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Chlorine in PDB 2c37: Rnase pH Core of the Archaeal Exosome in Complex with U8 Rna

Protein crystallography data

The structure of Rnase pH Core of the Archaeal Exosome in Complex with U8 Rna, PDB code: 2c37 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) 93.25 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 207.020, 212.940, 433.090, 90.00, 90.00, 90.00
R / Rfree (%) 26.6 / 28.2

Other elements in 2c37:

The structure of Rnase pH Core of the Archaeal Exosome in Complex with U8 Rna also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

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 U8 Rna (pdb code 2c37). 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 U8 Rna, PDB code: 2c37:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 2c37

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Chlorine binding site 1 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:55.4
occ:1.00
NE B:ARG139 3.3 48.6 1.0
OG B:SER138 3.3 48.8 1.0
N B:SER138 3.5 48.0 1.0
N B:ARG139 3.5 47.6 1.0
N B:GLY137 3.6 48.4 1.0
NH2 B:ARG139 3.7 47.5 1.0
NH1 B:ARG99 3.8 63.0 1.0
CZ B:ARG139 3.9 47.9 1.0
CA B:GLY137 4.0 48.2 1.0
C B:GLY137 4.0 48.3 1.0
CB B:ARG139 4.0 47.2 1.0
CG B:ARG139 4.2 47.5 1.0
CA B:SER138 4.3 48.0 1.0
CD B:ARG139 4.3 47.6 1.0
CB B:SER138 4.4 47.9 1.0
CA B:ARG139 4.4 47.3 1.0
C B:SER138 4.4 48.0 1.0
O5' B:U5P404 4.6 0.2 1.0
C B:ALA136 4.6 48.7 1.0
O2P B:U5P404 4.8 0.4 1.0
CZ B:ARG99 4.8 61.4 1.0
NH2 B:ARG99 4.9 61.5 1.0
OH B:TYR81 4.9 51.1 1.0
CA B:ALA136 4.9 49.0 1.0
O B:GLY137 4.9 48.2 1.0

Chlorine binding site 2 out of 12 in 2c37

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Chlorine binding site 2 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:76.4
occ:1.00
OG D:SER138 3.3 48.7 1.0
NH1 D:ARG99 3.5 62.9 1.0
N D:SER138 3.7 48.0 1.0
NE D:ARG139 3.8 48.2 1.0
N D:GLY137 3.8 48.5 1.0
NH2 D:ARG139 3.8 47.5 1.0
N D:ARG139 4.0 47.4 1.0
CZ D:ARG139 4.2 47.8 1.0
CA D:GLY137 4.3 48.3 1.0
C D:GLY137 4.4 48.2 1.0
CB D:SER138 4.4 48.0 1.0
CA D:SER138 4.5 48.0 1.0
CZ D:ARG99 4.5 61.5 1.0
CB D:ARG139 4.5 47.2 1.0
NH2 D:ARG99 4.6 61.5 1.0
C D:ALA136 4.6 48.7 1.0
CA D:ALA136 4.7 49.0 1.0
C D:SER138 4.7 48.0 1.0
CG D:ARG139 4.8 47.6 1.0
OD2 D:ASP182 4.8 59.4 1.0
CA D:ARG139 4.9 47.2 1.0
CD D:ARG139 4.9 47.3 1.0
OH D:TYR81 4.9 51.1 1.0

Chlorine binding site 3 out of 12 in 2c37

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Chlorine binding site 3 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:36.8
occ:1.00
OG F:SER138 3.3 48.6 1.0
N F:GLY137 3.4 48.4 1.0
N F:SER138 3.4 48.2 1.0
NE F:ARG139 3.6 48.3 1.0
N F:ARG139 3.6 47.3 1.0
CA F:GLY137 3.8 48.2 1.0
NH1 F:ARG99 3.9 62.9 1.0
NH2 F:ARG139 3.9 47.6 1.0
C F:GLY137 3.9 48.2 1.0
CZ F:ARG139 4.2 47.9 1.0
CA F:SER138 4.2 48.1 1.0
CB F:ARG139 4.3 47.0 1.0
CB F:SER138 4.3 47.9 1.0
C F:ALA136 4.4 48.6 1.0
CG F:ARG139 4.4 47.5 1.0
C F:SER138 4.4 47.9 1.0
O2P F:U5P404 4.5 0.3 1.0
CD F:ARG139 4.6 47.5 1.0
CA F:ARG139 4.6 47.1 1.0
CA F:ALA136 4.6 48.9 1.0
O3' F:U5P404 4.7 0.0 1.0
C5' F:U5P404 4.7 0.2 1.0
NH2 F:ARG99 4.9 61.4 1.0
CZ F:ARG99 4.9 61.4 1.0
O F:GLY137 4.9 48.3 1.0
OD2 F:ASP182 5.0 59.6 1.0
OH F:TYR81 5.0 51.0 1.0

Chlorine binding site 4 out of 12 in 2c37

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Chlorine binding site 4 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:66.8
occ:1.00
NH1 H:ARG99 3.4 62.8 1.0
OG H:SER138 3.4 48.8 1.0
NE H:ARG139 3.6 48.4 1.0
NH2 H:ARG139 3.6 47.6 1.0
N H:SER138 3.8 48.0 1.0
N H:GLY137 3.8 48.5 1.0
N H:ARG139 4.0 47.7 1.0
CZ H:ARG139 4.0 47.9 1.0
CA H:GLY137 4.3 48.3 1.0
CZ H:ARG99 4.4 61.4 1.0
C H:GLY137 4.4 48.3 1.0
CB H:ARG139 4.5 47.1 1.0
NH2 H:ARG99 4.5 61.6 1.0
CB H:SER138 4.6 47.8 1.0
CA H:SER138 4.6 48.0 1.0
CG H:ARG139 4.6 47.4 1.0
CD H:ARG139 4.7 47.5 1.0
C H:ALA136 4.7 48.7 1.0
C H:SER138 4.8 48.0 1.0
OD2 H:ASP182 4.8 59.5 1.0
CA H:ALA136 4.9 49.0 1.0
CA H:ARG139 4.9 47.2 1.0
OH H:TYR81 4.9 51.1 1.0

Chlorine binding site 5 out of 12 in 2c37

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Chlorine binding site 5 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl301

b:50.7
occ:1.00
OG J:SER138 3.2 48.7 1.0
NE J:ARG139 3.4 48.5 1.0
N J:SER138 3.4 48.1 1.0
N J:ARG139 3.5 47.5 1.0
N J:GLY137 3.6 48.4 1.0
NH2 J:ARG139 3.7 47.5 1.0
NH1 J:ARG99 3.9 63.0 1.0
C J:GLY137 3.9 48.3 1.0
CA J:GLY137 4.0 48.3 1.0
CZ J:ARG139 4.0 47.9 1.0
CB J:ARG139 4.0 47.0 1.0
CA J:SER138 4.1 48.1 1.0
CG J:ARG139 4.2 47.5 1.0
CB J:SER138 4.2 48.0 1.0
C J:SER138 4.3 47.9 1.0
CA J:ARG139 4.3 47.2 1.0
CD J:ARG139 4.4 47.6 1.0
C J:ALA136 4.6 48.7 1.0
OH J:TYR81 4.8 51.1 1.0
CZ J:ARG99 4.9 61.4 1.0
CA J:ALA136 4.9 48.9 1.0
NH2 J:ARG99 4.9 61.5 1.0
O J:GLY137 4.9 48.1 1.0

Chlorine binding site 6 out of 12 in 2c37

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Chlorine binding site 6 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl301

b:76.9
occ:1.00
N L:ARG139 3.0 47.4 1.0
OG L:SER138 3.0 48.6 1.0
N L:SER138 3.2 47.9 1.0
NE L:ARG139 3.5 48.5 1.0
N L:GLY137 3.7 48.4 1.0
CB L:ARG139 3.7 47.1 1.0
C L:GLY137 3.7 48.1 1.0
CA L:SER138 3.8 47.9 1.0
C L:SER138 3.8 48.0 1.0
CA L:GLY137 3.9 48.2 1.0
CA L:ARG139 3.9 47.2 1.0
CB L:SER138 3.9 47.7 1.0
NH1 L:ARG99 4.0 62.8 1.0
CG L:ARG139 4.0 47.4 1.0
NH2 L:ARG139 4.1 47.5 1.0
CZ L:ARG139 4.2 48.0 1.0
CD L:ARG139 4.4 47.5 1.0
OH L:TYR81 4.5 51.1 1.0
O L:GLY137 4.6 48.1 1.0
C L:ALA136 4.6 48.7 1.0
NH2 L:ARG99 4.8 61.5 1.0
CZ L:ARG99 4.9 61.3 1.0
CD1 L:LEU103 4.9 45.2 1.0
CA L:ALA136 5.0 49.0 1.0

Chlorine binding site 7 out of 12 in 2c37

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Chlorine binding site 7 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl301

b:59.2
occ:1.00
OG N:SER138 3.3 49.0 1.0
N N:SER138 3.3 48.0 1.0
N N:GLY137 3.4 48.5 1.0
NE N:ARG139 3.5 48.5 1.0
N N:ARG139 3.6 47.8 1.0
CA N:GLY137 3.8 48.4 1.0
NH2 N:ARG139 3.8 47.4 1.0
C N:GLY137 3.9 48.3 1.0
O3' N:RP5405 3.9 68.9 1.0
NH1 N:ARG99 3.9 62.9 1.0
O1X N:RP5405 4.0 68.5 1.0
O5' N:RP5405 4.1 67.2 1.0
CZ N:ARG139 4.1 47.9 1.0
CA N:SER138 4.2 48.0 1.0
CB N:ARG139 4.2 47.1 1.0
C5' N:RP5405 4.3 67.7 1.0
CB N:SER138 4.3 47.9 1.0
CG N:ARG139 4.3 47.5 1.0
C N:ALA136 4.4 48.7 1.0
C N:SER138 4.4 48.1 1.0
CD N:ARG139 4.5 47.6 1.0
CA N:ARG139 4.5 47.3 1.0
C3' N:RP5405 4.7 69.2 1.0
CA N:ALA136 4.7 49.0 1.0
P' N:RP5405 4.7 67.2 1.0
O N:GLY137 4.9 48.3 1.0
C4' N:RP5405 4.9 69.2 1.0
CZ N:ARG99 4.9 61.4 1.0
NH2 N:ARG99 5.0 61.6 1.0
OH N:TYR81 5.0 51.1 1.0

Chlorine binding site 8 out of 12 in 2c37

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Chlorine binding site 8 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl301

b:80.7
occ:1.00
N P:GLY137 3.4 48.4 1.0
OG P:SER138 3.6 48.4 1.0
NH1 P:ARG99 3.8 63.0 1.0
N P:SER138 3.9 48.0 1.0
NH2 P:ARG139 4.0 47.5 1.0
OD2 P:ASP182 4.0 59.4 1.0
CA P:GLY137 4.1 48.2 1.0
NE P:ARG139 4.2 48.5 1.0
CA P:ALA136 4.2 48.9 1.0
C P:ALA136 4.2 48.6 1.0
C P:GLY137 4.4 48.1 1.0
CZ P:ARG139 4.5 48.0 1.0
N P:ARG139 4.5 47.4 1.0
CB P:SER138 4.8 47.9 1.0
CA P:SER138 4.8 48.0 1.0
CZ P:ARG99 4.9 61.5 1.0
CB P:ALA136 4.9 48.5 1.0

Chlorine binding site 9 out of 12 in 2c37

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Chlorine binding site 9 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl301

b:63.0
occ:1.00
N R:SER138 3.1 48.1 1.0
OG R:SER138 3.1 48.8 1.0
N R:GLY137 3.1 48.4 1.0
CA R:GLY137 3.6 48.2 1.0
N R:ARG139 3.6 47.4 1.0
C R:GLY137 3.7 48.3 1.0
CA R:SER138 4.0 48.0 1.0
NE R:ARG139 4.0 48.5 1.0
C R:ALA136 4.0 48.7 1.0
CB R:SER138 4.1 47.8 1.0
NH1 R:ARG99 4.1 62.8 1.0
C R:SER138 4.3 47.8 1.0
NH2 R:ARG139 4.3 47.7 1.0
CA R:ALA136 4.3 49.0 1.0
CB R:ARG139 4.4 47.1 1.0
CZ R:ARG139 4.6 48.0 1.0
CA R:ARG139 4.6 47.2 1.0
CG R:ARG139 4.6 47.5 1.0
O R:GLY137 4.7 48.1 1.0
CD R:ARG139 4.9 47.4 1.0
OD2 R:ASP182 4.9 59.6 1.0
OH R:TYR81 5.0 50.9 1.0
NH2 R:ARG99 5.0 61.6 1.0

Chlorine binding site 10 out of 12 in 2c37

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Chlorine binding site 10 out of 12 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 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 U8 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl301

b:57.8
occ:1.00
NE T:ARG139 3.2 48.4 1.0
OG T:SER138 3.5 48.7 1.0
NH2 T:ARG139 3.5 47.6 1.0
N T:ARG139 3.6 47.4 1.0
N T:SER138 3.6 48.0 1.0
N T:GLY137 3.7 48.4 1.0
CZ T:ARG139 3.8 48.0 1.0
NH1 T:ARG99 3.8 62.9 1.0
CB T:ARG139 4.0 47.0 1.0
CA T:GLY137 4.0 48.3 1.0
C T:GLY137 4.1 48.3 1.0
CG T:ARG139 4.1 47.4 1.0
CD T:ARG139 4.2 47.4 1.0
CA T:SER138 4.4 48.0 1.0
CA T:ARG139 4.4 47.2 1.0
C T:SER138 4.5 47.8 1.0
CB T:SER138 4.5 47.8 1.0
C T:ALA136 4.7 48.7 1.0
CZ T:ARG99 4.8 61.4 1.0
NH2 T:ARG99 4.9 61.5 1.0
CD1 T:LEU103 4.9 45.3 1.0
OH T:TYR81 5.0 51.0 1.0

Reference:

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
Page generated: Sat Jul 20 06:05:17 2024

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