Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the EG5 Motor Domain in Complex with Stlc-Type Inhibitor PVEI0021 (C2 Type), PDB code: 5zo9:
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 (C2 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 (C2 Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:29.9 occ:1.00 O1B A:ADP600 1.9 30.1 1.0 OG1 A:THR112 2.3 36.6 1.0 O A:HOH704 2.7 33.3 1.0 PB A:ADP600 3.1 42.4 1.0 CB A:THR112 3.1 41.9 1.0 O3B A:ADP600 3.4 36.1 1.0 O1A A:ADP600 3.7 32.7 1.0 CG2 A:THR112 4.1 39.3 1.0 O3A A:ADP600 4.2 37.6 1.0 N A:THR112 4.2 47.3 1.0 PA A:ADP600 4.3 44.0 1.0 CA A:THR112 4.3 47.5 1.0 O2B A:ADP600 4.3 36.3 1.0 O2A A:ADP600 4.4 40.9 1.0 OD2 A:ASP265 4.5 47.7 1.0 O A:SER232 4.5 51.4 1.0 O A:HOH706 4.5 38.1 1.0 OD1 A:ASP265 4.9 51.0 1.0 CB A:SER232 5.0 40.1 0.5

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:31.8 occ:1.00 O2B B:ADP600 2.0 32.2 1.0 OG1 B:THR112 2.2 45.0 1.0 O B:HOH701 2.4 38.0 1.0 CB B:THR112 3.1 47.9 1.0 PB B:ADP600 3.2 41.6 1.0 O3B B:ADP600 3.4 37.9 1.0 O2A B:ADP600 3.6 29.2 1.0 CG2 B:THR112 4.0 44.9 1.0 O3A B:ADP600 4.2 38.0 1.0 PA B:ADP600 4.2 40.7 1.0 N B:THR112 4.2 52.4 1.0 CA B:THR112 4.2 50.9 1.0 O1A B:ADP600 4.3 38.7 1.0 O1B B:ADP600 4.4 39.4 1.0 OD2 B:ASP265 4.4 55.4 1.0 O B:SER232 4.5 46.6 1.0 OD1 B:ASP265 4.8 68.3 1.0 CB B:SER232 5.0 37.6 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