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Sodium 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:

Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Rnase pH Core of the Archaeal Exosome in Complex with U8 Rna, PDB code: 2c37:

Sodium binding site 1 out of 1 in 2c37

Go back to Sodium Binding Sites List in 2c37
Sodium binding site 1 out of 1 in the Rnase pH Core of the Archaeal Exosome in Complex with U8 Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
V:Na501

b:40.1
occ:1.00
O2P V:U5P404 2.3 85.7 1.0
O1P V:U5P403 2.7 74.6 1.0
P V:U5P404 3.3 86.5 1.0
NH2 V:ARG139 3.4 47.5 1.0
O1P V:U5P404 3.7 86.4 1.0
CD V:ARG99 3.8 53.9 1.0
O3' V:U5P403 3.9 85.3 1.0
CG V:ARG99 4.0 50.1 1.0
P V:U5P403 4.0 76.0 1.0
NH1 V:ARG99 4.1 62.9 1.0
NH1 U:ARG112 4.1 40.4 1.0
NH2 U:ARG112 4.2 41.2 1.0
O5' V:U5P403 4.5 77.3 1.0
CZ V:ARG139 4.5 47.9 1.0
C3' V:U5P403 4.5 83.7 1.0
C5' V:U5P403 4.6 80.1 1.0
CZ U:ARG112 4.7 40.5 1.0
O5' V:U5P404 4.7 87.1 1.0
O2P V:U5P403 4.8 75.4 1.0
NH1 V:ARG139 4.8 47.2 1.0
NE U:ARG116 4.8 47.6 1.0
NE V:ARG99 4.8 58.4 1.0
CZ V:ARG99 5.0 61.4 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: Tue Dec 15 05:46:30 2020

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