Manganese in PDB 4gv9: Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min

The structure of Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min, PDB code: 4gv9 was solved by X.Jiang, Q.Huang, W.Wang, H.Dong, H.Ly, Y.Liang, C.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.89 / 2.46
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.780, 44.780, 221.740, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 30.5

The structure of Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min (pdb code 4gv9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min, PDB code: 4gv9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:55.9 occ:1.00 OD1 A:ASP389 2.2 42.0 1.0 OP1 E:C11 2.4 78.3 1.0 O3' E:G10 2.5 75.8 1.0 P E:C11 3.0 75.4 1.0 CG A:ASP389 3.2 42.1 1.0 OD2 A:ASP389 3.7 42.9 1.0 MN E:MN103 3.7 78.2 1.0 C3' E:G10 3.8 74.8 1.0 O A:GLN462 3.9 53.3 1.0 OD2 A:ASP466 3.9 58.9 1.0 O A:ILE390 4.0 48.0 1.0 O5' E:C11 4.1 73.7 1.0 C5' E:C11 4.1 73.3 1.0 C4' E:G10 4.1 75.9 1.0 OP2 E:C11 4.2 73.6 1.0 O2' E:G10 4.4 75.5 1.0 N A:ILE390 4.5 44.6 1.0 C5' E:G10 4.5 76.8 1.0 OD1 A:ASP466 4.5 60.0 1.0 CB A:ASP389 4.5 42.0 1.0 CG A:ASP466 4.6 59.7 1.0 C2' E:G10 4.7 74.2 1.0 CA A:ASP389 4.8 42.8 1.0 O A:GLY463 4.9 56.0 1.0

Manganese binding site 2 out of 3 in the Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn102 b:81.5 occ:1.00 N7 E:G9 3.4 86.2 1.0 N4 F:C1 3.4 0.0 1.0 OP2 E:G9 3.9 86.8 1.0 O1B E:GTP8 4.0 0.7 1.0 C8 E:G9 4.1 85.2 1.0 C5 E:G9 4.3 85.3 1.0 O6 E:G9 4.5 88.7 1.0 C4 F:C1 4.5 0.9 1.0 C2' E:GTP8 4.5 0.2 1.0 C3' E:GTP8 4.6 0.9 1.0 C6 E:G9 4.7 86.2 1.0 N3 F:C1 4.8 0.4 1.0 O1A E:GTP8 4.9 0.1 1.0 O6 E:G10 5.0 80.4 1.0

Manganese binding site 3 out of 3 in the Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Lassa Nucleoprotein C-Terminal Domain in Complex with Triphosphated Dsrna Soaking For 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn103 b:78.2 occ:1.00 OP1 E:C11 1.7 78.3 1.0 OE2 A:GLU391 2.1 51.5 1.0 OD2 A:ASP533 2.3 50.4 1.0 OD2 A:ASP389 2.5 42.9 1.0 P E:C11 2.9 75.4 1.0 CD A:GLU391 3.1 51.6 1.0 CG A:ASP389 3.4 42.1 1.0 CG A:ASP533 3.5 50.7 1.0 OE1 A:GLU391 3.5 52.3 1.0 OP2 E:C11 3.5 73.6 1.0 O5' E:C11 3.6 73.7 1.0 OD1 A:ASP389 3.7 42.0 1.0 MN E:MN101 3.7 55.9 1.0 O A:ILE390 3.7 48.0 1.0 ND1 A:HIS528 4.1 64.8 1.0 C5' E:C11 4.2 73.3 1.0 CB A:ASP533 4.2 49.3 1.0 O3' E:G10 4.2 75.8 1.0 CB A:HIS528 4.3 61.5 1.0 NH2 A:ARG492 4.3 67.2 1.0 OD1 A:ASP533 4.4 51.7 1.0 CG A:GLU391 4.5 50.2 1.0 CG A:HIS528 4.6 64.2 1.0 C A:ILE390 4.7 47.1 1.0 O A:CYS529 4.8 51.7 1.0 CB A:ASP389 4.8 42.0 1.0 CA A:ALA530 4.9 48.4 1.0 C A:CYS529 4.9 50.9 1.0

X.Jiang, Q.Huang, W.Wang, H.Dong, H.Ly, Y.Liang, C.Dong. Structures of Arenaviral Nucleoproteins with Triphosphate Dsrna Reveal A Unique Mechanism of Immune Suppression. J.Biol.Chem. V. 288 16949 2013.
ISSN: ISSN 0021-9258
PubMed: 23615902
DOI: 10.1074/JBC.M112.420521