Magnesium 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:

Potassium

(K)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 1dul:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg704 b:26.4 occ:1.00 O B:HOH947 2.0 27.1 1.0 O B:HOH920 2.0 16.0 1.0 O B:HOH896 2.0 23.6 1.0 O B:HOH814 2.1 27.8 1.0 O B:HOH1011 2.1 27.0 1.0 O B:HOH909 2.1 24.4 1.0 O B:HOH927 4.1 19.3 1.0 OP2 B:C163 4.1 22.1 1.0 O B:HOH900 4.2 17.7 1.0 O4 B:U146 4.2 23.3 1.0 O B:HOH859 4.2 26.0 1.0 N7 B:G145 4.2 22.4 1.0 O B:HOH951 4.3 32.0 1.0 N4 B:C147 4.3 19.9 1.0 OP2 B:G144 4.3 30.6 1.0 OP1 B:G144 4.4 34.5 1.0 OP2 B:G145 4.4 30.8 1.0 P B:G144 4.8 34.6 1.0 O B:HOH982 4.9 34.2 1.0 N7 B:G144 4.9 27.4 1.0 C8 B:G145 4.9 23.2 1.0 OP1 B:C163 5.0 22.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg705 b:34.3 occ:1.00 O B:HOH963 1.9 29.9 1.0 O B:HOH805 2.0 22.6 1.0 OP1 B:C141 2.1 20.2 1.0 O B:HOH889 2.2 36.6 1.0 O B:HOH982 2.3 34.2 1.0 O B:HOH996 2.5 42.2 1.0 P B:C141 3.5 20.4 1.0 O B:HOH851 3.9 30.3 1.0 O B:HOH900 4.2 17.7 1.0 C5' B:C141 4.2 19.9 1.0 OP2 B:C142 4.2 22.8 1.0 OP2 B:A164 4.2 18.4 1.0 O5' B:C141 4.2 20.0 1.0 O B:HOH1031 4.2 59.1 1.0 O B:HOH927 4.2 19.3 1.0 O B:HOH876 4.2 15.2 1.0 O B:HOH1019 4.3 38.5 1.0 O3' B:A140 4.4 18.9 1.0 OP2 B:C141 4.5 19.5 1.0 OP1 B:A164 4.6 17.9 1.0 O B:HOH946 4.6 23.6 1.0 O6 B:G144 4.8 23.7 1.0 O B:HOH904 4.9 32.4 1.0 O B:HOH971 4.9 50.5 1.0 P B:A164 4.9 18.9 1.0

Magnesium binding site 3 out of 4 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg706 b:56.4 occ:1.00 OP2 B:G149 1.9 31.1 1.0 O B:HOH1005 2.1 32.5 1.0 O B:HOH842 2.1 44.6 1.0 O B:HOH812 2.2 41.2 1.0 O B:HOH908 2.2 13.5 1.0 O B:HOH948 2.3 43.7 1.0 P B:G149 3.2 30.9 1.0 O5' B:G149 3.8 30.0 1.0 OP1 B:G149 3.9 32.1 1.0 OP1 B:A148 4.0 29.5 1.0 N7 B:G150 4.1 22.6 1.0 O6 B:G150 4.2 24.4 1.0 O5' B:A148 4.4 28.8 1.0 O3' B:A148 4.4 30.3 1.0 P B:A148 4.5 29.4 1.0 OP2 B:A148 4.6 27.4 1.0 C8 B:G149 4.6 22.8 1.0 N7 B:G149 4.7 23.3 1.0 O4 B:U151 4.7 25.3 1.0 C3' B:A148 4.8 29.3 1.0 O B:HOH950 4.9 49.3 1.0 C5 B:G150 4.9 23.0 1.0 O B:HOH824 4.9 51.6 1.0 OP2 B:G150 4.9 28.4 1.0 C6 B:G150 4.9 22.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 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:Mg707 b:51.3 occ:1.00 O B:HOH821 1.9 35.5 1.0 O B:HOH864 2.1 31.4 1.0 O B:HOH1047 2.1 54.0 1.0 O B:HOH1046 2.1 45.2 1.0 O B:HOH875 2.6 31.2 1.0 O B:HOH1035 2.8 43.8 1.0 O6 B:G154 3.9 28.3 1.0 N7 B:G154 3.9 25.2 1.0 OP1 B:A156 4.1 34.5 1.0 O B:HOH858 4.2 50.9 1.0 O B:HOH1002 4.2 40.1 1.0 C6 B:G154 4.4 27.4 1.0 O B:HOH874 4.4 27.9 1.0 C5 B:G154 4.4 26.2 1.0 OP2 B:A156 4.6 30.7 1.0 O B:HOH992 4.8 46.4 1.0 P B:A156 4.8 32.4 1.0 C8 B:G154 4.9 25.6 1.0 O B:HOH972 4.9 48.1 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