Atomistry » Chlorine » PDB 2bwv-2c5h » 2c38
Atomistry »
  Chlorine »
    PDB 2bwv-2c5h »
      2c38 »

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

Protein crystallography data

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

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 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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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 2c38

Go back to Chlorine Binding Sites List in 2c38
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

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 Dec 12 09:01:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy