Sodium 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
Calcium	(Ca)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:78.2 occ:1.00 OE2 B:GLU113 2.8 94.2 1.0 OE1 B:GLU110 3.6 46.8 1.0 CD B:GLU113 3.8 87.7 1.0 OE1 B:GLU113 3.9 94.1 1.0 CD B:GLU110 4.4 56.1 1.0 OE2 B:GLU110 4.4 74.1 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:27.7 occ:1.00 O C:HOH641 2.1 33.5 1.0 O C:GLY44 2.3 37.3 1.0 OE1 C:GLU55 2.3 35.8 1.0 O C:THR41 2.4 40.0 1.0 OG1 C:THR41 2.4 42.0 1.0 OD1 C:ASP39 2.5 44.5 1.0 OE2 C:GLU55 2.5 40.5 1.0 OD2 C:ASP39 2.6 39.5 1.0 CD C:GLU55 2.8 43.7 1.0 CG C:ASP39 2.9 41.6 1.0 C C:THR41 3.4 39.6 1.0 C C:GLY44 3.5 36.5 1.0 CB C:THR41 3.5 43.9 1.0 CA C:THR41 3.8 40.8 1.0 O C:HOH604 3.9 56.2 1.0 N C:THR41 4.1 46.1 1.0 N C:GLY44 4.3 40.2 1.0 CG C:GLU55 4.3 27.0 1.0 CA C:GLY45 4.3 37.9 1.0 N C:GLY45 4.3 43.0 1.0 OD2 C:ASP47 4.4 38.9 1.0 CB C:ASP39 4.4 45.2 1.0 CA C:GLY44 4.5 37.2 1.0 O C:HOH697 4.6 37.5 1.0 NE2 C:HIS61 4.6 30.9 1.0 N C:ILE42 4.6 39.5 1.0 OD1 C:ASN50 4.7 24.8 1.0 CZ C:PHE49 4.7 30.7 1.0 CG2 C:THR41 4.8 29.4 1.0 CE1 C:PHE49 4.9 29.8 1.0 ND2 C:ASN50 4.9 24.9 1.0 O C:HOH721 4.9 47.3 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