Sodium in PDB 5v5g: Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4

All present enzymatic activity of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4:
2.7.7.48; 3.4.19.12;

The structure of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4, PDB code: 5v5g 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)	47.17 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.312, 64.312, 277.578, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.9

The binding sites of Sodium atom in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4 (pdb code 5v5g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4, PDB code: 5v5g:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4


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.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:33.7 occ:1.00 H A:MET1 2.5 53.0 1.0 H A:GLY0 2.7 56.6 1.0 HE1 A:PHE161 3.0 48.5 1.0 HG2 A:MET1 3.1 65.2 1.0 CA A:GLY-2 3.2 44.4 1.0 HA3 A:GLY0 3.2 57.4 1.0 N A:GLY0 3.3 47.2 1.0 C A:GLY-2 3.3 42.3 1.0 N A:MET1 3.3 44.2 1.0 CA A:GLY0 3.6 47.9 1.0 HD1 A:PHE161 3.6 53.5 1.0 O A:GLY-2 3.7 42.0 1.0 N A:PRO-1 3.7 45.0 1.0 CE1 A:PHE161 3.8 40.4 1.0 HB2 A:MET1 3.8 55.3 1.0 HD2 A:PRO-1 3.8 51.2 1.0 C A:GLY0 4.0 42.4 1.0 CG A:MET1 4.0 54.3 1.0 CD1 A:PHE161 4.1 44.6 1.0 CB A:MET1 4.2 46.1 1.0 CD A:PRO-1 4.3 42.7 1.0 C A:PRO-1 4.3 39.7 1.0 CA A:MET1 4.4 44.6 1.0 HG3 A:MET1 4.4 65.2 1.0 HA2 A:GLY0 4.5 57.4 1.0 CA A:PRO-1 4.6 42.8 1.0 HD3 A:PRO-1 4.6 51.2 1.0 H A:ASP2 4.8 53.2 1.0 HA A:MET1 4.9 53.5 1.0 CZ A:PHE161 5.0 42.2 1.0

Sodium binding site 2 out of 3 in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:34.0 occ:1.00 HE C:ARG63 2.2 43.4 1.0 HA C:TYR60 2.9 40.4 1.0 HH21 C:ARG63 3.0 49.8 1.0 HD1 C:TYR60 3.0 37.0 1.0 NE C:ARG63 3.0 36.2 1.0 HB2 C:TYR60 3.4 37.6 1.0 NH2 C:ARG63 3.7 41.5 1.0 CA C:TYR60 3.7 33.6 1.0 HB2 C:ARG63 3.8 39.7 1.0 HD2 C:ARG63 3.8 44.2 1.0 CZ C:ARG63 3.8 35.6 1.0 CD1 C:TYR60 3.9 30.8 1.0 N C:TYR60 4.0 31.3 1.0 CB C:TYR60 4.0 31.4 1.0 CD C:ARG63 4.0 36.8 1.0 HB3 C:ARG63 4.2 39.7 1.0 O C:HIS59 4.2 34.4 1.0 HB3 C:HIS59 4.2 43.3 1.0 C C:HIS59 4.2 34.2 1.0 H C:TYR60 4.3 37.5 1.0 CB C:ARG63 4.4 33.1 1.0 CG C:TYR60 4.4 31.3 1.0 HB2 C:HIS59 4.4 43.3 1.0 HH22 C:ARG63 4.5 49.8 1.0 CB C:HIS59 4.7 36.1 1.0 HD3 C:ARG63 4.8 44.2 1.0 CG C:ARG63 4.8 34.8 1.0 HB3 C:TYR60 4.8 37.6 1.0 CE1 C:TYR60 4.9 31.3 1.0 HE1 C:TYR60 4.9 37.5 1.0 C C:TYR60 5.0 29.9 1.0

Sodium binding site 3 out of 3 in the Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Otu Protease of Crimean Congo Hemorrhagic Fever Virus Bound to Ubiquitin Variant Cc.4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:35.1 occ:1.00 H3 C:GLY-2 2.3 58.6 1.0 H C:MET1 2.5 59.7 1.0 HE1 C:PHE161 2.8 55.1 1.0 H C:GLY0 2.8 54.8 1.0 N C:GLY-2 3.1 48.9 1.0 HA3 C:GLY-2 3.2 47.0 1.0 HA3 C:GLY0 3.3 57.4 1.0 N C:MET1 3.3 49.8 1.0 H2 C:GLY-2 3.4 58.6 1.0 CA C:GLY-2 3.4 39.1 1.0 N C:GLY0 3.4 45.7 1.0 C C:GLY-2 3.4 43.5 1.0 HB2 C:MET1 3.4 57.4 1.0 O C:GLY-2 3.6 43.1 1.0 CE1 C:PHE161 3.7 45.9 1.0 CA C:GLY0 3.7 47.9 1.0 HD1 C:PHE161 3.7 54.2 1.0 H1 C:GLY-2 3.8 58.6 1.0 N C:PRO-1 3.9 50.4 1.0 C C:GLY0 4.0 44.6 1.0 CD1 C:PHE161 4.1 45.1 1.0 CB C:MET1 4.1 47.8 1.0 HD2 C:PRO-1 4.2 50.7 1.0 HB3 C:MET1 4.2 57.4 1.0 CA C:MET1 4.3 48.0 1.0 HA2 C:GLY-2 4.3 47.0 1.0 C C:PRO-1 4.4 46.6 1.0 CD C:PRO-1 4.6 42.2 1.0 HA2 C:GLY0 4.6 57.4 1.0 CA C:PRO-1 4.8 47.7 1.0 HA C:MET1 4.8 57.7 1.0 CZ C:PHE161 4.8 44.0 1.0 H C:ASP2 4.8 46.1 1.0 HE21 C:GLN160 4.9 73.0 1.0 HZ C:PHE161 4.9 52.8 1.0

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