Magnesium in PDB 4o6h: 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain

The structure of 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain, PDB code: 4o6h 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)	47.26 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.856, 94.403, 145.124, 90.00, 102.30, 90.00
R / Rfree (%)	22.7 / 26.1

The structure of 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	8 atoms

The binding sites of Magnesium atom in the 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain (pdb code 4o6h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain, PDB code: 4o6h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 2.8A 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 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:70.1 occ:1.00 OD2 C:ASP522 2.4 66.1 1.0 OD2 C:ASP382 2.4 60.1 1.0 OE2 C:GLU384 2.8 64.5 1.0 OD1 C:ASP382 2.9 66.5 1.0 CG C:ASP382 3.0 64.5 1.0 O C:ILE383 3.4 72.0 1.0 CG C:ASP522 3.4 66.6 1.0 CD C:GLU384 3.7 64.9 1.0 HB2 C:ASP522 3.9 72.7 1.0 HB3 C:ASP522 3.9 72.7 1.0 HA C:ALA519 4.0 64.7 1.0 HB3 C:HIS517 4.0 85.6 1.0 CB C:ASP522 4.0 60.6 1.0 OE1 C:GLU384 4.0 68.1 1.0 H C:ILE383 4.0 66.3 1.0 HH22 C:ARG485 4.2 99.9 1.0 HZ C:PHE526 4.3 81.8 1.0 C C:ILE383 4.3 64.7 1.0 OD1 C:ASP522 4.4 70.6 1.0 HE2 C:PHE526 4.4 79.1 1.0 CB C:ASP382 4.5 56.1 1.0 N C:ILE383 4.6 55.3 1.0 HG2 C:GLU384 4.7 74.2 1.0 HA C:GLU384 4.7 73.6 1.0 HB3 C:ASP382 4.8 67.3 1.0 CG C:GLU384 4.8 61.9 1.0 NH2 C:ARG485 4.8 83.2 1.0 HH21 C:ARG485 4.9 99.9 1.0 CA C:ALA519 4.9 53.9 1.0 CB C:HIS517 4.9 71.4 1.0 CZ C:PHE526 4.9 68.2 1.0 HB2 C:ASP382 4.9 67.3 1.0 O C:CYS518 4.9 65.1 1.0 CE2 C:PHE526 5.0 65.9 1.0

Magnesium binding site 2 out of 4 in the 2.8A 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 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:65.3 occ:1.00 OD2 D:ASP382 2.3 54.8 1.0 OE2 D:GLU384 2.5 57.1 1.0 OD2 D:ASP522 2.9 67.4 1.0 OD1 D:ASP382 3.0 62.1 1.0 CG D:ASP382 3.0 59.7 1.0 O D:ILE383 3.1 54.4 1.0 CD D:GLU384 3.5 62.6 1.0 CG D:ASP522 3.8 59.5 1.0 H D:ILE383 3.9 64.2 1.0 HA D:ALA519 4.0 63.1 1.0 OE1 D:GLU384 4.0 63.3 1.0 HB3 D:HIS517 4.0 72.5 1.0 HB2 D:ASP522 4.1 65.4 1.0 C D:ILE383 4.1 50.5 1.0 HB3 D:ASP522 4.2 65.4 1.0 CB D:ASP522 4.3 54.5 1.0 HG2 D:GLU384 4.3 66.2 1.0 N D:ILE383 4.4 53.5 1.0 CB D:ASP382 4.5 53.2 1.0 HA D:GLU384 4.5 66.4 1.0 CG D:GLU384 4.6 55.1 1.0 HZ D:PHE526 4.6 84.4 1.0 HE2 D:PHE526 4.7 76.8 1.0 HB3 D:ASP382 4.8 63.8 1.0 OD1 D:ASP522 4.8 62.3 1.0 CA D:ALA519 4.9 52.6 1.0 CA D:ILE383 4.9 47.4 1.0 HH22 D:ARG485 5.0 0.3 1.0 CB D:HIS517 5.0 60.5 1.0

Magnesium binding site 3 out of 4 in the 2.8A 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 3 of 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:78.9 occ:1.00 OD2 G:ASP522 2.6 80.5 1.0 OD2 G:ASP382 2.8 73.3 1.0 OE2 G:GLU384 2.8 87.2 1.0 OD1 G:ASP382 3.3 84.7 1.0 CG G:ASP382 3.4 76.7 1.0 O G:ILE383 3.5 86.6 1.0 CD G:GLU384 3.6 92.5 1.0 CG G:ASP522 3.7 79.7 1.0 HB3 G:HIS517 3.8 0.5 1.0 OE1 G:GLU384 3.8 95.2 1.0 HB2 G:ASP522 4.2 91.5 1.0 HB3 G:ASP522 4.2 91.5 1.0 HA G:ALA519 4.3 80.8 1.0 CB G:ASP522 4.3 76.2 1.0 H G:ILE383 4.5 87.7 1.0 HZ G:PHE526 4.5 95.0 1.0 C G:ILE383 4.6 77.2 1.0 OD1 G:ASP522 4.6 76.0 1.0 HH22 G:ARG485 4.6 0.2 1.0 HA G:GLU384 4.6 0.7 1.0 CB G:HIS517 4.7 94.5 1.0 HG2 G:GLU384 4.7 99.8 1.0 HE2 G:PHE526 4.7 87.2 1.0 CG G:GLU384 4.8 83.1 1.0 ND1 G:HIS517 4.9 0.9 1.0 HB2 G:HIS517 4.9 0.5 1.0 CB G:ASP382 4.9 70.0 1.0 N G:ILE383 5.0 73.1 1.0

Magnesium binding site 4 out of 4 in the 2.8A 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 4 of 2.8A Crystal Structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:85.4 occ:1.00 OD2 H:ASP522 2.5 90.0 1.0 OD2 H:ASP382 2.8 82.3 1.0 OD1 H:ASP382 3.0 84.0 1.0 OE2 H:GLU384 3.3 87.1 1.0 CG H:ASP382 3.3 82.4 1.0 CG H:ASP522 3.7 85.2 1.0 O H:ILE383 3.7 88.5 1.0 CD H:GLU384 4.0 88.8 1.0 OE1 H:GLU384 4.1 90.1 1.0 HB3 H:ASP522 4.2 93.6 1.0 HB3 H:HIS517 4.2 0.2 1.0 HZ H:PHE526 4.3 0.4 1.0 H H:ILE383 4.3 93.8 1.0 HB2 H:ASP522 4.3 93.6 1.0 CB H:ASP522 4.3 78.0 1.0 HH21 H:ARG485 4.4 0.3 1.0 HA H:ALA519 4.5 91.0 1.0 HE2 H:PHE526 4.5 98.4 1.0 HH22 H:ARG485 4.5 0.3 1.0 OD1 H:ASP522 4.6 84.6 1.0 C H:ILE383 4.7 84.7 1.0 HD1 H:HIS517 4.7 0.9 1.0 HA H:GLU384 4.8 0.9 1.0 NH2 H:ARG485 4.8 0.6 1.0 CB H:ASP382 4.8 77.4 1.0 N H:ILE383 4.9 78.1 1.0 CZ H:PHE526 5.0 83.7 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