Calcium in PDB 5xlz: The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone

The structure of The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone, PDB code: 5xlz 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)	42.67 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.465, 158.439, 181.600, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.7

The structure of The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone (pdb code 5xlz). 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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone, PDB code: 5xlz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:62.1 occ:1.00 HG1 A:THR41 2.0 0.5 1.0 OE2 A:GLU55 2.3 62.7 1.0 O A:GLY44 2.4 61.3 1.0 OD2 A:ASP39 2.4 60.2 1.0 O A:HOH623 2.4 71.2 1.0 OE1 A:GLU55 2.5 69.1 1.0 OD1 A:ASP39 2.6 56.8 1.0 O A:THR41 2.7 72.5 1.0 CD A:GLU55 2.7 64.0 1.0 OG1 A:THR41 2.7 84.6 1.0 CG A:ASP39 2.8 58.8 1.0 HA3 A:GLY45 3.3 76.1 1.0 C A:GLY44 3.3 67.3 1.0 HZ A:PHE49 3.4 69.9 1.0 HD21 A:ASN50 3.5 60.1 1.0 HB A:THR41 3.6 84.1 1.0 H A:GLY44 3.6 84.3 1.0 CB A:THR41 3.7 70.0 1.0 C A:THR41 3.8 73.3 1.0 N A:GLY45 4.1 67.6 1.0 CA A:GLY45 4.1 63.4 1.0 H A:THR41 4.1 74.3 1.0 CG A:GLU55 4.2 61.8 1.0 CA A:THR41 4.2 66.0 1.0 CZ A:PHE49 4.2 58.2 1.0 N A:GLY44 4.3 70.3 1.0 CA A:GLY44 4.3 67.3 1.0 NE2 A:HIS61 4.3 60.9 1.0 OD1 A:ASN50 4.3 56.6 1.0 ND2 A:ASN50 4.3 50.1 1.0 HE1 A:PHE49 4.3 72.7 1.0 CB A:ASP39 4.3 57.3 1.0 HA2 A:GLY44 4.5 80.8 1.0 HG2 A:GLU55 4.6 74.2 1.0 HG3 A:GLU55 4.6 74.2 1.0 N A:THR41 4.6 62.0 1.0 HB2 A:ASP39 4.7 68.7 1.0 CE1 A:PHE49 4.7 60.6 1.0 HB3 A:ASP39 4.7 68.7 1.0 CG A:ASN50 4.8 53.3 1.0 HA2 A:GLY45 4.8 76.1 1.0 H A:GLY45 4.9 81.1 1.0 N A:ILE42 4.9 75.1 1.0 HA A:ILE42 4.9 83.3 1.0 HD22 A:ASN50 5.0 60.1 1.0 H A:GLY43 5.0 75.2 1.0 HB2 A:GLU55 5.0 75.5 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of Tubulin Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone


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 Complexed with A Benzylidene Derivative of 9(10H)-Anthracenone within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:40.8 occ:1.00 O C:THR41 2.4 57.6 1.0 OE2 C:GLU55 2.4 38.9 1.0 OG1 C:THR41 2.4 53.1 1.0 O C:HOH602 2.4 38.1 1.0 OD2 C:ASP39 2.5 39.5 1.0 O C:GLY44 2.6 44.4 1.0 OE1 C:GLU55 2.6 40.2 1.0 OD1 C:ASP39 2.7 47.1 1.0 CD C:GLU55 2.8 38.8 1.0 CG C:ASP39 2.9 41.6 1.0 HA3 C:GLY45 3.2 59.0 1.0 C C:THR41 3.4 51.8 1.0 CB C:THR41 3.4 53.8 1.0 HB C:THR41 3.5 64.5 1.0 C C:GLY44 3.5 45.1 1.0 CA C:THR41 3.9 52.9 1.0 H C:GLY44 3.9 57.7 1.0 H C:THR41 3.9 61.5 1.0 HD21 C:ASN50 3.9 36.2 1.0 HZ C:PHE49 4.0 45.5 1.0 CA C:GLY45 4.0 49.1 1.0 N C:GLY45 4.1 45.0 1.0 N C:THR41 4.2 51.3 1.0 HE1 C:PHE49 4.3 44.6 1.0 OD2 C:ASP47 4.3 47.8 1.0 CG C:GLU55 4.3 37.3 1.0 CB C:ASP39 4.4 43.6 1.0 HA2 C:GLY45 4.4 59.0 1.0 CA C:GLY44 4.5 48.0 1.0 N C:GLY44 4.5 48.1 1.0 N C:ILE42 4.6 48.7 1.0 HA C:ILE42 4.6 56.7 1.0 OD1 C:ASN50 4.6 32.7 1.0 NE2 C:HIS61 4.7 36.0 1.0 CZ C:PHE49 4.7 37.9 1.0 ND2 C:ASN50 4.7 30.2 1.0 HG3 C:GLU55 4.7 44.8 1.0 HA2 C:GLY44 4.7 57.6 1.0 HG2 C:GLU55 4.7 44.8 1.0 CG2 C:THR41 4.7 50.4 1.0 HB3 C:ASP39 4.8 52.4 1.0 HA C:THR41 4.8 63.4 1.0 CE1 C:PHE49 4.8 37.2 1.0 HB2 C:ASP39 4.8 52.4 1.0 H C:GLY45 4.9 54.0 1.0 HG21 C:THR41 4.9 60.5 1.0

J.Cheng, Y.Wu, Y.Wang, C.Wang, Y.Wang, C.Wu, S.Zeng, Y.Yu, Q.Chen. Structure of A Benzylidene Derivative of 9(10H)-Anthracenone in Complex with Tubulin Provides A Rationale For Drug Design. Biochem. Biophys. Res. V. 495 185 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29102632
DOI: 10.1016/J.BBRC.2017.10.104