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Sodium in PDB 4ovz: X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases

Enzymatic activity of X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases

All present enzymatic activity of X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases, PDB code: 4ovz was solved by Y.M.Baez-Santos, A.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.75 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.772, 73.508, 98.269, 90.00, 103.66, 90.00
R / Rfree (%) 18.2 / 24.3

Other elements in 4ovz:

The structure of X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases (pdb code 4ovz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases, PDB code: 4ovz:

Sodium binding site 1 out of 1 in 4ovz

Go back to Sodium Binding Sites List in 4ovz
Sodium binding site 1 out of 1 in the X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na903

b:31.8
occ:1.00
HH B:TYR311 2.4 26.1 1.0
HG1 B:THR313 2.5 35.3 1.0
O B:LYS218 2.6 18.4 1.0
OH B:TYR311 2.6 21.8 1.0
OG1 B:THR313 2.7 29.4 1.0
O B:LEU235 2.7 20.1 1.0
HA B:LYS218 2.9 29.2 1.0
HD12 B:ILE315 2.9 36.5 1.0
HB B:THR313 3.0 31.4 1.0
HB3 B:LYS218 3.0 24.3 1.0
C B:LYS218 3.3 20.6 1.0
HE2 B:TYR311 3.3 21.6 1.0
CB B:THR313 3.3 26.1 1.0
CA B:LYS218 3.4 24.3 1.0
HD1 B:TYR234 3.5 42.7 1.0
CB B:LYS218 3.6 20.3 1.0
CZ B:TYR311 3.6 19.1 1.0
HG2 B:LYS218 3.7 20.9 1.0
HB3 B:LEU235 3.8 24.4 1.0
H B:LEU235 3.8 29.6 1.0
HA B:THR313 3.8 33.5 1.0
CD1 B:ILE315 3.8 30.5 1.0
CE2 B:TYR311 3.9 18.0 1.0
C B:LEU235 3.9 26.7 1.0
HD11 B:ILE315 4.0 36.5 1.0
HB2 B:TYR234 4.1 34.2 1.0
CG B:LYS218 4.2 17.4 1.0
CA B:THR313 4.2 27.9 1.0
N B:LEU235 4.3 24.7 1.0
CD1 B:TYR234 4.3 35.6 1.0
HD13 B:ILE315 4.4 36.5 1.0
H B:THR314 4.4 37.9 1.0
CA B:LEU235 4.5 24.1 1.0
HB2 B:LYS218 4.5 24.3 1.0
HG21 B:THR313 4.5 37.3 1.0
HB B:ILE315 4.5 51.1 1.0
CB B:LEU235 4.5 20.3 1.0
CG2 B:THR313 4.6 31.1 1.0
HG13 B:ILE315 4.6 46.7 1.0
N B:THR219 4.6 15.2 1.0
HA B:THR219 4.6 24.0 1.0
HA B:VAL236 4.7 28.8 1.0
HG3 B:LYS218 4.8 20.9 1.0
CG1 B:ILE315 4.8 38.9 1.0
H B:ILE315 4.8 51.6 1.0
N B:LYS218 4.8 26.2 1.0
CE1 B:TYR311 4.9 15.0 1.0
HD23 B:LEU235 4.9 20.5 1.0
HE1 B:TYR234 4.9 46.6 1.0
CB B:TYR234 4.9 28.5 1.0
HG B:LEU235 5.0 19.9 1.0
N B:VAL236 5.0 20.4 1.0
O B:LEU217 5.0 19.7 1.0

Reference:

Y.M.Baez-Santos, S.J.Barraza, M.W.Wilson, M.P.Agius, A.M.Mielech, N.M.Davis, S.C.Baker, S.D.Larsen, A.D.Mesecar. X-Ray Structural and Biological Evaluation of A Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases. J.Med.Chem. V. 57 2393 2014.
ISSN: ISSN 1520-4804
PubMed: 24568342
DOI: 10.1021/JM401712T
Page generated: Tue Dec 15 06:57:20 2020

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