Sodium in PDB 5zo9: EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (C2 Type)

The structure of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (C2 Type), PDB code: 5zo9 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)	19.74 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.158, 50.729, 94.309, 90.00, 102.19, 90.00
R / Rfree (%)	22.7 / 28.3

The structure of EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (C2 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 (C2 Type) (pdb code 5zo9). 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 (C2 Type), PDB code: 5zo9:
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 (C2 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 (C2 Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:60.1 occ:1.00 OE1 A:GLU167 2.7 30.9 0.5 O1 A:SO4604 3.0 72.1 1.0 CD A:GLU167 3.8 32.9 0.5 OE2 A:GLU167 4.3 31.6 0.5 NH1 A:ARG181 4.4 43.8 1.0 S A:SO4604 4.5 69.2 1.0 CG A:GLU167 4.8 34.5 0.5

Sodium binding site 2 out of 2 in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (C2 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 (C2 Type) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:61.8 occ:1.00 OE1 B:GLU167 2.7 38.6 0.5 O4 B:SO4604 3.0 62.7 1.0 CD B:GLU167 3.6 40.3 0.5 OE2 B:GLU167 4.3 40.4 0.5 S B:SO4604 4.4 71.1 1.0 CG B:GLU167 4.6 39.5 0.5 NH1 B:ARG181 4.6 53.8 1.0 O1 B:SO4604 4.8 74.9 1.0

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