Calcium in PDB 5jcb: Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1

The structure of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1, PDB code: 5jcb was solved by Z.Guan, W.Zhao, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.357, 157.252, 179.631, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20

The structure of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 (pdb code 5jcb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1, PDB code: 5jcb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:53.5 occ:1.00 O A:GLY44 2.2 54.6 1.0 OD2 A:ASP39 2.3 47.7 1.0 OG1 A:THR41 2.4 56.7 1.0 OE2 A:GLU55 2.5 50.2 1.0 O A:HOH624 2.5 47.7 1.0 O A:THR41 2.5 76.2 1.0 OD1 A:ASP39 2.5 61.6 1.0 CG A:ASP39 2.7 60.5 1.0 OE1 A:GLU55 2.7 64.4 1.0 CD A:GLU55 2.9 60.4 1.0 C A:GLY44 3.4 62.1 1.0 C A:THR41 3.5 75.3 1.0 CB A:THR41 3.6 63.5 1.0 CA A:THR41 3.9 70.5 1.0 N A:THR41 4.1 68.1 1.0 CA A:GLY45 4.2 65.7 1.0 N A:GLY45 4.2 62.4 1.0 CB A:ASP39 4.2 55.6 1.0 N A:GLY44 4.3 63.7 1.0 CZ A:PHE49 4.4 48.7 1.0 CG A:GLU55 4.4 58.3 1.0 CA A:GLY44 4.5 64.9 1.0 OD2 A:ASP47 4.6 58.3 1.0 OD1 A:ASN50 4.6 44.7 1.0 NE2 A:HIS61 4.7 63.8 1.0 N A:ILE42 4.7 74.1 1.0 CG2 A:THR41 4.8 55.5 1.0 CE1 A:PHE49 4.9 53.0 1.0

Calcium binding site 2 out of 2 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:0.5 occ:1.00 O C:TYR282 3.2 47.2 1.0 O C:GLU279 3.7 61.9 1.0 O C:LYS280 4.1 49.0 1.0 C C:TYR282 4.4 37.2 1.0 CA C:LYS280 4.6 42.3 1.0 C C:LYS280 4.6 38.6 1.0 CB C:HIS283 4.6 82.4 1.0 C C:GLU279 4.8 50.7 1.0 CD2 C:TYR282 4.9 47.3 1.0 O C:HIS283 5.0 55.4 1.0

W.Zhao, C.Zhou, Z.Y.Guan, P.Yin, F.Chen, Y.J.Tang. Structural Insights Into the Inhibition of Tubulin By the Antitumor Agent 4 Beta-(1,2,4-Triazol-3-Ylthio)-4-Deoxypodophyllotoxin. Acs Chem. Biol. V. 12 746 2017.
ISSN: ESSN 1554-8937
PubMed: 28035796
DOI: 10.1021/ACSCHEMBIO.6B00842