Sodium in PDB 4kbf: Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera

The structure of Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera, PDB code: 4kbf was solved by M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.645, 119.645, 107.095, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.8

The binding sites of Sodium atom in the Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera (pdb code 4kbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera, PDB code: 4kbf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.0 occ:1.00 O A:HOH503 2.3 34.6 1.0 O A:PHE6 2.4 27.5 1.0 O A:HOH521 2.4 30.5 1.0 O A:LYS4 2.4 30.8 1.0 C A:LYS4 3.4 35.4 1.0 C A:PHE6 3.4 32.0 1.0 C A:ASP5 4.0 31.9 1.0 N A:PHE6 4.0 26.8 1.0 N A:LEU8 4.2 31.9 1.0 CA A:PRO7 4.2 29.9 1.0 N A:ASP5 4.2 27.6 1.0 N A:PRO7 4.3 29.1 1.0 CA A:ASP5 4.3 31.3 1.0 O A:ASP5 4.3 30.8 1.0 CA A:LYS4 4.3 29.8 1.0 CA A:PHE6 4.4 25.8 1.0 O A:PHE3 4.6 30.3 1.0 O A:LEU8 4.7 37.1 1.0 C A:PRO7 4.8 37.4 1.0 O A:HOH516 4.9 42.1 1.0

Sodium binding site 2 out of 2 in the Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Two Different Open Conformations of the Helicase Core of the Rna Helicase Hera within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:51.2 occ:1.00 O A:HOH590 2.3 50.4 1.0 O A:HOH591 2.4 44.2 1.0 O A:THR47 2.4 43.4 1.0 O A:PRO210 2.4 52.6 1.0 OG1 A:THR212 2.6 56.2 1.0 OG1 A:THR47 2.6 45.5 1.0 C A:THR47 3.3 51.1 1.0 CB A:THR212 3.4 47.2 1.0 C A:PRO210 3.7 57.1 1.0 CB A:THR47 3.7 45.1 1.0 N A:THR212 3.7 42.9 1.0 CA A:THR47 3.8 41.1 1.0 N A:THR47 4.0 43.8 1.0 O A:HOH574 4.0 40.4 1.0 CA A:THR212 4.2 47.8 1.0 N A:GLY48 4.3 46.8 1.0 C A:VAL211 4.3 43.3 1.0 CB A:GLU209 4.4 53.3 1.0 CA A:VAL211 4.4 42.4 1.0 N A:PRO210 4.5 70.7 1.0 N A:VAL211 4.5 45.7 1.0 CA A:GLY48 4.6 48.3 1.0 CG2 A:THR212 4.6 56.8 1.0 CA A:PRO210 4.6 66.7 1.0 OE1 A:GLU209 4.6 50.6 1.0 CD A:PRO210 4.7 73.8 1.0 C A:GLU209 4.8 62.8 1.0 CG2 A:THR47 5.0 42.7 1.0 CB A:PRO210 5.0 72.0 1.0

D.Klostermeier, M.G.Rudolph, D.Klostermeier. N/A N/A.
ISSN: ISSN 0006-3525
PubMed: 23765433
DOI: 10.1002/BIP.22316