Sodium in PDB 5zo8: EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type)

The structure of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type), PDB code: 5zo8 was solved by H.Yokoyama, K.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.293, 50.724, 83.355, 90.00, 112.99, 90.00
R / Rfree (%)	20.5 / 24.4

The structure of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type) (pdb code 5zo8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type), PDB code: 5zo8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:52.6 occ:1.00 O A:HOH759 2.4 29.3 1.0 O1 A:SO4604 2.7 43.9 1.0 OE1 A:GLU167 2.8 11.6 0.5 CD A:GLU167 3.7 12.5 0.5 OE2 A:GLU167 4.1 11.7 0.5 S A:SO4604 4.2 42.5 1.0 O4 A:SO4604 4.5 42.4 1.0 NH1 A:ARG181 4.7 20.0 1.0 O2 A:SO4604 4.7 38.9 1.0 CG A:GLU167 4.8 13.6 0.5

Sodium binding site 2 out of 2 in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:43.8 occ:1.00 O4 B:SO4604 2.6 45.4 1.0 OE1 B:GLU167 2.8 13.9 0.5 CD B:GLU167 3.6 15.1 0.5 S B:SO4604 4.0 41.9 1.0 OE2 B:GLU167 4.0 14.2 0.5 O B:HOH742 4.4 30.6 1.0 O3 B:SO4604 4.4 46.1 1.0 O2 B:SO4604 4.6 42.6 1.0 NH1 B:ARG181 4.7 21.9 1.0 CG B:GLU167 4.7 15.6 0.5

H.Yokoyama, J.I.Sawada, K.Sato, N.Ogo, N.Kamei, Y.Ishikawa, K.Hara, A.Asai, H.Hashimoto. Structural and Thermodynamic Basis of the Enhanced Interaction Between Kinesin Spindle Protein EG5 and Stlc-Type Inhibitors. Acs Omega V. 3 12284 2018.
ISSN: ESSN 2470-1343
PubMed: 31459302
DOI: 10.1021/ACSOMEGA.8B00778