Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (P21 Type), PDB code: 5zo8:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:20.4 occ:1.00 O A:HOH709 2.0 12.2 1.0 O A:HOH714 2.0 17.2 1.0 O1B A:ADP600 2.1 19.7 1.0 O A:HOH749 2.1 15.1 1.0 OG1 A:THR112 2.1 19.6 1.0 O A:HOH704 2.2 13.5 1.0 CB A:THR112 3.1 20.8 1.0 PB A:ADP600 3.4 20.1 1.0 O3B A:ADP600 3.7 21.0 1.0 N A:THR112 4.0 19.3 1.0 OD2 A:ASP265 4.0 18.1 1.0 CA A:THR112 4.1 19.9 1.0 O A:HOH711 4.1 18.8 1.0 CG2 A:THR112 4.1 19.4 1.0 O2A A:ADP600 4.1 18.9 1.0 O A:HOH758 4.2 29.4 1.0 OD1 A:ASP265 4.2 17.8 1.0 O2B A:ADP600 4.3 16.6 1.0 O A:SER232 4.4 29.7 1.0 O A:HOH743 4.4 15.8 1.0 O3A A:ADP600 4.5 20.0 1.0 CG A:ASP265 4.5 18.6 1.0 PA A:ADP600 4.6 19.6 1.0 O1A A:ADP600 4.7 19.4 1.0 O A:HOH723 4.7 24.3 1.0 CB A:LYS111 4.9 17.7 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:24.4 occ:1.00 O3B B:ADP600 2.0 19.8 1.0 OG1 B:THR112 2.1 22.3 1.0 O B:HOH702 2.1 15.6 1.0 O B:HOH745 2.2 19.1 1.0 O B:HOH711 2.2 15.9 1.0 O B:HOH712 2.2 19.7 1.0 CB B:THR112 3.0 21.5 1.0 PB B:ADP600 3.3 20.3 1.0 O1B B:ADP600 3.7 19.8 1.0 N B:THR112 3.9 21.1 1.0 O1A B:ADP600 4.0 20.3 1.0 CA B:THR112 4.0 20.4 1.0 CG2 B:THR112 4.0 20.5 1.0 OD2 B:ASP265 4.0 23.7 1.0 OD1 B:ASP265 4.2 21.7 1.0 O B:HOH728 4.2 17.9 1.0 O2B B:ADP600 4.3 21.0 1.0 O3A B:ADP600 4.3 21.8 1.0 O B:SER232 4.5 29.5 1.0 PA B:ADP600 4.5 20.6 1.0 CG B:ASP265 4.5 23.8 1.0 O B:HOH727 4.6 20.0 1.0 O B:HOH744 4.6 24.4 1.0 O2A B:ADP600 4.7 23.4 1.0 CB B:LYS111 4.9 23.6 1.0 C B:LYS111 4.9 21.3 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