Potassium in PDB 1dul: Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 1dul was solved by R.T.Batey, R.P.Rambo, L.Lucast, B.Rha, J.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.83 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.567, 78.291, 32.849, 90.00, 96.14, 90.00
R / Rfree (%)	19.9 / 22.1

The structure of Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Potassium atom in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 1dul). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 1dul:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:K701 b:20.7 occ:1.00 O B:HOH929 2.6 25.8 1.0 O6 B:G165 2.7 21.2 1.0 O2 B:C147 2.7 22.9 1.0 O B:HOH945 2.8 17.8 1.0 N3 B:C147 3.0 21.7 1.0 C2 B:C147 3.1 22.0 1.0 N7 B:A164 3.1 20.4 1.0 O4 B:U146 3.2 23.3 1.0 O B:HOH900 3.5 17.7 1.0 C6 B:G165 3.6 20.6 1.0 C5 B:C163 3.8 17.9 1.0 N7 B:G165 3.9 19.2 1.0 C8 B:A164 4.0 18.6 1.0 N3 B:U146 4.0 23.6 1.0 C4 B:U146 4.0 25.2 1.0 C5 B:G165 4.1 18.1 1.0 C4 B:C147 4.1 20.5 1.0 N6 B:A164 4.1 19.6 1.0 C5 B:A164 4.1 20.8 1.0 O B:HOH920 4.2 16.0 1.0 N1 B:C147 4.3 24.5 1.0 C4 B:C163 4.4 20.0 1.0 C6 B:C163 4.4 18.6 1.0 N4 B:C163 4.4 19.2 1.0 OP2 B:C163 4.5 22.1 1.0 O6 B:G145 4.5 21.7 1.0 OP2 B:A164 4.6 18.4 1.0 C6 B:A164 4.6 19.4 1.0 N4 B:C147 4.6 19.9 1.0 N1 B:G165 4.7 19.1 1.0 N4 B:C166 4.9 17.6 1.0 C1' B:C147 5.0 26.6 1.0

Potassium binding site 2 out of 3 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:K702 b:31.7 occ:1.00 O B:HOH934 2.6 34.4 1.0 O B:HOH1024 2.7 41.7 1.0 O6 B:G136 2.7 18.5 1.0 O B:HOH957 2.7 22.0 1.0 O B:HOH1028 2.8 34.9 1.0 O4 B:U135 3.0 21.5 1.0 O B:HOH991 3.1 32.0 1.0 O4 B:U137 3.2 19.1 1.0 C6 B:G136 3.7 20.6 1.0 C4 B:U135 3.8 21.4 1.0 O B:HOH1042 3.8 40.0 1.0 N7 B:G136 3.9 20.0 1.0 O B:HOH918 3.9 19.5 1.0 C4 B:U137 4.1 18.6 1.0 O B:HOH861 4.1 21.2 1.0 C5 B:G136 4.2 21.2 1.0 N4 B:C172 4.3 21.2 1.0 N6 B:A173 4.4 22.1 1.0 O6 B:G171 4.4 23.1 1.0 C5 B:U135 4.4 22.9 1.0 N3 B:U137 4.5 18.1 1.0 N3 B:U135 4.6 21.2 1.0 O B:HOH879 4.9 34.5 1.0 N1 B:G136 5.0 20.1 1.0 O B:HOH967 5.0 38.1 1.0

Potassium binding site 3 out of 3 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:K703 b:42.6 occ:1.00 O2' B:G162 2.8 20.0 1.0 O6 B:G149 2.8 20.3 1.0 O A:GLY57 3.0 18.0 1.0 N3 B:G162 3.0 20.4 1.0 N2 B:G150 3.3 19.6 1.0 C2' B:G162 3.3 21.2 1.0 C1' B:G162 3.3 21.9 1.0 O A:HOH114 3.4 31.6 1.0 C6 B:C163 3.5 18.6 1.0 C5 B:C163 3.6 17.9 1.0 C2 B:G150 3.7 21.4 1.0 N1 B:G150 3.7 22.3 1.0 N1 B:C163 3.8 19.9 1.0 C A:GLY57 3.8 18.0 1.0 C6 B:G149 3.8 22.8 1.0 C4 B:G162 3.9 20.3 1.0 C2 B:G162 3.9 20.4 1.0 N2 B:G162 4.0 18.0 1.0 C4 B:C163 4.0 20.0 1.0 CA A:GLY57 4.0 17.6 1.0 N9 B:G162 4.1 20.8 1.0 C2 B:C163 4.1 21.3 1.0 N1 B:G149 4.2 20.6 1.0 N3 B:C163 4.2 21.4 1.0 N1 B:A161 4.3 21.2 1.0 O4' B:C163 4.4 18.2 1.0 C2 B:A161 4.5 22.8 1.0 O4' B:G162 4.5 23.3 1.0 C1' B:C163 4.5 19.2 1.0 N3 B:G150 4.6 22.6 1.0 O B:HOH883 4.6 21.7 1.0 O A:ALA56 4.7 19.4 1.0 N4 B:C163 4.7 19.2 1.0 C6 B:G150 4.7 22.9 1.0 C3' B:G162 4.8 20.8 1.0 O2 B:C163 4.9 20.3 1.0

R.T.Batey, R.P.Rambo, L.Lucast, B.Rha, J.A.Doudna. Crystal Structure of the Ribonucleoprotein Core of the Signal Recognition Particle. Science V. 287 1232 2000.
ISSN: ISSN 0036-8075
PubMed: 10678824
DOI: 10.1126/SCIENCE.287.5456.1232