Zinc in PDB 8eho: Prrsv-1 PLP2 Domain Bound to Ubiquitin

The structure of Prrsv-1 PLP2 Domain Bound to Ubiquitin, PDB code: 8eho 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)	43.94 / 2.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.686, 159.492, 147.325, 90, 90, 90
R / Rfree (%)	21.2 / 24.7

The binding sites of Zinc atom in the Prrsv-1 PLP2 Domain Bound to Ubiquitin (pdb code 8eho). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Prrsv-1 PLP2 Domain Bound to Ubiquitin, PDB code: 8eho:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Prrsv-1 PLP2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prrsv-1 PLP2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:45.1 occ:1.00 SG A:CYS516 2.3 45.7 1.0 SG A:CYS525 2.3 49.0 1.0 SG A:CYS485 2.3 44.8 1.0 SG A:CYS521 2.3 45.9 1.0 CB A:CYS521 3.2 47.8 1.0 CB A:CYS525 3.2 50.7 1.0 CB A:CYS516 3.3 46.1 1.0 CB A:CYS485 3.3 43.7 1.0 CA A:CYS516 3.8 46.3 1.0 CA A:CYS485 4.0 42.5 1.0 NH1 A:ARG483 4.2 49.6 1.0 CD A:PRO486 4.4 42.0 1.0 ND2 A:ASN487 4.5 43.9 1.0 CA A:CYS521 4.6 48.6 1.0 CA A:CYS525 4.7 51.6 1.0 C A:CYS485 4.7 41.9 1.0 N A:CYS516 4.7 47.0 1.0 N A:PRO486 4.8 42.0 1.0 C A:CYS516 4.8 45.2 1.0 O A:CYS516 4.9 43.9 1.0

Zinc binding site 2 out of 3 in the Prrsv-1 PLP2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prrsv-1 PLP2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:41.5 occ:1.00 SG C:CYS516 2.3 41.6 1.0 SG C:CYS485 2.3 42.5 1.0 SG C:CYS521 2.3 41.5 1.0 SG C:CYS525 2.3 44.6 1.0 CB C:CYS521 3.2 41.4 1.0 CB C:CYS525 3.2 45.0 1.0 CB C:CYS516 3.3 40.6 1.0 CB C:CYS485 3.3 42.5 1.0 CA C:CYS516 3.8 39.6 1.0 CA C:CYS485 4.0 42.2 1.0 NH1 C:ARG483 4.2 56.1 1.0 CD C:PRO486 4.4 41.1 1.0 ND2 C:ASN487 4.5 42.2 1.0 C C:CYS485 4.7 41.8 1.0 CA C:CYS525 4.7 45.5 1.0 CA C:CYS521 4.7 41.6 1.0 N C:CYS516 4.7 40.1 1.0 N C:PRO486 4.8 41.0 1.0 C C:CYS516 4.8 38.1 1.0 O C:CYS516 4.9 37.5 1.0

Zinc binding site 3 out of 3 in the Prrsv-1 PLP2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prrsv-1 PLP2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:40.1 occ:1.00 SG E:CYS485 2.3 39.8 1.0 SG E:CYS525 2.3 42.9 1.0 SG E:CYS521 2.3 41.4 1.0 SG E:CYS516 2.3 40.5 1.0 CB E:CYS521 3.2 43.0 1.0 CB E:CYS525 3.2 43.7 1.0 CB E:CYS485 3.3 39.0 1.0 CB E:CYS516 3.3 41.2 1.0 CA E:CYS516 3.8 42.4 1.0 CA E:CYS485 3.9 38.4 1.0 NH2 E:ARG483 4.2 54.2 1.0 CD E:PRO486 4.4 37.0 1.0 ND2 E:ASN487 4.5 36.3 1.0 C E:CYS485 4.6 38.0 1.0 CA E:CYS521 4.7 43.9 1.0 CA E:CYS525 4.7 44.3 1.0 N E:CYS516 4.7 44.3 1.0 N E:PRO486 4.8 37.3 1.0 C E:CYS516 4.9 42.0 1.0 O E:CYS516 4.9 41.7 1.0

B.A.Bailey-Elkin, R.C.M.Knaap, A.De Silva, I.M.Boekhoud, S.Mous, N.Van Vught, M.Khajehpour, E.Van Den Born, M.Kikkert, B.L.Mark. Demonstrating the Importance of Porcine Reproductive and Respiratory Syndrome Virus Papain-Like Protease 2 Deubiquitinating Activity in Viral Replication By Structure-Guided Mutagenesis Plos Pathog. 2023.
ISSN: ESSN 1553-7374