Sodium in PDB 5ogh: Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions

All present enzymatic activity of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions:
3.1.27.5;

The structure of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions, PDB code: 5ogh was solved by J.A.Blanco, G.Prats-Ejarque, V.A.Salazar, M.Moussaoui, E.Boix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.65 / 1.16
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.060, 64.060, 64.058, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 13.5

The structure of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions (pdb code 5ogh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions, PDB code: 5ogh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:22.4 occ:1.00 H A:LEU51 2.3 14.4 1.0 CL A:CL205 2.8 21.0 0.7 HA A:SER50 2.9 14.5 1.0 CL A:CL206 3.0 20.6 0.6 N A:LEU51 3.1 12.1 1.0 HB2 A:SER50 3.1 15.8 1.0 O A:HOH479 3.3 47.8 1.0 HB3 A:LEU51 3.4 17.6 1.0 O A:HOH477 3.5 51.9 0.9 HB3 A:SER15 3.6 19.3 1.0 CA A:SER50 3.6 12.1 1.0 HB2 A:LEU51 3.7 17.6 1.0 OG A:SER15 3.7 14.4 1.0 CB A:SER50 3.8 13.2 1.0 C A:SER50 3.9 11.8 1.0 CB A:LEU51 3.9 14.7 1.0 HB2 A:SER15 3.9 19.3 1.0 CB A:SER15 3.9 16.1 1.0 HG A:SER15 4.0 17.3 1.0 CA A:LEU51 4.1 12.2 1.0 H A:ALA52 4.1 15.2 1.0 HB3 A:SER50 4.1 15.8 1.0 O A:HOH474 4.4 33.9 0.7 O A:HOH472 4.6 53.9 1.0 O A:HOH459 4.7 29.3 0.9 HA A:LEU51 4.8 14.6 1.0 N A:ALA52 4.8 12.7 1.0 N A:SER50 4.9 11.6 1.0 OG A:SER50 5.0 13.5 1.0

Sodium binding site 2 out of 2 in the Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rnase A at High Resolution (1.16 A) in Complex with 3'- Cmp and Sulphate Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:15.8 occ:0.40 O A:HOH388 2.2 26.1 0.6 O A:HOH455 2.4 29.1 1.0 HA A:SER32 2.4 25.4 0.6 O A:HOH313 2.4 17.7 0.7 OD1 A:ASN34 2.6 25.6 1.0 O A:HOH449 2.6 26.9 0.7 O A:HOH420 2.7 39.7 0.8 HA A:SER32 2.8 23.9 0.4 O A:SER32 3.0 16.5 0.4 O A:LYS31 3.0 24.9 1.0 CA A:SER32 3.3 21.1 0.6 C A:SER32 3.5 17.5 0.4 CA A:SER32 3.5 19.9 0.4 O A:SER32 3.5 21.8 0.6 CG A:ASN34 3.6 20.9 1.0 O A:HOH355 3.6 27.9 0.6 C A:SER32 3.6 19.8 0.6 HD21 A:ASN34 3.8 25.8 1.0 C A:LYS31 3.8 22.5 1.0 H A:ASN34 3.8 18.8 1.0 HE2 A:LYS37 4.0 44.7 0.5 N A:SER32 4.1 20.5 0.6 ND2 A:ASN34 4.1 21.5 1.0 N A:SER32 4.1 20.4 0.4 HG2 A:LYS31 4.1 31.6 0.5 HA A:ASN34 4.3 20.9 1.0 HB2 A:SER32 4.3 21.2 0.6 CB A:SER32 4.3 17.6 0.6 HZ2 A:LYS31 4.3 39.9 0.5 N A:ASN34 4.4 15.7 1.0 HB3 A:SER32 4.5 21.2 0.6 N A:ARG33 4.7 16.1 1.0 CA A:ASN34 4.7 17.4 1.0 O A:HOH382 4.7 17.8 0.9 HZ1 A:LYS31 4.8 39.9 0.5 CB A:ASN34 4.8 18.9 1.0 CB A:SER32 4.8 19.5 0.4 HB3 A:SER32 4.9 23.4 0.4 H A:SER32 4.9 24.6 0.6 HD22 A:ASN34 4.9 25.8 1.0 H A:SER32 4.9 24.4 0.4 CE A:LYS37 5.0 37.2 0.4 NZ A:LYS31 5.0 33.3 0.4

G.Prats-Ejarque, J.A.Blanco, V.A.Salazar, V.M.Nogues, M.Moussaoui, E.Boix. Characterization of An Rnase with Two Catalytic Centers. Human RNASE6 Catalytic and Phosphate-Binding Site Arrangement Favors the Endonuclease Cleavage of Polymeric Substrates. Biochim Biophys Acta Gen V.1863 105 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 30287244
DOI: 10.1016/J.BBAGEN.2018.09.021