Calcium in PDB 4i50: Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex, PDB code: 4i50 was solved by A.E.Prota, K.Bargsten, D.Zurwerra, J.J.Field, J.F.Diaz, K.H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.57 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.620, 155.130, 180.410, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.6

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A 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-Stathmin-Ttl-Epothilone A Complex (pdb code 4i50). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex, PDB code: 4i50:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A 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-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:72.8 occ:1.00 HG1 A:THR41 2.2 98.0 1.0 O A:HOH650 2.5 63.1 1.0 O A:GLY44 2.6 84.5 1.0 OD2 A:ASP39 2.6 66.6 1.0 O A:THR41 2.6 77.0 1.0 OD1 A:ASP39 2.6 74.7 1.0 OE1 A:GLU55 2.7 86.0 1.0 OE2 A:GLU55 2.7 61.7 1.0 OG1 A:THR41 3.0 81.7 1.0 CG A:ASP39 3.0 66.3 1.0 CD A:GLU55 3.0 80.0 1.0 H A:GLY44 3.5 0.8 1.0 HZ A:PHE49 3.6 93.8 1.0 C A:THR41 3.6 82.2 1.0 C A:GLY44 3.6 89.0 1.0 H A:THR41 3.7 88.3 1.0 HA3 A:GLY45 3.8 92.8 1.0 HE2 A:HIS61 3.8 0.3 1.0 CB A:THR41 3.9 76.5 1.0 HB A:THR41 4.1 91.8 1.0 CA A:THR41 4.1 76.5 1.0 N A:THR41 4.2 73.5 1.0 N A:GLY44 4.2 97.3 1.0 HD22 A:ASN50 4.2 84.6 1.0 HE1 A:PHE49 4.3 90.1 1.0 CZ A:PHE49 4.4 78.1 1.0 CA A:GLY44 4.4 98.8 1.0 CB A:ASP39 4.5 55.5 1.0 N A:GLY45 4.5 79.0 1.0 CG A:GLU55 4.5 72.5 1.0 NE2 A:HIS61 4.6 89.4 1.0 OD1 A:ASP47 4.6 72.6 1.0 CA A:GLY45 4.6 77.3 1.0 HA A:ILE42 4.6 0.9 1.0 OD1 A:ASN50 4.6 82.3 1.0 H A:GLY43 4.6 95.3 1.0 N A:ILE42 4.7 95.8 1.0 HA2 A:GLY44 4.7 0.6 1.0 CE1 A:PHE49 4.8 75.1 1.0 HB2 A:ASP39 4.8 66.6 1.0 HG2 A:GLU55 4.8 87.0 1.0 HB3 A:ASP39 4.9 66.6 1.0 N A:GLY43 5.0 79.4 1.0 HG3 A:GLU55 5.0 87.0 1.0 H A:LYS40 5.0 0.4 1.0 ND2 A:ASN50 5.0 70.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A 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-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:97.6 occ:1.00 O A:HOH656 2.8 63.4 1.0 O A:HOH620 3.0 77.4 1.0 O A:HOH657 3.1 67.1 1.0 O A:HOH655 3.7 64.9 1.0 HZ1 A:LYS166 3.9 87.2 1.0 HA A:HIS197 3.9 47.6 1.0 O A:GLU196 4.1 54.5 1.0 OD2 E:ASP44 4.1 0.3 1.0 O A:HOH658 4.2 62.2 1.0 HB3 A:SER158 4.4 54.9 1.0 OG A:SER158 4.4 52.1 1.0 HZ3 A:LYS166 4.5 87.2 1.0 HG A:SER158 4.6 62.5 1.0 NZ A:LYS166 4.6 72.7 1.0 HD1 A:HIS197 4.6 75.4 1.0 O A:GLY162 4.8 64.5 1.0 CA A:HIS197 4.9 39.7 1.0 CB A:SER158 4.9 45.7 1.0 HZ2 A:LYS166 4.9 87.2 1.0 O A:HIS197 4.9 50.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A 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-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:91.3 occ:1.00 OE2 B:GLU113 2.9 0.9 1.0 CD B:GLU113 3.8 0.6 1.0 OE1 B:GLU113 3.9 0.5 1.0 OE1 B:GLU110 4.3 58.0 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A 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-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:72.5 occ:1.00 OD2 C:ASP39 2.5 55.4 1.0 OE2 C:GLU55 2.6 60.4 1.0 OG1 C:THR41 2.7 71.4 1.0 O C:GLY44 2.7 66.6 1.0 OE1 C:GLU55 2.7 65.6 1.0 O C:THR41 2.7 65.6 1.0 HG1 C:THR41 2.9 85.7 1.0 OD1 C:ASP39 2.9 65.5 1.0 CD C:GLU55 3.0 60.3 1.0 CG C:ASP39 3.1 62.7 1.0 HA3 C:GLY45 3.2 90.4 1.0 HB C:THR41 3.5 96.5 1.0 C C:GLY44 3.5 78.3 1.0 C C:THR41 3.5 76.4 1.0 CB C:THR41 3.5 80.4 1.0 HZ C:PHE49 3.7 82.9 1.0 H C:GLY44 3.8 98.9 1.0 HE2 C:HIS61 3.8 70.2 1.0 H C:THR41 3.9 63.0 1.0 OD1 C:ASP47 3.9 84.5 1.0 CA C:THR41 3.9 64.7 1.0 CA C:GLY45 4.0 75.3 1.0 HD22 C:ASN50 4.0 63.5 1.0 N C:GLY45 4.1 60.1 1.0 N C:THR41 4.3 52.5 1.0 OD1 C:ASN50 4.4 67.4 1.0 CZ C:PHE49 4.5 69.1 1.0 HA2 C:GLY45 4.5 90.4 1.0 N C:GLY44 4.5 82.5 1.0 CA C:GLY44 4.5 79.8 1.0 O C:HOH699 4.5 57.3 1.0 CG C:GLU55 4.5 64.2 1.0 N C:ILE42 4.5 72.8 1.0 CB C:ASP39 4.6 61.0 1.0 NE2 C:HIS61 4.6 58.5 1.0 HA C:ILE42 4.6 81.9 1.0 HA2 C:GLY44 4.7 95.8 1.0 HE1 C:PHE49 4.7 85.5 1.0 ND2 C:ASN50 4.8 53.0 1.0 H C:GLY45 4.8 72.2 1.0 HG3 C:GLU55 4.9 77.1 1.0 HA C:THR41 4.9 77.6 1.0 CG2 C:THR41 4.9 82.8 1.0 HB2 C:ASP39 4.9 73.2 1.0 HB3 C:ASP39 4.9 73.2 1.0 HG2 C:GLU55 4.9 77.1 1.0 CE1 C:PHE49 5.0 71.3 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:0.3 occ:1.00 HZ3 C:LYS163 3.1 0.1 1.0 HD2 C:LYS163 3.1 0.3 1.0 O C:GLU196 3.6 37.4 1.0 O C:HOH672 3.7 53.1 1.0 OD2 C:ASP199 3.7 72.1 1.0 HA C:HIS197 3.8 37.7 1.0 HE2 C:LYS163 3.8 0.1 1.0 CD C:LYS163 3.9 0.2 1.0 NZ C:LYS163 3.9 0.2 1.0 HZ E:PHE93 3.9 62.6 1.0 CE C:LYS163 4.1 0.7 1.0 HD3 C:LYS163 4.1 0.3 1.0 HA C:LYS163 4.2 0.6 1.0 CZ E:PHE93 4.3 52.1 1.0 OD1 C:ASP199 4.3 41.7 1.0 CG C:ASP199 4.3 64.9 1.0 C C:HIS197 4.3 44.2 1.0 O C:HIS197 4.3 40.9 1.0 HZ1 C:LYS163 4.4 0.1 1.0 HZ2 C:LYS163 4.4 0.1 1.0 HE2 E:PHE93 4.5 57.4 1.0 CA C:HIS197 4.5 31.4 1.0 HZ3 C:LYS166 4.5 52.0 1.0 CE2 E:PHE93 4.6 47.9 1.0 C C:GLU196 4.6 38.5 1.0 HZ1 C:LYS166 4.7 52.0 1.0 N C:SER198 4.8 49.2 1.0 HG C:SER158 4.9 53.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:97.3 occ:1.00 HB3 C:ASP431 3.7 46.9 1.0 HB3 C:TYR262 3.9 46.2 1.0 O C:HOH621 4.0 33.3 1.0 HB2 C:TYR262 4.2 46.2 1.0 CG C:TYR262 4.2 43.6 1.0 CD2 C:TYR262 4.3 48.0 1.0 HD2 C:TYR262 4.3 57.6 1.0 CB C:TYR262 4.3 38.5 1.0 CG C:ASP431 4.4 42.4 1.0 HG12 C:ILE265 4.4 36.6 1.0 CB C:ASP431 4.5 39.0 1.0 OD1 C:ASP431 4.5 68.8 1.0 HG13 C:VAL435 4.5 45.9 1.0 HD3 C:ARG264 4.7 31.9 1.0 OD2 C:ASP431 4.7 52.5 1.0 HA C:ASP431 4.7 37.5 1.0 HG11 C:VAL435 4.7 45.9 1.0 HG12 C:VAL435 4.7 45.9 1.0 CD1 C:TYR262 4.8 40.6 1.0 HG13 C:ILE265 4.8 36.6 1.0 HD11 C:ILE265 4.8 55.1 1.0 CE2 C:TYR262 4.8 51.8 1.0 HB2 C:ARG264 4.8 42.7 1.0 CG1 C:VAL435 4.9 38.2 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