1.0 OE2 A:GLU55 2.6 38.7 1.0 O A:HOH702 2.6 38.3 1.0 OD1 A:ASP39 2.7 54.6 1.0 CD A:GLU55 2.9 42.3 1.0 CG A:ASP39 3.0 56.2 1.0 CB A:THR41 3.4 55.4 1.0 HB A:THR41 3.4 66.4 1.0 C A:THR41 3.5 66.7 1.0 C A:GLY44 3.5 70.1 1.0 H A:GLY44 3.6 72.8 1.0 HA3 A:GLY45 3.6 68.9 1.0 H A:THR41 3.7 67.9 1.0 HZ A:PHE49 3.7 54.9 1.0 CA A:THR41 3.9 56.8 1.0 HE2 A:HIS61 4.1 57.6 1.0 N A:THR41 4.2 56.6 1.0 HD21 A:ASN50 4.2 45.8 1.0 O A:HOH716 4.3 48.0 1.0 N A:GLY44 4.3 60.7 1.0 HE1 A:PHE49 4.3 53.4 1.0 N A:GLY45 4.3 56.3 1.0 CG A:GLU55 4.4 42.2 1.0 CA A:GLY45 4.4 57.4 1.0 CA A:GLY44 4.4 68.6 1.0 CB A:ASP39 4.5 44.5 1.0 CZ A:PHE49 4.5 45.7 1.0 OD1 A:ASN50 4.6 45.3 1.0 OD1 A:ASP47 4.6 46.0 1.0 HA2 A:GLY44 4.7 82.3 1.0 N A:ILE42 4.7 57.2 1.0 HG2 A:GLU55 4.7 50.7 1.0 CG2 A:THR41 4.8 57.6 1.0 HA A:ILE42 4.8 65.1 1.0 H A:GLY43 4.8 58.6 1.0 HA A:THR41 4.8 68.1 1.0 HG3 A:GLU55 4.8 50.7 1.0 CE1 A:PHE49 4.8 44.5 1.0 NE2 A:HIS61 4.8 48.0 1.0 HB3 A:ASP39 4.9 53.4 1.0 HB2 A:ASP39 4.9 53.4 1.0 HG21 A:THR41 4.9 69.1 1.0 HA2 A:GLY45 4.9 68.9 1.0 ND2 A:ASN50 5.0 38.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:80.9 occ:1.00 O E:HOH258 2.6 55.2 1.0 O A:HOH916 2.7 71.1 1.0 HO2 A:GOL507 2.8 64.8 1.0 O A:HOH712 2.9 44.4 1.0 O A:HOH900 2.9 63.1 1.0 O A:HOH901 3.1 39.0 1.0 HO3 A:GOL507 3.2 0.2 1.0 O2 A:GOL507 3.2 54.0 1.0 O3 A:GOL507 3.5 91.9 1.0 H31 A:GOL507 3.6 0.3 1.0 O A:HOH902 3.7 69.8 1.0 C3 A:GOL507 3.9 94.4 1.0 HZ3 A:LYS166 4.0 33.5 1.0 HZ1 A:LYS166 4.0 33.5 1.0 C2 A:GOL507 4.2 89.7 1.0 HA A:HIS197 4.2 36.3 1.0 OD2 E:ASP44 4.3 62.7 1.0 OD2 A:ASP199 4.3 35.0 1.0 NZ A:LYS166 4.4 27.9 1.0 HG A:SER158 4.4 41.7 1.0 O A:GLU196 4.5 36.8 1.0 O A:GLY162 4.5 49.2 1.0 OG A:SER158 4.5 34.7 1.0 HZ2 A:LYS166 4.6 33.5 1.0 HB3 A:SER158 4.7 41.1 1.0 O A:HIS197 4.7 37.9 1.0 H2 A:GOL507 4.9 0.7 1.0 OD1 A:ASP199 4.9 31.7 1.0 H32 A:GOL507 5.0 0.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:76.3 occ:1.00 OE2 B:GLU113 2.4 57.2 1.0 O B:HOH833 2.4 48.2 1.0 O B:HOH729 2.5 61.3 1.0 O B:HOH741 2.5 44.6 1.0 O B:HOH677 2.6 37.8 1.0 CD B:GLU113 3.4 47.8 1.0 OE1 B:GLU113 3.7 53.2 1.0 OE1 B:GLU110 3.8 38.1 1.0 OE2 B:GLU110 4.5 46.2 1.0 CD B:GLU110 4.5 43.5 1.0 HB2 B:GLU113 4.6 34.4 1.0 HA B:GLU110 4.6 34.2 1.0 HG B:SER97 4.7 0.9 1.0 HB3 B:GLU113 4.7 34.4 1.0 CG B:GLU113 4.7 38.4 1.0 O B:HOH655 4.7 44.1 1.0 CB B:GLU113 4.9 28.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:39.9 occ:1.00 O C:THR41 2.4 38.5 1.0 O C:HOH792 2.5 32.6 1.0 OG1 C:THR41 2.5 39.1 1.0 OE2 C:GLU55 2.6 36.3 1.0 OE1 C:GLU55 2.6 39.7 1.0 O C:GLY44 2.6 48.3 1.0 OD2 C:ASP39 2.6 45.9 1.0 OD1 C:ASP39 2.6 45.8 1.0 CD C:GLU55 2.9 42.2 1.0 CG C:ASP39 2.9 47.6 1.0 C C:THR41 3.4 51.1 1.0 CB C:THR41 3.5 56.4 1.0 C C:GLY44 3.5 53.3 1.0 HA3 C:GLY45 3.6 63.3 1.0 H C:THR41 3.6 47.2 1.0 HB C:THR41 3.6 67.7 1.0 H C:GLY44 3.7 56.5 1.0 HZ C:PHE49 3.8 43.2 1.0 CA C:THR41 3.8 43.7 1.0 HE2 C:HIS61 3.9 42.5 1.0 N C:THR41 4.1 39.4 1.0 HD21 C:ASN50 4.1 40.7 1.0 HE1 C:PHE49 4.2 44.5 1.0 N C:GLY45 4.3 49.9 1.0 O C:HOH613 4.3 38.5 1.0 CA C:GLY45 4.3 52.8 1.0 N C:GLY44 4.4 47.1 1.0 CG C:GLU55 4.4 38.6 1.0 CB C:ASP39 4.4 41.4 1.0 CA C:GLY44 4.4 47.5 1.0 OD1 C:ASP47 4.5 47.0 1.0 CZ C:PHE49 4.6 36.0 1.0 HA C:ILE42 4.6 49.0 1.0 OD1 C:ASN50 4.6 36.4 1.0 N C:ILE42 4.6 45.4 1.0 NE2 C:HIS61 4.6 35.5 1.0 HA2 C:GLY44 4.7 57.0 1.0 HG2 C:GLU55 4.8 46.3 1.0 HB3 C:ASP39 4.8 49.7 1.0 HG3 C:GLU55 4.8 46.3 1.0 CE1 C:PHE49 4.8 37.1 1.0 HA C:THR41 4.8 52.4 1.0 HA2 C:GLY45 4.8 63.3 1.0 H C:GLY43 4.8 46.3 1.0 CG2 C:THR41 4.9 51.0 1.0 ND2 C:ASN50 4.9 33.9 1.0 HB2 C:ASP39 4.9 49.7 1.0 O C:HOH735 4.9 40.9 1.0

A.E.Prota, K.Bargsten, D.Zurwerra, J.J.Field, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science V. 339 587 2013.
ISSN: ISSN 0036-8075
PubMed: 23287720
DOI: 10.1126/SCIENCE.1230582