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Chlorine in PDB 2br2: Rnase pH Core of the Archaeal Exosome

Protein crystallography data

The structure of Rnase pH Core of the Archaeal Exosome, PDB code: 2br2 was solved by E.Lorentzen, S.Fribourg, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 218.22 / 2.8
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 206.880, 212.720, 434.050, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.7

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine atom in the Rnase pH Core of the Archaeal Exosome (pdb code 2br2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Rnase pH Core of the Archaeal Exosome, PDB code: 2br2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 2br2

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Chlorine binding site 1 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1249

b:67.2
occ:1.00
 N B:ARG139 3.1 30.6 1.0
N B:SER138 3.2 31.5 1.0
NE B:ARG139 3.3 29.6 1.0
NH2 B:ARG99 3.3 50.8 1.0
O B:HOH2005 3.6 17.6 1.0
C B:GLY137 3.7 31.6 1.0
N B:GLY137 3.7 31.6 1.0
CB B:ARG139 3.7 29.7 1.0
OG B:SER138 3.8 33.8 1.0
CG B:ARG139 3.9 29.4 1.0
CA B:GLY137 3.9 31.5 1.0
CA B:SER138 3.9 31.4 1.0
NH2 B:ARG139 3.9 28.0 1.0
CB B:SER138 3.9 31.2 1.0
C B:SER138 4.0 31.1 1.0
CA B:ARG139 4.0 29.8 1.0
CZ B:ARG139 4.1 28.3 1.0
CD B:ARG139 4.2 29.3 1.0
CZ B:ARG99 4.5 50.8 1.0
OH B:TYR81 4.5 33.8 1.0
O B:GLY137 4.5 31.9 1.0
C B:ALA136 4.8 31.6 1.0
CD1 B:LEU103 4.9 28.4 1.0
NH1 B:ARG99 5.0 52.5 1.0

Chlorine binding site 2 out of 13 in 2br2

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Chlorine binding site 2 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1249

b:50.0
occ:1.00
 NE D:ARG139 3.2 29.4 1.0
N D:SER138 3.3 31.5 1.0
N D:ARG139 3.3 30.5 1.0
NH2 D:ARG99 3.5 50.8 1.0
N D:GLY137 3.6 31.6 1.0
C D:GLY137 3.7 31.6 1.0
NH2 D:ARG139 3.8 28.0 1.0
CA D:GLY137 3.8 31.5 1.0
CG D:ARG139 3.8 29.3 1.0
CB D:ARG139 3.9 29.8 1.0
CZ D:ARG139 3.9 28.4 1.0
CA D:SER138 4.1 31.4 1.0
OG D:SER138 4.1 33.8 1.0
CD D:ARG139 4.1 29.1 1.0
C D:SER138 4.2 31.2 1.0
CB D:SER138 4.2 31.2 1.0
CA D:ARG139 4.2 29.9 1.0
O D:GLY137 4.5 31.9 1.0
CZ D:ARG99 4.6 50.8 1.0
C D:ALA136 4.7 31.7 1.0
OH D:TYR81 4.9 33.7 1.0
CD1 D:LEU103 5.0 28.4 1.0
NH1 D:ARG99 5.0 52.5 1.0

Chlorine binding site 3 out of 13 in 2br2

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Chlorine binding site 3 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1249

b:48.7
occ:1.00
 NE F:ARG139 2.9 29.6 1.0
N F:ARG139 3.2 30.5 1.0
N F:SER138 3.4 31.5 1.0
CG F:ARG139 3.5 29.4 1.0
CB F:ARG139 3.6 29.6 1.0
C F:GLY137 3.7 31.6 1.0
N F:GLY137 3.7 31.5 1.0
NH2 F:ARG99 3.7 50.8 1.0
CA F:GLY137 3.7 31.5 1.0
CD F:ARG139 3.8 29.2 1.0
NH2 F:ARG139 3.8 27.9 1.0
CZ F:ARG139 3.8 28.4 1.0
CA F:ARG139 4.0 29.8 1.0
CA F:SER138 4.1 31.4 1.0
C F:SER138 4.1 31.1 1.0
OG F:SER138 4.3 33.8 1.0
CB F:SER138 4.3 31.3 1.0
O F:GLY137 4.5 32.0 1.0
CZ F:ARG99 4.8 50.8 1.0
N F:LEU140 4.9 29.2 1.0
C F:ALA136 4.9 31.7 1.0
OH F:TYR81 5.0 33.8 1.0
CD1 F:LEU103 5.0 28.4 1.0
C F:ARG139 5.0 29.7 1.0

Chlorine binding site 4 out of 13 in 2br2

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Chlorine binding site 4 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1249

b:52.3
occ:1.00
 NE H:ARG139 3.0 29.6 1.0
N H:ARG139 3.2 30.6 1.0
N H:SER138 3.3 31.4 1.0
C H:GLY137 3.6 31.6 1.0
CG H:ARG139 3.6 29.2 1.0
NH2 H:ARG99 3.6 50.8 1.0
CB H:ARG139 3.7 29.7 1.0
N H:GLY137 3.7 31.6 1.0
CA H:GLY137 3.7 31.6 1.0
NH2 H:ARG139 3.8 28.0 1.0
CZ H:ARG139 3.8 28.4 1.0
CD H:ARG139 3.9 29.2 1.0
CA H:ARG139 4.0 29.8 1.0
CA H:SER138 4.0 31.4 1.0
C H:SER138 4.1 31.2 1.0
OG H:SER138 4.2 33.8 1.0
CB H:SER138 4.2 31.3 1.0
O H:GLY137 4.4 31.9 1.0
CZ H:ARG99 4.8 50.7 1.0
C H:ALA136 4.8 31.7 1.0
OH H:TYR81 4.9 33.9 1.0
N H:LEU140 4.9 29.1 1.0

Chlorine binding site 5 out of 13 in 2br2

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Chlorine binding site 5 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl1249

b:47.4
occ:1.00
 NE J:ARG139 3.0 29.5 1.0
NH2 J:ARG99 3.2 50.9 1.0
N J:ARG139 3.3 30.5 1.0
NH2 J:ARG139 3.5 28.0 1.0
N J:SER138 3.6 31.4 1.0
CB J:ARG139 3.7 29.7 1.0
CZ J:ARG139 3.7 28.3 1.0
CG J:ARG139 3.8 29.3 1.0
CD J:ARG139 3.9 29.2 1.0
C J:GLY137 4.0 31.6 1.0
N J:GLY137 4.1 31.6 1.0
CA J:ARG139 4.1 29.8 1.0
OG J:SER138 4.1 33.7 1.0
CA J:SER138 4.2 31.5 1.0
CB J:SER138 4.2 31.3 1.0
C J:SER138 4.2 31.2 1.0
CA J:GLY137 4.2 31.5 1.0
CZ J:ARG99 4.3 50.8 1.0
OH J:TYR81 4.6 33.7 1.0
CD1 J:LEU103 4.6 28.4 1.0
NH1 J:ARG99 4.8 52.5 1.0
O J:GLY137 4.8 31.8 1.0
NH1 J:ARG139 5.0 27.3 1.0

Chlorine binding site 6 out of 13 in 2br2

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Chlorine binding site 6 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1249

b:45.2
occ:1.00
 NE L:ARG139 3.0 29.4 1.0
N L:ARG139 3.3 30.5 1.0
N L:SER138 3.4 31.4 1.0
CG L:ARG139 3.6 29.3 1.0
NH2 L:ARG139 3.7 28.1 1.0
CB L:ARG139 3.7 29.7 1.0
NH2 L:ARG99 3.7 50.9 1.0
N L:GLY137 3.7 31.6 1.0
C L:GLY137 3.7 31.5 1.0
CZ L:ARG139 3.8 28.3 1.0
CA L:GLY137 3.8 31.5 1.0
CD L:ARG139 3.8 29.1 1.0
CA L:ARG139 4.1 29.8 1.0
CA L:SER138 4.2 31.4 1.0
C L:SER138 4.2 31.1 1.0
CB L:SER138 4.4 31.2 1.0
OG L:SER138 4.4 33.8 1.0
O L:GLY137 4.5 31.9 1.0
CZ L:ARG99 4.8 50.8 1.0
C L:ALA136 4.9 31.7 1.0
N L:LEU140 4.9 29.2 1.0
CD1 L:LEU103 5.0 28.4 1.0

Chlorine binding site 7 out of 13 in 2br2

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Chlorine binding site 7 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl1276

b:45.3
occ:1.00
 NH2 M:ARG112 2.6 24.8 1.0
CZ M:ARG112 3.8 24.6 1.0
CD N:ARG99 4.0 39.3 1.0
CG N:ARG99 4.2 33.9 1.0
NH1 M:ARG112 4.3 25.2 1.0
CB N:ARG99 4.4 31.6 1.0
NH1 N:ARG99 4.5 52.6 1.0
NE M:ARG112 4.9 24.5 1.0

Chlorine binding site 8 out of 13 in 2br2

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Chlorine binding site 8 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl1249

b:56.4
occ:1.00
 N N:SER138 3.2 31.4 1.0
NH2 N:ARG99 3.3 50.8 1.0
N N:ARG139 3.3 30.6 1.0
NE N:ARG139 3.4 29.5 1.0
N N:GLY137 3.6 31.6 1.0
O N:HOH2003 3.7 16.2 1.0
C N:GLY137 3.7 31.6 1.0
CA N:GLY137 3.8 31.6 1.0
OG N:SER138 3.8 33.9 1.0
NH2 N:ARG139 3.9 27.9 1.0
CA N:SER138 3.9 31.4 1.0
CB N:ARG139 4.0 29.8 1.0
CB N:SER138 4.0 31.3 1.0
CG N:ARG139 4.0 29.3 1.0
C N:SER138 4.1 31.2 1.0
CZ N:ARG139 4.1 28.3 1.0
CA N:ARG139 4.2 29.8 1.0
CD N:ARG139 4.3 29.2 1.0
CZ N:ARG99 4.5 50.7 1.0
O N:GLY137 4.6 31.8 1.0
OH N:TYR81 4.6 33.8 1.0
C N:ALA136 4.7 31.7 1.0
NH1 N:ARG99 4.9 52.6 1.0
CD1 N:LEU103 4.9 28.4 1.0

Chlorine binding site 9 out of 13 in 2br2

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Chlorine binding site 9 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl1249

b:59.6
occ:1.00
 N P:SER138 3.2 31.4 1.0
N P:ARG139 3.3 30.6 1.0
NH2 P:ARG99 3.3 50.9 1.0
NE P:ARG139 3.3 29.6 1.0
N P:GLY137 3.7 31.6 1.0
C P:GLY137 3.8 31.5 1.0
NH2 P:ARG139 3.8 28.0 1.0
OG P:SER138 3.8 33.8 1.0
CA P:GLY137 3.9 31.4 1.0
CB P:ARG139 3.9 29.7 1.0
CG P:ARG139 3.9 29.3 1.0
CA P:SER138 3.9 31.4 1.0
CB P:SER138 4.0 31.1 1.0
CZ P:ARG139 4.0 28.4 1.0
C P:SER138 4.1 31.1 1.0
CA P:ARG139 4.2 29.9 1.0
CD P:ARG139 4.2 29.2 1.0
CZ P:ARG99 4.4 50.8 1.0
O P:GLY137 4.6 31.7 1.0
OH P:TYR81 4.6 33.8 1.0
C P:ALA136 4.8 31.7 1.0
CD1 P:LEU103 4.8 28.4 1.0
NH1 P:ARG99 4.9 52.5 1.0

Chlorine binding site 10 out of 13 in 2br2

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Chlorine binding site 10 out of 13 in the Rnase pH Core of the Archaeal Exosome


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl1249

b:46.1
occ:1.00
 NE R:ARG139 3.2 29.6 1.0
N R:SER138 3.3 31.3 1.0
N R:ARG139 3.4 30.5 1.0
NH2 R:ARG99 3.5 50.8 1.0
N R:GLY137 3.5 31.6 1.0
C R:GLY137 3.7 31.5 1.0
CA R:GLY137 3.7 31.5 1.0
NH2 R:ARG139 3.8 27.9 1.0
CG R:ARG139 3.9 29.4 1.0
CB R:ARG139 4.0 29.7 1.0
CZ R:ARG139 4.0 28.4 1.0
CA R:SER138 4.1 31.3 1.0
OG R:SER138 4.1 33.8 1.0
CD R:ARG139 4.2 29.2 1.0
C R:SER138 4.3 31.1 1.0
CB R:SER138 4.3 31.2 1.0
CA R:ARG139 4.3 29.7 1.0
O R:GLY137 4.6 31.9 1.0
C R:ALA136 4.6 31.7 1.0
CZ R:ARG99 4.7 50.7 1.0
NH1 R:ARG99 5.0 52.4 1.0
OH R:TYR81 5.0 33.8 1.0

Reference:

E.Lorentzen, P.Walter, S.Fribourg, E.Evguenieva-Hackenberg, G.Klug, E.Conti. The Archaeal Exosome Core Is A Hexameric Ring Structure with Three Catalytic Subunits. Nat.Struct.Mol.Biol. V. 12 575 2005.
ISSN: ISSN 1545-9993
PubMed: 15951817
DOI: 10.1038/NSMB952
Page generated: Sat Jul 20 05:52:38 2024

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