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Magnesium in PDB 2c0b: Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna

Protein crystallography data

The structure of Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna, PDB code: 2c0b was solved by M.J.Marcaida, A.J.Callaghan, W.G.Scott, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.18
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 196.049, 196.049, 142.660, 90.00, 90.00, 120.00
R / Rfree (%) 25.2 / 28.2

Other elements in 2c0b:

The structure of Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna (pdb code 2c0b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna, PDB code: 2c0b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2c0b

Go back to Magnesium Binding Sites List in 2c0b
Magnesium binding site 1 out of 2 in the Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1510

b:21.8
occ:1.00
O L:HOH2023 2.2 33.7 1.0
O L:HOH2028 2.2 57.1 1.0
O L:HOH2029 2.2 22.6 1.0
O L:HOH2024 2.2 36.4 1.0
OD2 L:ASP346 2.7 29.8 1.0
OD2 L:ASP303 2.9 20.1 1.0
CG L:ASP303 3.8 18.6 1.0
CG L:ASP346 4.0 18.9 1.0
O L:ILE304 4.0 18.4 1.0
OD1 L:ASP303 4.0 26.9 1.0
O L:ASP346 4.6 15.3 1.0
OD1 L:ASP346 4.7 38.0 1.0
N L:ILE304 4.8 15.0 1.0
C L:ILE304 5.0 15.0 1.0
CB L:ASP346 5.0 15.0 1.0

Magnesium binding site 2 out of 2 in 2c0b

Go back to Magnesium Binding Sites List in 2c0b
Magnesium binding site 2 out of 2 in the Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of E. Coli Rnase E in Complex with 13-Mer Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1512

b:30.8
occ:0.50
O L:SER295 3.7 16.1 1.0
O L:GLY409 4.2 28.7 1.0
O L:THR410 4.7 42.4 1.0
C L:SER295 4.9 15.0 1.0
OD1 L:ASP294 5.0 34.2 1.0

Reference:

A.J.Callaghan, M.J.Marcaida, J.A.Stead, K.J.Mcdowall, W.G.Scott, B.F.Luisi. Structure of E. Coli Rnase E Catalytic Domain and Implications For Rna Processing and Turnover Nature V. 437 1187 2005.
ISSN: ISSN 0028-0836
PubMed: 16237448
DOI: 10.1038/NATURE04084
Page generated: Mon Dec 14 07:17:59 2020

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