Zinc in PDB 4a2x: Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna

The structure of Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna, PDB code: 4a2x was solved by E.Kowalinski, T.Lunardi, A.A.Mccarthy, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.01 / 4.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	216.020, 90.640, 62.960, 90.00, 90.38, 90.00
R / Rfree (%)	20.4 / 24.8

The binding sites of Zinc atom in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna (pdb code 4a2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna, PDB code: 4a2x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:55.5 occ:1.00 SG A:CYS815 1.9 58.8 1.0 SG A:CYS866 2.1 53.4 1.0 SG A:CYS871 2.3 59.8 1.0 SG A:CYS812 2.5 52.6 1.0 CB A:CYS815 3.0 63.7 1.0 CB A:CYS866 3.1 51.5 1.0 CB A:CYS871 3.2 63.5 1.0 CB A:CYS812 3.2 50.9 1.0 N A:CYS815 3.8 62.2 1.0 CA A:CYS815 3.9 64.1 1.0 CB A:ASN868 4.3 63.7 1.0 C A:CYS815 4.5 62.9 1.0 CA A:CYS866 4.5 49.9 1.0 NE1 A:TRP875 4.6 46.0 1.0 CB A:ALA817 4.6 55.9 1.0 CA A:CYS871 4.6 67.1 1.0 CB A:HIS873 4.6 54.5 1.0 CA A:CYS812 4.7 50.0 1.0 CZ2 A:TRP875 4.7 45.3 1.0 N A:LYS816 4.8 60.2 1.0 N A:ALA817 4.9 56.8 1.0 C A:LYS814 4.9 64.9 1.0 ND2 A:ASN868 4.9 69.2 1.0 N A:GLN872 5.0 61.9 1.0 CE2 A:TRP875 5.0 44.6 1.0 CB A:LYS814 5.0 63.0 1.0 N A:HIS873 5.0 56.4 1.0

Zinc binding site 2 out of 4 in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:76.9 occ:1.00 SG B:CYS815 1.8 81.0 1.0 SG B:CYS871 2.3 85.6 1.0 SG B:CYS812 2.4 69.4 1.0 SG B:CYS866 2.4 73.5 1.0 CB B:CYS815 2.8 88.9 1.0 CB B:CYS812 3.1 65.1 1.0 CB B:CYS871 3.2 92.7 1.0 CB B:CYS866 3.4 71.9 1.0 N B:CYS815 3.5 84.9 1.0 CA B:CYS815 3.6 88.2 1.0 C B:CYS815 4.2 84.9 1.0 CB B:ASN868 4.5 91.3 1.0 N B:LYS816 4.5 79.4 1.0 CA B:CYS812 4.6 61.8 1.0 CB B:ALA817 4.6 73.3 1.0 CA B:CYS871 4.6 0.2 1.0 C B:LYS814 4.6 89.0 1.0 CB B:HIS873 4.7 76.3 1.0 N B:ALA817 4.7 73.6 1.0 NE1 B:TRP875 4.7 59.1 1.0 CB B:LYS814 4.8 87.8 1.0 CA B:CYS866 4.8 69.8 1.0 ND2 B:ASN868 4.9 98.9 1.0 CZ2 B:TRP875 4.9 56.8 1.0 O B:CYS815 4.9 88.1 1.0

Zinc binding site 3 out of 4 in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:53.6 occ:1.00 SG C:CYS815 2.0 54.5 1.0 SG C:CYS871 2.1 58.6 1.0 SG C:CYS812 2.2 51.4 1.0 SG C:CYS866 2.3 53.1 1.0 CB C:CYS815 3.0 58.1 1.0 CB C:CYS812 3.1 49.1 1.0 CB C:CYS871 3.1 62.0 1.0 CB C:CYS866 3.1 53.5 1.0 N C:CYS815 3.6 57.5 1.0 CA C:CYS815 3.8 58.0 1.0 CB C:HIS873 4.4 57.5 1.0 C C:CYS815 4.5 56.2 1.0 NE1 C:TRP875 4.5 48.7 1.0 CA C:CYS871 4.5 66.8 1.0 CB C:ASN868 4.6 60.8 1.0 CA C:CYS812 4.6 48.6 1.0 CA C:CYS866 4.6 53.6 1.0 CB C:LYS814 4.7 61.5 1.0 C C:LYS814 4.7 60.2 1.0 N C:LYS816 4.7 54.4 1.0 CZ2 C:TRP875 4.8 46.8 1.0 N C:HIS873 4.8 61.0 1.0 CB C:ALA817 4.8 51.4 1.0 N C:GLN872 4.9 65.2 1.0 C C:CYS871 4.9 66.9 1.0 N C:ALA817 5.0 51.4 1.0 CE2 C:TRP875 5.0 47.3 1.0

Zinc binding site 4 out of 4 in the Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Duck Rig-I C-Terminal Domain (Ctd) with 14-Mer Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1000 b:76.2 occ:1.00 SG D:CYS815 2.1 77.0 1.0 SG D:CYS812 2.2 73.8 1.0 SG D:CYS871 2.3 83.7 1.0 SG D:CYS866 2.4 74.5 1.0 CB D:CYS812 3.0 69.8 1.0 CB D:CYS815 3.1 82.0 1.0 CB D:CYS866 3.2 75.3 1.0 CB D:CYS871 3.2 87.2 1.0 N D:CYS815 3.6 81.6 1.0 CA D:CYS815 3.8 81.8 1.0 CB D:HIS873 4.4 82.0 1.0 C D:CYS815 4.4 78.6 1.0 NE1 D:TRP875 4.5 68.9 1.0 CA D:CYS812 4.5 68.6 1.0 CB D:ASN868 4.6 83.0 1.0 CA D:CYS866 4.6 74.3 1.0 CA D:CYS871 4.7 93.2 1.0 N D:LYS816 4.7 75.9 1.0 C D:LYS814 4.7 85.2 1.0 CB D:LYS814 4.7 87.4 1.0 CZ2 D:TRP875 4.7 65.0 1.0 CB D:ALA817 4.8 69.9 1.0 N D:ALA817 4.9 70.7 1.0 N D:HIS873 4.9 85.9 1.0 CE2 D:TRP875 4.9 66.2 1.0 C D:CYS812 4.9 72.0 1.0

E.Kowalinski, T.Lunardi, A.A.Mccarthy, J.Louber, J.Brunel, B.Grigorov, D.Gerlier, S.Cusack. Structural Basis For the Activation of Innate Immune Pattern-Recognition Receptor Rig-I By Viral Rna. Cell V. 147 423 2011.
ISSN: ISSN 1097-4172
PubMed: 22000019
DOI: 10.1016/J.CELL.2011.09.039