Sodium in PDB 7vh4: Crystal Structure of Oligoribonuclease of Escherichia Coli

All present enzymatic activity of Crystal Structure of Oligoribonuclease of Escherichia Coli:
3.1.13.3;

The structure of Crystal Structure of Oligoribonuclease of Escherichia Coli, PDB code: 7vh4 was solved by P.Badhwar, B.Taneja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.63 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.574, 100.574, 147.831, 90, 90, 90
R / Rfree (%)	19.4 / 24.5

The structure of Crystal Structure of Oligoribonuclease of Escherichia Coli also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Oligoribonuclease of Escherichia Coli (pdb code 7vh4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Oligoribonuclease of Escherichia Coli, PDB code: 7vh4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Oligoribonuclease of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Oligoribonuclease of Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:73.1 occ:1.00 O D:PHE127 2.6 47.1 1.0 O D:GLU124 3.1 47.3 1.0 NH2 D:ARG113 3.2 50.4 1.0 O D:HOH337 3.2 50.4 1.0 OE1 D:GLU124 3.3 41.1 1.0 O D:HOH327 3.4 43.5 1.0 O D:HOH325 3.4 45.5 1.0 O D:ALA125 3.5 60.1 1.0 C D:PHE127 3.6 48.3 1.0 CA D:ALA125 3.7 49.2 1.0 C D:ALA125 3.8 48.0 1.0 CD D:GLU124 3.8 44.8 1.0 OE2 D:GLU124 3.8 39.7 1.0 C D:GLU124 4.0 42.2 1.0 C D:HIS128 4.2 44.1 1.0 O D:HIS128 4.2 49.1 1.0 N D:ALA125 4.2 45.5 1.0 N D:PHE127 4.3 49.6 1.0 N D:TYR129 4.3 44.2 1.0 CA D:PHE127 4.3 46.3 1.0 CA D:TYR129 4.4 48.2 1.0 CB D:PHE127 4.4 45.8 1.0 CZ D:ARG113 4.5 45.9 1.0 N D:HIS128 4.6 45.6 1.0 N D:TYR126 4.8 48.1 1.0 CA D:HIS128 4.8 46.2 1.0 CB D:ALA125 4.9 48.6 1.0 NE D:ARG113 5.0 46.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Oligoribonuclease of Escherichia Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Oligoribonuclease of Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:84.8 occ:1.00 O D:HOH306 2.3 56.1 1.0 O B:PHE127 2.5 53.5 1.0 O B:GLU124 3.0 47.3 1.0 NH2 B:ARG113 3.1 52.8 1.0 O B:HOH704 3.2 54.5 1.0 O B:HOH732 3.2 67.7 1.0 OE2 B:GLU124 3.3 47.5 1.0 C B:PHE127 3.5 49.6 1.0 O B:HOH724 3.6 50.1 1.0 O B:ALA125 3.6 52.6 1.0 OE1 B:GLU124 3.6 54.7 1.0 CA B:ALA125 3.7 57.8 1.0 CD B:GLU124 3.7 54.8 1.0 C B:ALA125 3.8 53.0 1.0 C B:GLU124 3.9 48.7 1.0 O B:HIS128 4.0 44.4 1.0 C B:HIS128 4.1 51.7 1.0 N B:ALA125 4.2 53.4 1.0 N B:PHE127 4.2 50.1 1.0 CA B:PHE127 4.2 46.4 1.0 N B:TYR129 4.2 52.9 1.0 CB B:PHE127 4.2 45.7 1.0 CZ B:ARG113 4.3 51.6 1.0 CA B:TYR129 4.3 59.2 1.0 N B:HIS128 4.5 45.8 1.0 OD2 D:ASP60 4.7 75.5 1.0 CA B:HIS128 4.7 50.9 1.0 N B:TYR126 4.8 54.1 1.0 NE B:ARG113 4.8 54.5 1.0 CG B:GLU124 5.0 50.9 1.0 CB B:ALA125 5.0 64.8 1.0

P.Badhwar, S.H.Khan, B.Taneja. Three-Dimensional Structure of A Mycobacterial Oligoribonuclease Reveals A Unique C-Terminal Tail That Stabilizes the Homodimer. J.Biol.Chem. V. 298 02595 2022.
ISSN: ESSN 1083-351X
PubMed: 36244449
DOI: 10.1016/J.JBC.2022.102595