Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 2.0A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain, PDB code: 4o6i:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:70.0 occ:1.00 OD1 A:ASP382 2.1 61.9 1.0 OD2 A:ASP522 2.1 67.6 1.0 OE2 A:GLU384 2.1 73.2 1.0 CG A:ASP382 3.0 56.4 1.0 O A:HOH770 3.1 77.6 1.0 CG A:ASP522 3.1 66.3 1.0 OD2 A:ASP382 3.2 63.7 1.0 HB2 A:ASP522 3.3 71.0 1.0 CD A:GLU384 3.4 63.9 1.0 HA A:ALA519 3.4 57.7 1.0 HB3 A:ASP522 3.5 71.0 1.0 CB A:ASP522 3.6 59.2 1.0 HB3 A:HIS517 3.7 80.4 1.0 O A:ILE383 3.7 53.3 1.0 HG2 A:GLU384 3.8 70.9 1.0 HD2 A:HIS517 3.8 94.1 1.0 CG A:GLU384 4.2 59.1 1.0 OD1 A:ASP522 4.2 65.0 1.0 O A:CYS518 4.2 54.2 1.0 OE1 A:GLU384 4.3 64.5 1.0 O A:HOH771 4.3 63.7 1.0 CA A:ALA519 4.3 48.1 1.0 CB A:ASP382 4.4 54.7 1.0 HB3 A:ASP382 4.4 65.7 1.0 HE2 A:PHE526 4.4 79.0 1.0 C A:ILE383 4.5 56.7 1.0 C A:CYS518 4.5 52.8 1.0 H A:ILE383 4.6 62.6 1.0 N A:ALA519 4.6 54.2 1.0 CB A:HIS517 4.6 67.0 1.0 HG3 A:GLU384 4.6 70.9 1.0 CD2 A:HIS517 4.6 78.4 1.0 HZ A:PHE526 4.7 82.6 1.0 HB2 A:ALA519 4.8 64.7 1.0 N A:ILE383 4.9 52.2 1.0 HB2 A:ASP382 4.9 65.7 1.0 HH12 A:ARG485 4.9 0.3 1.0 HA A:GLU384 4.9 67.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:69.6 occ:1.00 O B:HOH771 2.1 78.8 1.0 OD2 B:ASP522 2.1 71.2 1.0 OE2 B:GLU384 2.1 68.3 1.0 OD1 B:ASP382 2.1 67.0 1.0 CG B:ASP382 3.1 63.4 1.0 CG B:ASP522 3.2 63.2 1.0 CD B:GLU384 3.3 68.9 1.0 OD2 B:ASP382 3.4 73.1 1.0 HA B:ALA519 3.4 61.5 1.0 HB2 B:ASP522 3.5 71.2 1.0 O B:ILE383 3.5 60.9 1.0 HG2 B:GLU384 3.7 71.8 1.0 HB3 B:HIS517 3.7 78.7 1.0 CB B:ASP522 3.7 59.4 1.0 HB3 B:ASP522 3.8 71.2 1.0 CG B:GLU384 4.1 59.8 1.0 OE1 B:GLU384 4.3 58.9 1.0 OD1 B:ASP522 4.3 64.7 1.0 CA B:ALA519 4.3 51.3 1.0 O B:CYS518 4.4 54.3 1.0 C B:ILE383 4.4 59.9 1.0 CB B:ASP382 4.4 59.3 1.0 HB3 B:ASP382 4.4 71.2 1.0 H B:ILE383 4.4 64.5 1.0 HD2 B:HIS517 4.5 90.0 1.0 N B:ALA519 4.6 56.5 1.0 HG3 B:GLU384 4.6 71.8 1.0 C B:CYS518 4.6 53.7 1.0 CB B:HIS517 4.7 65.5 1.0 HB2 B:ALA519 4.7 67.6 1.0 N B:ILE383 4.7 53.8 1.0 HA B:GLU384 4.8 66.8 1.0 HE2 B:PHE526 4.8 80.9 1.0 HZ B:PHE526 4.9 80.0 1.0 HB2 B:ASP382 5.0 71.2 1.0 CB B:ALA519 5.0 56.3 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