Chlorine in PDB 2c38: Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna

The structure of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna, PDB code: 2c38 was solved by E.Lorentzen, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.78 / 3.1
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	206.260, 213.610, 434.040, 90.00, 90.00, 90.00
R / Rfree (%)	27.6 / 28.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna (pdb code 2c38). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna, PDB code: 2c38:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:25.1 occ:1.00 OG B:SER138 3.0 56.4 1.0 N B:SER138 3.2 56.5 1.0 N B:GLY137 3.2 57.4 1.0 O3' B:AMP404 3.3 89.2 1.0 NH2 B:ARG139 3.3 54.8 1.0 C5' B:AMP404 3.5 89.7 1.0 NH2 B:ARG99 3.5 64.3 1.0 O1P B:AMP404 3.7 86.8 1.0 NE B:ARG139 3.7 54.6 1.0 CA B:GLY137 3.8 57.0 1.0 C3' B:AMP404 3.9 90.6 1.0 CB B:SER138 3.9 55.9 1.0 C B:GLY137 3.9 56.7 1.0 O5' B:AMP404 4.0 88.0 1.0 NH1 B:ARG99 4.0 65.2 1.0 CZ B:ARG139 4.0 54.4 1.0 C B:ALA136 4.0 57.5 1.0 CA B:SER138 4.1 56.1 1.0 N B:ARG139 4.1 55.3 1.0 CA B:ALA136 4.1 57.7 1.0 C4' B:AMP404 4.2 90.5 1.0 CZ B:ARG99 4.2 63.8 1.0 P B:AMP404 4.4 86.7 1.0 C B:SER138 4.7 55.8 1.0 OD2 B:ASP182 4.8 63.2 1.0 O2P B:AMP404 4.9 86.3 1.0 CB B:ARG139 4.9 54.9 1.0 N B:ALA136 5.0 57.8 1.0 OH B:TYR81 5.0 56.6 1.0 CD B:ARG139 5.0 54.5 1.0

Chlorine binding site 2 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:21.0 occ:1.00 NH2 D:ARG139 3.1 54.8 1.0 OG D:SER138 3.1 56.6 1.0 N D:SER138 3.2 56.5 1.0 N D:GLY137 3.3 57.4 1.0 NH2 D:ARG99 3.4 64.3 1.0 NE D:ARG139 3.5 54.6 1.0 CZ D:ARG139 3.8 54.5 1.0 CA D:GLY137 3.8 57.0 1.0 NH1 D:ARG99 3.9 65.3 1.0 CB D:SER138 3.9 56.0 1.0 N D:ARG139 4.0 55.2 1.0 C D:GLY137 4.0 56.7 1.0 CA D:SER138 4.1 56.1 1.0 CZ D:ARG99 4.1 63.9 1.0 C D:ALA136 4.2 57.5 1.0 CA D:ALA136 4.3 57.6 1.0 C D:SER138 4.6 55.8 1.0 CB D:ARG139 4.7 54.9 1.0 CD D:ARG139 4.8 54.5 1.0 OD2 D:ASP182 4.9 63.2 1.0 CG D:ARG139 4.9 54.9 1.0 OH D:TYR81 4.9 56.4 1.0 CA D:ARG139 5.0 54.8 1.0

Chlorine binding site 3 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl301 b:15.7 occ:1.00 N F:GLY137 3.0 57.4 1.0 NH2 F:ARG139 3.1 54.9 1.0 N F:SER138 3.1 56.4 1.0 C5' F:AMP404 3.4 91.6 1.0 OG F:SER138 3.4 56.5 1.0 O5' F:AMP404 3.4 90.0 1.0 NE F:ARG139 3.4 54.7 1.0 CA F:GLY137 3.5 57.0 1.0 CZ F:ARG139 3.7 54.4 1.0 C F:GLY137 3.7 56.7 1.0 NH2 F:ARG99 3.9 64.3 1.0 N F:ARG139 4.0 55.3 1.0 C F:ALA136 4.0 57.5 1.0 CA F:SER138 4.1 56.1 1.0 O1P F:AMP404 4.1 88.5 1.0 CB F:SER138 4.1 56.0 1.0 O3' F:AMP404 4.2 92.0 1.0 CA F:ALA136 4.2 57.6 1.0 NH1 F:ARG99 4.3 65.2 1.0 P F:AMP404 4.4 88.8 1.0 C4' F:AMP404 4.5 92.5 1.0 CZ F:ARG99 4.6 63.9 1.0 C3' F:AMP404 4.6 92.8 1.0 C F:SER138 4.6 55.8 1.0 CD F:ARG139 4.6 54.5 1.0 CB F:ARG139 4.7 54.8 1.0 OD2 F:ASP182 4.7 63.2 1.0 CG F:ARG139 4.8 54.8 1.0 O F:GLY137 4.9 56.6 1.0 CA F:ARG139 5.0 54.8 1.0

Chlorine binding site 4 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:23.2 occ:1.00 O5' H:AMP404 3.0 75.2 1.0 N H:SER138 3.1 56.4 1.0 N H:GLY137 3.1 57.4 1.0 OG H:SER138 3.2 56.6 1.0 NH2 H:ARG139 3.2 54.8 1.0 C5' H:AMP404 3.4 77.0 1.0 NE H:ARG139 3.5 54.6 1.0 CA H:GLY137 3.6 57.0 1.0 NH2 H:ARG99 3.7 64.2 1.0 O1P H:AMP404 3.7 74.5 1.0 C H:GLY137 3.8 56.7 1.0 CZ H:ARG139 3.8 54.4 1.0 N H:ARG139 3.9 55.3 1.0 CB H:SER138 3.9 56.0 1.0 P H:AMP404 3.9 74.1 1.0 O3' H:AMP404 3.9 77.1 1.0 CA H:SER138 4.0 56.1 1.0 C H:ALA136 4.0 57.5 1.0 NH1 H:ARG99 4.2 65.3 1.0 CA H:ALA136 4.2 57.6 1.0 C3' H:AMP404 4.3 77.8 1.0 C4' H:AMP404 4.4 77.8 1.0 CZ H:ARG99 4.4 63.9 1.0 C H:SER138 4.5 55.8 1.0 O2P H:AMP404 4.5 74.1 1.0 CB H:ARG139 4.7 54.8 1.0 CD H:ARG139 4.7 54.4 1.0 CG H:ARG139 4.8 54.8 1.0 OD2 H:ASP182 4.9 63.1 1.0 CA H:ARG139 4.9 54.8 1.0 O H:GLY137 4.9 56.6 1.0 OH H:TYR81 4.9 56.5 1.0

Chlorine binding site 5 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl301 b:19.4 occ:1.00 NH2 J:ARG139 3.0 54.9 1.0 OG J:SER138 3.2 56.5 1.0 O5' J:AMP404 3.3 88.7 1.0 C5' J:AMP404 3.3 90.1 1.0 NH2 J:ARG99 3.3 64.4 1.0 N J:SER138 3.3 56.4 1.0 NE J:ARG139 3.4 54.6 1.0 N J:GLY137 3.5 57.4 1.0 CZ J:ARG139 3.7 54.4 1.0 NH1 J:ARG99 3.8 65.3 1.0 CB J:SER138 4.0 56.0 1.0 N J:ARG139 4.0 55.3 1.0 CA J:GLY137 4.0 57.0 1.0 O1P J:AMP404 4.0 88.3 1.0 CZ J:ARG99 4.0 63.9 1.0 C J:GLY137 4.1 56.7 1.0 CA J:SER138 4.2 56.0 1.0 P J:AMP404 4.2 88.2 1.0 O3' J:AMP404 4.3 90.8 1.0 C J:ALA136 4.4 57.5 1.0 C4' J:AMP404 4.4 90.9 1.0 C3' J:AMP404 4.5 91.3 1.0 CA J:ALA136 4.5 57.6 1.0 C J:SER138 4.6 55.8 1.0 CB J:ARG139 4.6 54.9 1.0 CD J:ARG139 4.7 54.5 1.0 O2P J:AMP404 4.8 88.4 1.0 OH J:TYR81 4.8 56.5 1.0 CG J:ARG139 4.8 54.8 1.0 CA J:ARG139 4.9 54.8 1.0 NH1 J:ARG139 5.0 53.6 1.0

Chlorine binding site 6 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl301 b:44.1 occ:1.00 NH2 L:ARG139 3.2 54.8 1.0 OG L:SER138 3.2 56.6 1.0 NH2 L:ARG99 3.2 64.3 1.0 N L:SER138 3.5 56.4 1.0 N L:GLY137 3.5 57.4 1.0 NE L:ARG139 3.7 54.6 1.0 NH1 L:ARG99 3.7 65.2 1.0 CZ L:ARG139 3.9 54.4 1.0 CZ L:ARG99 3.9 63.9 1.0 CB L:SER138 4.0 55.9 1.0 CA L:GLY137 4.1 57.1 1.0 N L:ARG139 4.2 55.4 1.0 C L:GLY137 4.2 56.7 1.0 CA L:SER138 4.3 56.0 1.0 C L:ALA136 4.3 57.4 1.0 CA L:ALA136 4.3 57.6 1.0 C L:SER138 4.8 55.8 1.0 CB L:ARG139 4.9 54.9 1.0 OH L:TYR81 4.9 56.4 1.0 OD2 L:ASP182 4.9 63.3 1.0 CD L:ARG139 5.0 54.5 1.0

Chlorine binding site 7 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl301 b:13.0 occ:1.00 N N:SER138 3.0 56.4 1.0 OG N:SER138 3.1 56.7 1.0 N N:GLY137 3.1 57.3 1.0 C5' N:AMP404 3.2 86.9 1.0 NH2 N:ARG139 3.2 54.9 1.0 NE N:ARG139 3.4 54.6 1.0 O5' N:AMP404 3.5 86.6 1.0 CA N:GLY137 3.6 57.0 1.0 O3' N:AMP404 3.6 86.2 1.0 NH2 N:ARG99 3.7 64.3 1.0 C N:GLY137 3.7 56.7 1.0 N N:ARG139 3.8 55.3 1.0 CZ N:ARG139 3.8 54.5 1.0 CB N:SER138 3.9 56.0 1.0 CA N:SER138 3.9 56.1 1.0 C3' N:AMP404 4.0 86.6 1.0 C N:ALA136 4.0 57.4 1.0 C4' N:AMP404 4.1 87.1 1.0 NH1 N:ARG99 4.3 65.2 1.0 O1P N:AMP404 4.3 87.2 1.0 CA N:ALA136 4.3 57.6 1.0 C N:SER138 4.4 55.8 1.0 CZ N:ARG99 4.4 63.8 1.0 P N:AMP404 4.5 86.7 1.0 CB N:ARG139 4.5 54.9 1.0 CD N:ARG139 4.6 54.5 1.0 CG N:ARG139 4.7 54.9 1.0 CA N:ARG139 4.8 54.8 1.0 O N:GLY137 4.9 56.7 1.0 OH N:TYR81 4.9 56.4 1.0 OD2 N:ASP182 4.9 63.2 1.0

Chlorine binding site 8 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ P:Cl301 b:28.0 occ:1.00 N P:GLY137 3.1 57.4 1.0 OG P:SER138 3.2 56.5 1.0 N P:SER138 3.3 56.5 1.0 NH2 P:ARG139 3.4 54.8 1.0 NH2 P:ARG99 3.5 64.3 1.0 CA P:GLY137 3.8 57.0 1.0 C P:ALA136 3.9 57.5 1.0 CA P:ALA136 3.9 57.6 1.0 NE P:ARG139 3.9 54.6 1.0 NH1 P:ARG99 4.0 65.3 1.0 CB P:SER138 4.0 56.0 1.0 C P:GLY137 4.1 56.7 1.0 CZ P:ARG139 4.1 54.4 1.0 CA P:SER138 4.2 56.1 1.0 CZ P:ARG99 4.2 63.9 1.0 N P:ARG139 4.3 55.2 1.0 OD2 P:ASP182 4.6 63.2 1.0 N P:ALA136 4.8 57.7 1.0 C P:SER138 4.8 55.7 1.0 CB P:ALA136 4.9 57.8 1.0 O P:ALA136 5.0 57.3 1.0

Chlorine binding site 9 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ R:Cl301 b:22.1 occ:1.00 NH2 R:ARG139 3.1 54.9 1.0 OG R:SER138 3.3 56.5 1.0 N R:SER138 3.3 56.3 1.0 NE R:ARG139 3.4 54.7 1.0 N R:GLY137 3.4 57.5 1.0 NH2 R:ARG99 3.5 64.3 1.0 CZ R:ARG139 3.7 54.4 1.0 CA R:GLY137 3.8 57.0 1.0 NH1 R:ARG99 3.9 65.2 1.0 N R:ARG139 3.9 55.3 1.0 C R:GLY137 4.0 56.6 1.0 CB R:SER138 4.0 56.0 1.0 CA R:SER138 4.2 56.0 1.0 CZ R:ARG99 4.2 63.9 1.0 C R:ALA136 4.3 57.6 1.0 CA R:ALA136 4.4 57.7 1.0 CB R:ARG139 4.6 54.8 1.0 C R:SER138 4.6 55.7 1.0 CD R:ARG139 4.6 54.5 1.0 CG R:ARG139 4.8 54.8 1.0 OH R:TYR81 4.9 56.4 1.0 CA R:ARG139 4.9 54.8 1.0 OD2 R:ASP182 4.9 63.3 1.0 NH1 R:ARG139 5.0 53.4 1.0

Chlorine binding site 10 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Rnase pH Core of the Archaeal Exosome in Complex with A5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ T:Cl301 b:10.9 occ:1.00 OG T:SER138 3.1 56.6 1.0 N T:SER138 3.2 56.5 1.0 NH2 T:ARG139 3.2 54.8 1.0 N T:GLY137 3.3 57.4 1.0 NH2 T:ARG99 3.5 64.4 1.0 NE T:ARG139 3.5 54.8 1.0 CA T:GLY137 3.8 57.0 1.0 CZ T:ARG139 3.8 54.4 1.0 C T:GLY137 3.9 56.8 1.0 CB T:SER138 3.9 56.0 1.0 N T:ARG139 3.9 55.2 1.0 NH1 T:ARG99 4.0 65.3 1.0 CA T:SER138 4.0 56.1 1.0 C T:ALA136 4.2 57.5 1.0 CZ T:ARG99 4.2 63.9 1.0 CA T:ALA136 4.3 57.7 1.0 C T:SER138 4.5 55.8 1.0 CB T:ARG139 4.6 54.7 1.0 CD T:ARG139 4.7 54.6 1.0 CG T:ARG139 4.8 54.8 1.0 OH T:TYR81 4.9 56.6 1.0 CA T:ARG139 4.9 54.7 1.0 OD2 T:ASP182 4.9 63.1 1.0

E.Lorentzen, E.Conti. Structural Basis of 3' End Rna Recognition and Exoribonucleolytic Cleavage By An Exosome Rnase pH Core. Mol.Cell V. 20 473 2005.
ISSN: ISSN 1097-2765
PubMed: 16285928
DOI: 10.1016/J.MOLCEL.2005.10.020