Calcium in PDB 5xlt: The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin

The structure of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin, PDB code: 5xlt was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.86 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.473, 156.926, 180.868, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.9

The structure of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin (pdb code 5xlt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin, PDB code: 5xlt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:86.1 occ:1.00 HG1 A:THR41 1.8 0.3 1.0 OE2 A:GLU55 2.3 80.5 1.0 OD1 A:ASP39 2.4 66.0 1.0 O A:GLY44 2.4 67.0 1.0 OD2 A:ASP39 2.4 64.3 1.0 OE1 A:GLU55 2.5 80.0 1.0 O A:THR41 2.6 84.6 1.0 OG1 A:THR41 2.6 95.2 1.0 CG A:ASP39 2.7 60.2 1.0 CD A:GLU55 2.7 76.0 1.0 HZ A:PHE49 3.4 96.0 1.0 C A:GLY44 3.4 71.7 1.0 HB A:THR41 3.6 95.8 1.0 CB A:THR41 3.6 79.9 1.0 HA3 A:GLY45 3.6 87.9 1.0 HD21 A:ASN50 3.6 62.0 1.0 C A:THR41 3.6 87.7 1.0 H A:GLY44 3.6 92.5 1.0 H A:THR41 4.0 87.6 1.0 CA A:THR41 4.0 82.1 1.0 CZ A:PHE49 4.2 80.0 1.0 CB A:ASP39 4.2 64.8 1.0 CG A:GLU55 4.2 75.5 1.0 NE2 A:HIS61 4.2 90.7 1.0 HE1 A:PHE49 4.3 74.9 1.0 N A:GLY44 4.3 77.1 1.0 N A:GLY45 4.3 78.8 1.0 CA A:GLY44 4.3 76.3 1.0 CA A:GLY45 4.4 73.2 1.0 N A:THR41 4.4 73.0 1.0 ND2 A:ASN50 4.4 51.7 1.0 HB2 A:ASP39 4.4 77.7 1.0 OD1 A:ASN50 4.5 78.5 1.0 HA2 A:GLY44 4.5 91.5 1.0 HG2 A:GLU55 4.6 90.6 1.0 HG3 A:GLU55 4.6 90.6 1.0 HB3 A:ASP39 4.6 77.7 1.0 CE1 A:PHE49 4.6 62.4 1.0 N A:ILE42 4.8 88.3 1.0 HA A:ILE42 4.8 86.8 1.0 H A:GLY43 4.8 73.6 1.0 CG A:ASN50 4.9 63.0 1.0 CG2 A:THR41 4.9 68.7 1.0 HA A:ASP39 4.9 85.4 1.0 HA A:THR41 5.0 98.5 1.0 HB3 A:GLU55 5.0 99.5 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Tubulin in Complex with 4'- Demethylepipodophyllotoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:42.9 occ:1.00 OE2 C:GLU55 2.4 47.9 1.0 OG1 C:THR41 2.4 54.2 1.0 O C:THR41 2.4 54.2 1.0 OD2 C:ASP39 2.5 43.0 1.0 O C:GLY44 2.5 50.7 1.0 OE1 C:GLU55 2.5 49.8 1.0 O C:HOH603 2.7 44.2 1.0 OD1 C:ASP39 2.7 48.4 1.0 CD C:GLU55 2.8 43.2 1.0 CG C:ASP39 2.9 48.1 1.0 HA3 C:GLY45 3.3 71.1 1.0 C C:GLY44 3.5 53.7 1.0 C C:THR41 3.5 48.3 1.0 CB C:THR41 3.5 51.9 1.0 HB C:THR41 3.7 62.2 1.0 HZ C:PHE49 3.8 51.9 1.0 HD21 C:ASN50 3.9 40.2 1.0 H C:THR41 3.9 61.4 1.0 CA C:THR41 4.0 52.7 1.0 H C:GLY44 4.1 67.3 1.0 CA C:GLY45 4.1 59.2 1.0 N C:GLY45 4.2 58.0 1.0 HE1 C:PHE49 4.2 46.8 1.0 O C:HOH611 4.3 37.5 1.0 N C:THR41 4.3 51.2 1.0 CG C:GLU55 4.3 39.8 1.0 OD1 C:ASN50 4.4 47.4 1.0 OD2 C:ASP47 4.4 54.1 1.0 CB C:ASP39 4.4 53.2 1.0 CA C:GLY44 4.5 53.4 1.0 HA2 C:GLY45 4.5 71.1 1.0 CZ C:PHE49 4.5 43.3 1.0 NE2 C:HIS61 4.5 43.5 1.0 N C:GLY44 4.6 56.1 1.0 HA C:ILE42 4.6 57.9 1.0 HA2 C:GLY44 4.7 64.0 1.0 N C:ILE42 4.7 45.8 1.0 HG3 C:GLU55 4.7 47.8 1.0 ND2 C:ASN50 4.7 33.5 1.0 HG2 C:GLU55 4.7 47.8 1.0 CE1 C:PHE49 4.7 39.0 1.0 HB3 C:ASP39 4.8 63.9 1.0 CG2 C:THR41 4.8 54.9 1.0 HB2 C:ASP39 4.8 63.9 1.0 HA C:THR41 4.9 63.3 1.0 HG21 C:THR41 4.9 65.9 1.0 H C:GLY45 4.9 69.7 1.0 CG C:ASN50 5.0 40.5 1.0

L.Niu, Y.Wang, C.Wang, Y.Wang, X.Jiang, L.Ma, C.Wu, Y.Yu, Q.Chen. Structure of 4'-Demethylepipodophyllotoxin in Complex with Tubulin Provides A Rationale For Drug Design Biochem. Biophys. Res. V. 493 718 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28864414
DOI: 10.1016/J.BBRC.2017.08.125