Calcium in PDB 7e4y: Crystal Structure of Tubulin in Complex with L-DM4-Sme

The structure of Crystal Structure of Tubulin in Complex with L-DM4-Sme, PDB code: 7e4y 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)	39.51 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.991, 156.034, 182.357, 90, 90, 90
R / Rfree (%)	19.6 / 23.9

The structure of Crystal Structure of Tubulin in Complex with L-DM4-Sme also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Crystal Structure of Tubulin in Complex with L-DM4-Sme (pdb code 7e4y). 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-DM4-Sme, PDB code: 7e4y:
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-DM4-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-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:71.2 occ:1.00 O A:THR41 2.3 72.3 1.0 HG1 A:THR41 2.3 89.5 1.0 OD2 A:ASP39 2.4 70.7 1.0 OE2 A:GLU55 2.4 81.6 1.0 OD1 A:ASP39 2.4 66.3 1.0 OE1 A:GLU55 2.7 80.2 1.0 CG A:ASP39 2.7 65.5 1.0 O A:GLY44 2.8 74.4 1.0 CD A:GLU55 2.9 79.6 1.0 OG1 A:THR41 3.0 74.6 1.0 HB A:THR41 3.1 90.8 1.0 HA3 A:GLY45 3.2 84.0 1.0 C A:THR41 3.4 77.9 1.0 CB A:THR41 3.4 75.7 1.0 C A:GLY44 3.5 72.5 1.0 HZ A:PHE49 3.6 94.7 1.0 CA A:GLY45 3.8 70.0 1.0 CA A:THR41 3.9 77.7 1.0 HA2 A:GLY45 3.9 84.0 1.0 H A:GLY44 4.0 101.2 1.0 H A:THR41 4.0 90.6 1.0 HD21 A:ASN50 4.0 80.4 1.0 N A:GLY45 4.0 69.4 1.0 CB A:ASP39 4.2 63.6 1.0 N A:THR41 4.3 75.5 1.0 CG A:GLU55 4.3 75.5 1.0 CZ A:PHE49 4.4 79.0 1.0 HA A:ILE42 4.5 90.7 1.0 N A:GLY44 4.5 84.3 1.0 N A:ILE42 4.5 82.6 1.0 CA A:GLY44 4.6 85.7 1.0 HG3 A:GLU55 4.6 90.6 1.0 HB2 A:ASP39 4.6 76.3 1.0 OD2 A:ASP47 4.6 77.4 1.0 HB3 A:ASP39 4.6 76.3 1.0 OD1 A:ASN50 4.7 74.4 1.0 NE2 A:HIS61 4.7 78.9 1.0 H A:GLY45 4.7 83.3 1.0 HA A:THR41 4.8 93.2 1.0 ND2 A:ASN50 4.8 67.0 1.0 HG2 A:GLU55 4.8 90.6 1.0 HA2 A:GLY44 4.8 102.8 1.0 CG2 A:THR41 4.9 64.9 1.0 HE1 A:PHE49 4.9 88.9 1.0 HA A:ASP39 5.0 85.4 1.0 CA A:ILE42 5.0 75.6 1.0 H A:GLY43 5.0 80.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Tubulin in Complex with L-DM4-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-DM4-Sme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:54.5 occ:1.00 O C:GLY44 2.4 54.0 1.0 O C:THR41 2.4 60.7 1.0 OD2 C:ASP39 2.4 47.5 1.0 OE2 C:GLU55 2.4 48.9 1.0 OG1 C:THR41 2.5 58.4 1.0 OE1 C:GLU55 2.5 53.3 1.0 OD1 C:ASP39 2.7 50.0 1.0 CD C:GLU55 2.8 49.2 1.0 CG C:ASP39 2.9 46.8 1.0 HA3 C:GLY45 3.3 65.4 1.0 HB C:THR41 3.4 60.7 1.0 C C:GLY44 3.4 52.4 1.0 CB C:THR41 3.4 50.6 1.0 C C:THR41 3.4 54.8 1.0 HZ C:PHE49 3.8 57.7 1.0 H C:THR41 3.8 64.2 1.0 H C:GLY44 3.9 64.3 1.0 CA C:THR41 3.9 53.8 1.0 HD21 C:ASN50 4.0 45.7 1.0 CA C:GLY45 4.1 54.5 1.0 N C:GLY45 4.1 57.1 1.0 N C:THR41 4.3 53.5 1.0 O C:HOH620 4.3 40.5 1.0 CG C:GLU55 4.3 39.2 1.0 OD1 C:ASN50 4.4 38.2 1.0 CA C:GLY44 4.4 49.5 1.0 HE1 C:PHE49 4.4 54.8 1.0 OD2 C:ASP47 4.4 65.1 1.0 CB C:ASP39 4.4 52.6 1.0 N C:GLY44 4.5 53.6 1.0 CZ C:PHE49 4.5 48.1 1.0 HA2 C:GLY44 4.5 59.4 1.0 NE2 C:HIS61 4.6 39.8 1.0 HA2 C:GLY45 4.6 65.4 1.0 N C:ILE42 4.6 51.4 1.0 HA C:ILE42 4.7 60.2 1.0 HG3 C:GLU55 4.7 47.1 1.0 CG2 C:THR41 4.7 46.9 1.0 HG2 C:GLU55 4.7 47.1 1.0 ND2 C:ASN50 4.7 38.1 1.0 HB3 C:ASP39 4.8 63.1 1.0 HA C:THR41 4.8 64.5 1.0 HB2 C:ASP39 4.8 63.1 1.0 CE1 C:PHE49 4.9 45.7 1.0 HG21 C:THR41 4.9 56.3 1.0 H C:GLY45 4.9 68.5 1.0

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