Magnesium in PDB 5f6c: The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound

All present enzymatic activity of The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound:
3.1.26.12;

The structure of The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound, PDB code: 5f6c was solved by K.J.Bandyra, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.62 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.619, 122.562, 122.195, 90.00, 99.77, 90.00
R / Rfree (%)	17.5 / 25

The structure of The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound (pdb code 5f6c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound, PDB code: 5f6c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:53.9 occ:1.00 OD1 A:ASP338 2.2 76.1 1.0 O A:LEU27 2.2 77.5 1.0 OD1 A:ASP26 2.2 68.5 1.0 O A:ARG335 2.4 74.0 1.0 OD1 A:ASP28 2.5 90.3 1.0 CG A:ASP338 2.9 82.3 1.0 OD2 A:ASP338 3.1 81.0 1.0 HH11 A:ARG371 3.1 0.2 1.0 CG A:ASP26 3.2 73.1 1.0 H A:LEU27 3.4 81.0 1.0 OD2 A:ASP26 3.4 79.4 1.0 C A:LEU27 3.4 67.0 1.0 C A:ARG335 3.5 75.8 1.0 CG A:ASP28 3.7 91.5 1.0 HA A:ARG335 3.7 82.1 1.0 HB3 A:ARG335 3.7 75.9 1.0 NH1 A:ARG371 3.8 0.7 1.0 HA A:ASP28 3.9 63.0 1.0 N A:LEU27 4.0 67.5 1.0 CA A:ARG335 4.0 68.5 1.0 H A:ASP338 4.1 81.0 1.0 HA A:ASP338 4.1 86.1 1.0 HH12 A:ARG371 4.1 0.2 1.0 CB A:ASP338 4.3 79.2 1.0 HE A:ARG371 4.3 0.1 1.0 N A:ASP28 4.3 53.8 1.0 HH22 A:ARG389 4.3 97.2 1.0 CA A:LEU27 4.3 64.9 1.0 HA A:LEU336 4.3 72.2 1.0 OD2 A:ASP28 4.4 90.5 1.0 CB A:ARG335 4.4 63.2 1.0 CA A:ASP28 4.4 52.5 1.0 CA A:ASP338 4.5 71.7 1.0 N A:LEU336 4.5 67.4 1.0 N A:ASP338 4.6 67.5 1.0 CB A:ASP26 4.6 53.5 1.0 CB A:ASP28 4.7 61.7 1.0 HB3 A:LEU27 4.7 74.3 1.0 HA A:ASP26 4.7 76.1 1.0 CZ A:ARG371 4.8 0.6 1.0 HB2 A:ASP338 4.8 95.0 1.0 CA A:LEU336 4.8 60.2 1.0 C A:ASP26 4.9 62.9 1.0 HB3 A:ASP338 4.9 95.0 1.0 NE A:ARG371 4.9 0.8 1.0 C A:LEU336 5.0 71.8 1.0

Magnesium binding site 2 out of 2 in the The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of E. Coli Rnase E Catalytically Inactive Mutant with Rna Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:99.0 occ:1.00 OD1 B:ASP28 2.1 0.8 1.0 HB2 B:SER393 2.8 0.3 1.0 OG B:SER393 2.9 0.5 1.0 CB B:SER393 3.2 0.2 1.0 CG B:ASP28 3.2 89.0 1.0 HB3 B:SER393 3.2 0.3 1.0 HH11 B:ARG216 3.3 0.2 1.0 HH12 B:ARG216 3.4 0.2 1.0 HH12 B:ARG371 3.5 0.7 1.0 HG B:SER393 3.6 0.3 1.0 OD2 B:ASP28 3.6 93.5 1.0 NH1 B:ARG216 3.7 0.1 1.0 NH1 B:ARG371 4.2 0.9 1.0 HH11 B:ARG371 4.4 0.7 1.0 OD2 B:ASP338 4.5 0.1 1.0 CB B:ASP28 4.5 61.2 1.0 HB2 B:ASP28 4.6 73.5 1.0 CA B:SER393 4.7 0.6 1.0 OH B:TYR221 4.7 93.1 1.0 HA B:ASP28 4.7 71.6 1.0 CG B:ASP338 4.7 0.6 1.0 HB2 B:ASP338 4.8 0.4 1.0 HH B:TYR221 4.9 0.7 1.0 HA B:SER393 4.9 0.9 1.0 HH22 B:ARG371 4.9 0.5 1.0 CZ B:ARG216 5.0 0.1 1.0

K.J.Bandyra, J.M.Wandzik, B.F.Luisi. Substrate Recognition and Autoinhibition in the Central Ribonuclease Rnase E. Mol. Cell V. 72 275 2018.
ISSN: ISSN 1097-4164
PubMed: 30270108
DOI: 10.1016/J.MOLCEL.2018.08.039