Zinc in PDB 3m85: Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site

The structure of Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site, PDB code: 3m85 was solved by S.Hartung, K.-P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 3.00
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	138.020, 138.020, 262.250, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 27.8

The binding sites of Zinc atom in the Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site (pdb code 3m85). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site, PDB code: 3m85:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn180 b:62.8 occ:1.00 SG A:CYS143 2.2 67.4 1.0 SG A:CYS159 2.3 69.8 1.0 SG A:CYS162 2.4 77.5 1.0 SG A:CYS146 2.5 68.4 1.0 CB A:CYS143 2.8 64.8 1.0 CB A:CYS162 2.9 69.8 1.0 CB A:CYS159 3.2 67.8 1.0 CB A:CYS146 3.5 64.8 1.0 N A:CYS146 3.7 65.5 1.0 CA A:CYS162 4.0 65.0 1.0 CA A:CYS146 4.1 61.6 1.0 N A:CYS162 4.2 67.3 1.0 ND2 A:ASN145 4.2 76.9 1.0 CA A:CYS143 4.3 57.3 1.0 CB A:ASN145 4.4 68.4 1.0 CB A:ARG164 4.6 71.1 1.0 CA A:CYS159 4.6 68.1 1.0 C A:CYS162 4.7 74.6 1.0 C A:CYS146 4.7 62.2 1.0 CG A:ASN145 4.7 75.7 1.0 C A:ASN145 4.7 64.1 1.0 N A:LYS147 4.8 61.3 1.0 C A:CYS143 4.9 61.8 1.0 CB A:THR148 4.9 60.5 1.0 CA A:ASN145 4.9 65.9 1.0 N A:ASN145 5.0 65.4 1.0 N A:THR148 5.0 49.5 1.0

Zinc binding site 2 out of 3 in the Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn180 b:0.1 occ:1.00 SG B:CYS146 2.1 98.0 1.0 CB B:CYS159 2.5 0.0 1.0 CB B:CYS162 2.6 0.8 1.0 SG B:CYS159 2.7 0.5 1.0 CB B:CYS146 2.7 0.4 1.0 SG B:CYS162 3.5 0.6 1.0 N B:CYS162 3.6 0.7 1.0 CA B:CYS162 3.7 0.8 1.0 CA B:CYS159 4.0 0.1 1.0 CB B:CYS143 4.0 0.5 1.0 SG B:CYS143 4.2 0.1 1.0 CA B:CYS146 4.2 0.1 1.0 OD1 B:ASN145 4.2 0.2 1.0 N B:GLY163 4.2 0.2 1.0 CE B:MET150 4.4 0.7 1.0 C B:CYS162 4.4 0.7 1.0 ND2 B:ASN145 4.5 0.9 1.0 N B:CYS159 4.5 0.1 1.0 N B:CYS146 4.5 0.1 1.0 C B:CYS159 4.6 0.4 1.0 CG B:ASN145 4.7 0.9 1.0 C B:GLU161 4.7 0.8 1.0 N B:ARG164 4.9 0.9 1.0 CB B:ARG164 4.9 0.1 1.0 O B:CYS159 5.0 0.4 1.0

Zinc binding site 3 out of 3 in the Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Archaeoglobus Fulgidus Exosome Y70A with Rna Bound to the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn180 b:81.4 occ:1.00 SG C:CYS146 2.4 83.2 1.0 SG C:CYS159 2.5 85.3 1.0 CB C:CYS162 2.7 89.2 1.0 SG C:CYS143 2.7 85.1 1.0 O C:ASN145 2.8 81.8 1.0 CB C:CYS146 2.9 76.8 1.0 CB C:CYS143 3.1 79.7 1.0 SG C:CYS162 3.5 95.9 1.0 CB C:CYS159 3.7 81.5 1.0 CA C:CYS162 3.9 84.6 1.0 C C:ASN145 3.9 77.8 1.0 N C:CYS162 4.0 92.7 1.0 CA C:CYS146 4.0 79.0 1.0 OD1 C:ASN145 4.2 77.8 1.0 N C:LYS147 4.3 84.7 1.0 OG1 C:THR148 4.3 80.3 1.0 C C:CYS146 4.4 84.1 1.0 N C:CYS146 4.5 73.7 1.0 CA C:CYS143 4.6 79.7 1.0 N C:THR148 4.6 78.0 1.0 C C:CYS162 4.9 84.5 1.0 N C:GLY163 4.9 85.6 1.0

S.Hartung, T.Niederberger, M.Hartung, A.Tresch, K.-P.Hopfner. Quantitative Analysis of Processive Rna Degradation By the Archaeal Rna Exosome Nucleic Acids Res. V. 38 5166 2010.
ISSN: ISSN 0305-1048
PubMed: 20392821
DOI: 10.1093/NAR/GKQ238