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

Protein crystallography data

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

Other elements in 5zo9:

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

Sodium Binding Sites:

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 5zo9

Go back to Sodium Binding Sites List in 5zo9
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 5zo9

Go back to Sodium Binding Sites List in 5zo9
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

Reference:

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
Page generated: Tue Dec 15 11:53:09 2020

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