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Sodium in PDB 5v69: Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4

Protein crystallography data

The structure of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4, PDB code: 5v69 was solved by B.A.Bailey-Elkin, B.L.Mark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.55
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.207, 110.965, 185.898, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.6

Other elements in 5v69:

The structure of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4 (pdb code 5v69). 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 Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4, PDB code: 5v69:

Sodium binding site 1 out of 1 in 5v69

Go back to Sodium Binding Sites List in 5v69
Sodium binding site 1 out of 1 in the Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Middle East Respiratory Syndrome Coronavirus Papain-Like Protease Bound to Ubiquitin Variant Me.4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1903

b:32.1
occ:1.00
O A:HOH2051 2.4 31.0 1.0
O A:HOH2079 2.8 35.4 1.0
NZ A:LYS1568 4.0 25.7 1.0
CD A:LYS1568 4.1 28.8 1.0
CE A:LYS1568 4.1 29.1 1.0
CD1 A:TYR1565 4.1 30.7 1.0
CA A:GLY1518 4.3 31.7 1.0
CG A:TYR1565 4.5 24.6 1.0
CE1 A:TYR1565 4.5 29.3 1.0
N A:GLY1518 4.7 38.2 1.0
CG A:TYR1536 4.7 31.4 1.0
CB A:PHE1515 4.8 25.2 1.0
CB A:TYR1565 4.8 27.7 1.0
CB A:TYR1536 4.9 25.0 1.0
CG A:LYS1568 4.9 27.1 1.0
CD1 A:PHE1515 4.9 22.9 1.0
CA A:TYR1565 4.9 28.4 1.0
CD2 A:TYR1536 5.0 28.7 1.0
CD1 A:TYR1536 5.0 27.4 1.0

Reference:

W.Zhang, B.A.Bailey-Elkin, R.C.M.Knaap, B.Khare, T.J.Dalebout, G.G.Johnson, P.B.Van Kasteren, N.J.Mcleish, J.Gu, W.He, M.Kikkert, B.L.Mark, S.S.Sidhu. Potent and Selective Inhibition of Pathogenic Viruses By Engineered Ubiquitin Variants. Plos Pathog. V. 13 06372 2017.
ISSN: ESSN 1553-7374
PubMed: 28542609
DOI: 10.1371/JOURNAL.PPAT.1006372
Page generated: Tue Dec 15 11:44:23 2020

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