Calcium in PDB 7e4q: Crystal Structure of Tubulin in Complex with L-DM1-Sme

The structure of Crystal Structure of Tubulin in Complex with L-DM1-Sme, PDB code: 7e4q was solved by Y.Wang, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.88 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.893, 157.209, 181.658, 90, 90, 90
R / Rfree (%)	20.5 / 25.2

The structure of Crystal Structure of Tubulin in Complex with L-DM1-Sme also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Tubulin in Complex with L-DM1-Sme (pdb code 7e4q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Tubulin in Complex with L-DM1-Sme, PDB code: 7e4q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Tubulin in Complex with L-DM1-Sme


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 in Complex with L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:79.4 occ:1.00 HG1 A:THR41 2.2 108.7 1.0 OD1 A:ASP39 2.4 68.2 1.0 OE2 A:GLU55 2.5 85.4 1.0 O A:THR41 2.5 82.5 1.0 O A:GLY44 2.6 74.0 1.0 OD2 A:ASP39 2.6 74.4 1.0 OE1 A:GLU55 2.8 87.5 1.0 OG1 A:THR41 2.9 90.6 1.0 CG A:ASP39 2.9 69.6 1.0 HA3 A:GLY45 2.9 104.1 1.0 HB A:THR41 3.0 98.5 1.0 CD A:GLU55 3.0 76.7 1.0 CB A:THR41 3.3 82.1 1.0 C A:GLY44 3.4 77.5 1.0 HZ A:PHE49 3.4 91.6 1.0 C A:THR41 3.5 84.6 1.0 CA A:GLY45 3.6 86.8 1.0 HA2 A:GLY45 3.7 104.1 1.0 N A:GLY45 3.9 83.0 1.0 CA A:THR41 3.9 81.3 1.0 H A:GLY44 3.9 102.5 1.0 HD21 A:ASN50 3.9 86.6 1.0 H A:THR41 4.0 86.3 1.0 OD2 A:ASP47 4.2 75.1 1.0 CZ A:PHE49 4.3 76.3 1.0 N A:THR41 4.3 71.9 1.0 CB A:ASP39 4.4 66.9 1.0 CG A:GLU55 4.5 77.3 1.0 OD1 A:ASN50 4.5 85.8 1.0 CA A:GLY44 4.5 88.7 1.0 N A:GLY44 4.5 85.4 1.0 H A:GLY45 4.6 99.7 1.0 N A:ILE42 4.7 82.2 1.0 HB2 A:ASP39 4.7 80.3 1.0 HG3 A:GLU55 4.7 92.7 1.0 CG2 A:THR41 4.7 77.5 1.0 ND2 A:ASN50 4.7 72.2 1.0 NE2 A:HIS61 4.7 79.2 1.0 HA A:ILE42 4.8 96.5 1.0 HA A:THR41 4.8 97.5 1.0 HG21 A:THR41 4.8 93.0 1.0 HA2 A:GLY44 4.8 106.4 1.0 HB3 A:ASP39 4.9 80.3 1.0 HE2 A:PHE49 4.9 88.5 1.0 HG2 A:GLU55 4.9 92.7 1.0 C A:GLY45 4.9 83.5 1.0 HE1 A:PHE49 4.9 95.2 1.0 HA A:ASP39 5.0 89.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Tubulin in Complex with L-DM1-Sme


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 in Complex with L-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:61.1 occ:1.00 OD2 C:ASP39 2.4 62.5 1.0 O C:THR41 2.4 79.1 1.0 OG1 C:THR41 2.5 66.9 1.0 O C:HOH606 2.5 49.1 1.0 OE2 C:GLU55 2.5 52.2 1.0 OD1 C:ASP39 2.6 54.0 1.0 OE1 C:GLU55 2.6 54.0 1.0 O C:GLY44 2.7 67.8 1.0 CG C:ASP39 2.8 58.3 1.0 CD C:GLU55 2.9 56.2 1.0 HA3 C:GLY45 3.3 77.5 1.0 CB C:THR41 3.4 69.0 1.0 HB C:THR41 3.4 82.8 1.0 C C:THR41 3.5 70.0 1.0 C C:GLY44 3.6 69.2 1.0 H C:THR41 3.7 74.9 1.0 HZ C:PHE49 3.8 51.9 1.0 CA C:THR41 3.9 68.5 1.0 HD21 C:ASN50 4.0 58.4 1.0 H C:GLY44 4.1 84.8 1.0 CA C:GLY45 4.2 64.6 1.0 N C:THR41 4.2 62.4 1.0 N C:GLY45 4.2 63.9 1.0 CB C:ASP39 4.3 60.2 1.0 O C:HOH631 4.4 57.8 1.0 CG C:GLU55 4.4 48.9 1.0 HE1 C:PHE49 4.4 54.9 1.0 OD2 C:ASP47 4.4 68.8 1.0 OD1 C:ASN50 4.5 48.4 1.0 CZ C:PHE49 4.5 43.2 1.0 CA C:GLY44 4.6 74.7 1.0 NE2 C:HIS61 4.6 52.0 1.0 HA2 C:GLY45 4.6 77.5 1.0 N C:GLY44 4.6 70.7 1.0 N C:ILE42 4.7 70.7 1.0 HB3 C:ASP39 4.7 72.2 1.0 HA C:ILE42 4.7 75.2 1.0 HA2 C:GLY44 4.7 89.6 1.0 HB2 C:ASP39 4.7 72.2 1.0 HG2 C:GLU55 4.7 58.6 1.0 CG2 C:THR41 4.8 50.5 1.0 HG3 C:GLU55 4.8 58.6 1.0 HA C:THR41 4.8 82.1 1.0 ND2 C:ASN50 4.8 48.7 1.0 CE1 C:PHE49 4.9 45.7 1.0 HG21 C:THR41 4.9 60.6 1.0 O C:HOH635 5.0 52.7 1.0 H C:GLY45 5.0 76.7 1.0

W.Li, M.Huang, Y.Li, A.Xia, L.Tan, Z.Zhang, Y.Wang, J.Yang. C3 Ester Side Chain Plays A Pivotal Role in the Antitumor Activity of Maytansinoids. Biochem.Biophys.Res.Commun. V. 566 197 2021.
ISSN: ESSN 1090-2104
PubMed: 34144258
DOI: 10.1016/J.BBRC.2021.05.071