Sodium in PDB 5v5h: Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2

Enzymatic activity of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2

All present enzymatic activity of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2:
2.7.7.48; 3.4.19.12;

Protein crystallography data

The structure of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2, PDB code: 5v5h was solved by B.Khare, B.L.Mark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	43.43 / 1.50
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	101.398, 33.599, 71.248, 90.00, 96.51, 90.00
*R / R_free (%)*	15.6 / 17.8

Other elements in 5v5h:

The structure of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2 (pdb code 5v5h). 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 Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2, PDB code: 5v5h:

Sodium binding site 1 out of 1 in 5v5h

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Sodium Binding Sites List in 5v5h

Sodium binding site 1 out of 1 in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.2 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na201 b:27.2 occ:1.00	OE1	A:GLU78	2.7	19.9	1.0
	O	A:HOH360	2.8	23.2	1.0
	HA	A:LEU103	2.9	20.2	1.0
	HB2	A:GLU78	2.9	23.6	1.0
	HB2	A:SER106	2.9	20.8	1.0
	HE1	A:PHE133	3.0	21.2	1.0
	HE22	A:GLN16	3.0	34.4	1.0
	O	A:THR102	3.0	16.0	1.0
	HB3	A:GLU78	3.1	23.6	1.0
	HB	A:THR102	3.4	17.4	1.0
	CB	A:GLU78	3.4	19.7	1.0
	HB3	A:SER106	3.5	20.8	1.0
	C	A:THR102	3.5	17.5	1.0
	CD	A:GLU78	3.6	22.2	1.0
	NE2	A:GLN16	3.6	28.7	1.0
	CB	A:SER106	3.6	17.3	1.0
	CE1	A:PHE133	3.6	17.6	1.0
	HH12	B:ARG42	3.7	24.6	1.0
	CA	A:LEU103	3.7	16.9	1.0
	N	A:LEU103	3.9	15.9	1.0
	NH1	B:ARG42	3.9	20.5	1.0
	HG	A:SER106	3.9	25.9	1.0
	HZ	A:PHE133	3.9	19.1	1.0
	HE21	A:GLN16	4.0	34.4	1.0
	HH11	B:ARG42	4.1	24.6	1.0
	CG	A:GLU78	4.1	21.7	1.0
	CZ	A:PHE133	4.1	15.9	1.0
	H	A:GLU78	4.2	25.9	1.0
	H	A:SER106	4.2	19.1	1.0
	CD	A:GLN16	4.2	26.9	1.0
	OE1	A:GLN16	4.3	23.6	1.0
	OG	A:SER106	4.3	21.6	1.0
	CB	A:THR102	4.3	14.4	1.0
	HD12	A:LEU103	4.3	23.9	1.0
	CZ	B:ARG42	4.4	20.5	1.0
	O	A:HOH373	4.4	19.4	1.0
	HH22	B:ARG42	4.5	26.4	1.0
	H	A:LEU103	4.5	19.1	1.0
	HB2	A:LEU103	4.5	21.7	1.0
	OE2	A:GLU78	4.5	19.7	1.0
	CA	A:THR102	4.5	14.0	1.0
	CD1	A:PHE133	4.5	17.9	1.0
	OE1	A:GLU76	4.6	25.5	1.0
	C	A:LEU103	4.6	18.7	1.0
	HG2	A:GLU78	4.6	26.0	1.0
	O	A:LEU103	4.6	17.2	1.0
	HD1	A:PHE133	4.6	21.5	1.0
	NH2	B:ARG42	4.6	22.0	1.0
	HD13	A:LEU103	4.7	23.9	1.0
	CA	A:GLU78	4.7	23.1	1.0
	CB	A:LEU103	4.7	18.1	1.0
	HG3	A:GLU78	4.8	26.0	1.0
	N	A:GLU78	4.8	21.6	1.0
	CA	A:SER106	4.8	16.4	1.0
	N	A:SER106	4.8	15.9	1.0
	OG1	A:THR102	4.9	17.7	1.0
	HA	A:THR102	4.9	16.8	1.0
	CD1	A:LEU103	4.9	19.9	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: Mon Aug 18 02:43:52 2025

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