Calcium in PDB 7e4r: Crystal Structure of Tubulin in Complex with D-DM1-Sme

The structure of Crystal Structure of Tubulin in Complex with D-DM1-Sme, PDB code: 7e4r 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)	45.45 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.982, 157.229, 182.574, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

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

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Tubulin in Complex with D-DM1-Sme (pdb code 7e4r). 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 D-DM1-Sme, PDB code: 7e4r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Tubulin in Complex with D-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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:67.8 occ:1.00 HG1 A:THR41 1.8 102.6 1.0 OE2 A:GLU55 2.4 79.5 1.0 OD2 A:ASP39 2.4 74.2 1.0 O A:GLY44 2.5 64.9 1.0 OD1 A:ASP39 2.6 55.5 1.0 OG1 A:THR41 2.6 85.5 1.0 OE1 A:GLU55 2.7 79.5 1.0 O A:THR41 2.7 77.8 1.0 CG A:ASP39 2.8 56.1 1.0 CD A:GLU55 2.9 69.4 1.0 HZ A:PHE49 3.3 91.8 1.0 HA3 A:GLY45 3.3 86.3 1.0 C A:GLY44 3.4 78.5 1.0 HD21 A:ASN50 3.5 77.1 1.0 HB A:THR41 3.6 95.6 1.0 CB A:THR41 3.6 79.7 1.0 C A:THR41 3.7 78.5 1.0 H A:GLY44 3.9 96.0 1.0 H A:THR41 4.0 83.9 1.0 CA A:GLY45 4.1 71.9 1.0 CZ A:PHE49 4.1 76.5 1.0 N A:GLY45 4.1 61.8 1.0 CA A:THR41 4.1 82.8 1.0 NE2 A:HIS61 4.2 84.8 1.0 ND2 A:ASN50 4.3 64.3 1.0 CB A:ASP39 4.3 54.1 1.0 CG A:GLU55 4.4 70.8 1.0 CA A:GLY44 4.4 89.7 1.0 HE1 A:PHE49 4.4 81.2 1.0 N A:THR41 4.4 69.9 1.0 OD1 A:ASN50 4.4 57.3 1.0 OD2 A:ASP47 4.4 55.1 1.0 N A:GLY44 4.5 80.0 1.0 HA2 A:GLY44 4.5 107.6 1.0 HB2 A:ASP39 4.6 64.9 1.0 CE1 A:PHE49 4.7 67.7 1.0 HA2 A:GLY45 4.7 86.3 1.0 HG3 A:GLU55 4.7 85.0 1.0 HB3 A:ASP39 4.7 64.9 1.0 HG2 A:GLU55 4.8 85.0 1.0 HE1 A:HIS61 4.8 110.0 1.0 CG A:ASN50 4.8 57.8 1.0 H A:GLY45 4.9 74.1 1.0 CG2 A:THR41 4.9 58.6 1.0 CE1 A:HIS61 4.9 91.7 1.0 N A:ILE42 4.9 66.9 1.0 HD22 A:ASN50 4.9 77.1 1.0 HG21 A:THR41 5.0 70.3 1.0 HA A:ILE42 5.0 83.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Tubulin in Complex with D-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 D-DM1-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:42.4 occ:1.00 OE2 C:GLU55 2.4 58.0 1.0 OG1 C:THR41 2.4 53.7 1.0 O C:THR41 2.4 54.7 1.0 OD2 C:ASP39 2.4 42.0 1.0 O C:GLY44 2.5 50.2 1.0 OE1 C:GLU55 2.5 37.5 1.0 OD1 C:ASP39 2.6 38.6 1.0 O C:HOH602 2.6 41.4 1.0 CD C:GLU55 2.8 42.5 1.0 CG C:ASP39 2.8 40.1 1.0 HA3 C:GLY45 3.3 71.5 1.0 C C:GLY44 3.4 54.1 1.0 C C:THR41 3.5 44.8 1.0 CB C:THR41 3.5 57.5 1.0 HB C:THR41 3.6 69.0 1.0 HD21 C:ASN50 3.9 48.5 1.0 CA C:THR41 3.9 49.1 1.0 H C:GLY44 4.0 53.1 1.0 H C:THR41 4.0 60.7 1.0 HZ C:PHE49 4.0 44.0 1.0 CA C:GLY45 4.1 59.6 1.0 N C:GLY45 4.1 54.7 1.0 HE1 C:PHE49 4.2 39.7 1.0 N C:THR41 4.3 50.6 1.0 CG C:GLU55 4.3 41.4 1.0 OD2 C:ASP47 4.3 52.3 1.0 CB C:ASP39 4.4 41.6 1.0 CA C:GLY44 4.4 48.1 1.0 N C:GLY44 4.5 44.2 1.0 O C:HOH647 4.5 42.3 1.0 HA2 C:GLY45 4.5 71.5 1.0 HA2 C:GLY44 4.6 57.7 1.0 NE2 C:HIS61 4.6 45.7 1.0 OD1 C:ASN50 4.6 39.4 1.0 HA C:ILE42 4.6 54.0 1.0 N C:ILE42 4.7 45.3 1.0 HG2 C:GLU55 4.7 49.6 1.0 HG3 C:GLU55 4.7 49.6 1.0 ND2 C:ASN50 4.7 40.4 1.0 CZ C:PHE49 4.7 36.7 1.0 HB2 C:ASP39 4.7 50.0 1.0 HB3 C:ASP39 4.7 50.0 1.0 CG2 C:THR41 4.8 63.3 1.0 CE1 C:PHE49 4.8 33.1 1.0 HA C:THR41 4.8 59.0 1.0 HG21 C:THR41 4.9 75.9 1.0 H C:GLY45 4.9 65.7 1.0 HG23 C:THR41 5.0 75.9 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