Zinc in PDB 4o6i: 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain

The structure of 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain, PDB code: 4o6i was solved by B.R.West, K.M.Hastie, E.O.Saphire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.95 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	89.962, 89.962, 145.941, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 22.8

The structure of 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain (pdb code 4o6i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain, PDB code: 4o6i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:54.0 occ:1.00 OE2 A:GLU392 2.0 51.7 1.0 NE2 A:HIS502 2.0 61.6 1.0 SG A:CYS518 2.2 49.7 1.0 SG A:CYS499 2.3 48.1 1.0 CD A:GLU392 2.9 48.9 1.0 CD2 A:HIS502 3.0 55.7 1.0 HB2 A:CYS518 3.1 66.6 1.0 CE1 A:HIS502 3.1 55.2 1.0 HD2 A:HIS502 3.1 66.9 1.0 OE1 A:GLU392 3.1 51.7 1.0 CB A:CYS518 3.2 55.5 1.0 HB3 A:CYS499 3.2 65.6 1.0 CB A:CYS499 3.3 54.7 1.0 HE1 A:HIS502 3.3 66.2 1.0 HE2 A:HIS405 3.4 68.6 1.0 HA A:CYS518 3.4 65.4 1.0 HB2 A:CYS499 3.5 65.6 1.0 HE1 A:TYR407 3.6 66.9 1.0 HE1 A:HIS405 3.7 67.5 1.0 H A:ALA519 3.8 65.0 1.0 CA A:CYS518 3.8 54.5 1.0 HH A:TYR407 4.0 67.5 1.0 NE2 A:HIS405 4.0 57.2 1.0 HB3 A:CYS518 4.0 66.6 1.0 H A:LEU520 4.0 56.6 1.0 HB2 A:MET501 4.1 71.3 1.0 CG A:HIS502 4.1 61.9 1.0 ND1 A:HIS502 4.1 61.6 1.0 CE1 A:HIS405 4.2 56.3 1.0 N A:ALA519 4.3 54.2 1.0 CG A:GLU392 4.3 56.6 1.0 HB3 A:LEU520 4.4 59.7 1.0 C A:CYS518 4.4 52.8 1.0 HG3 A:GLU392 4.5 67.9 1.0 CE1 A:TYR407 4.5 55.7 1.0 H A:MET501 4.7 71.7 1.0 HG2 A:GLU392 4.7 67.9 1.0 CA A:CYS499 4.7 52.0 1.0 HH2 A:TRP492 4.8 64.6 1.0 OH A:TYR407 4.8 56.3 1.0 HG2 A:MET521 4.8 54.1 1.0 N A:LEU520 4.9 47.2 1.0 H A:MET521 4.9 61.3 1.0 HD1 A:HIS502 4.9 73.9 1.0

Zinc binding site 2 out of 2 in the 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:54.0 occ:1.00 OE2 B:GLU392 2.0 51.9 1.0 NE2 B:HIS502 2.0 60.6 1.0 SG B:CYS518 2.2 52.4 1.0 SG B:CYS499 2.3 55.0 1.0 CD B:GLU392 2.9 51.1 1.0 CD2 B:HIS502 3.0 57.7 1.0 HB2 B:CYS518 3.0 70.9 1.0 CE1 B:HIS502 3.1 57.3 1.0 OE1 B:GLU392 3.1 54.2 1.0 HD2 B:HIS502 3.1 69.2 1.0 CB B:CYS518 3.2 59.1 1.0 HB3 B:CYS499 3.2 64.3 1.0 HE1 B:HIS502 3.3 68.7 1.0 CB B:CYS499 3.3 53.6 1.0 HE2 B:HIS405 3.3 69.1 1.0 HA B:CYS518 3.4 69.8 1.0 HB2 B:CYS499 3.5 64.3 1.0 HE1 B:TYR407 3.5 64.5 1.0 HE1 B:HIS405 3.7 70.0 1.0 CA B:CYS518 3.8 58.1 1.0 H B:ALA519 3.9 67.8 1.0 HB2 B:MET501 3.9 71.7 1.0 NE2 B:HIS405 4.0 57.6 1.0 HB3 B:CYS518 4.0 70.9 1.0 HH B:TYR407 4.0 66.4 1.0 CG B:HIS502 4.1 61.7 1.0 ND1 B:HIS502 4.1 61.0 1.0 H B:LEU520 4.2 65.2 1.0 CE1 B:HIS405 4.2 58.3 1.0 CG B:GLU392 4.3 54.3 1.0 N B:ALA519 4.4 56.5 1.0 CE1 B:TYR407 4.5 53.8 1.0 HG3 B:GLU392 4.5 65.1 1.0 C B:CYS518 4.5 53.7 1.0 HB3 B:LEU520 4.5 59.6 1.0 H B:MET501 4.6 64.2 1.0 HG2 B:GLU392 4.7 65.1 1.0 CA B:CYS499 4.7 51.5 1.0 HH2 B:TRP492 4.8 68.2 1.0 HE2 B:MET426 4.8 71.5 1.0 OH B:TYR407 4.8 55.3 1.0 HG2 B:MET521 4.8 57.8 1.0 CB B:MET501 4.9 59.8 1.0 HD1 B:HIS502 4.9 73.2 1.0 HG3 B:MET501 5.0 72.0 1.0 HA B:CYS499 5.0 61.8 1.0

B.R.West, K.M.Hastie, E.O.Saphire. Structure of the Lcmv Nucleoprotein Provides A Template For Understanding Arenavirus Replication and Immunosuppression. Acta Crystallogr.,Sect.D V. 70 1764 2014.
ISSN: ISSN 0907-4449
PubMed: 24914986
DOI: 10.1107/S1399004714007883