Cobalt in PDB 2pxe: Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxe was solved by A.Y.Keel, R.P.Rambo, R.T.Batey, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.480, 73.410, 33.160, 90.00, 94.65, 90.00
R / Rfree (%)	23.4 / 27.7

The binding sites of Cobalt atom in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxe). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxe:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:32.8 occ:0.95 CO B:NCO201 0.0 32.8 0.9 N4 B:NCO201 2.0 31.1 0.9 N2 B:NCO201 2.0 30.4 0.9 N3 B:NCO201 2.0 30.9 0.9 N1 B:NCO201 2.0 30.0 0.9 N5 B:NCO201 2.0 30.6 0.9 N6 B:NCO201 2.0 31.2 0.9 O4 B:U137 3.9 22.3 1.0 O6 B:G170 4.3 18.4 1.0 N7 B:G170 4.5 17.8 1.0 O6 B:G171 4.6 15.3 1.0

Cobalt binding site 2 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:40.3 occ:0.86 CO B:NCO202 0.0 40.3 0.9 N4 B:NCO202 2.0 38.6 0.9 N1 B:NCO202 2.0 38.9 0.9 N5 B:NCO202 2.0 38.4 0.9 N6 B:NCO202 2.0 37.2 0.9 N2 B:NCO202 2.0 38.1 0.9 N3 B:NCO202 2.0 38.5 0.9 O4 B:U146 4.0 21.7 1.0 OP2 B:C163 4.0 16.6 1.0 OP1 B:C163 4.1 16.5 1.0 O6 B:G145 4.2 11.6 1.0 O6 B:G144 4.5 26.8 1.0 OP2 B:A164 4.5 12.8 1.0 P B:C163 4.6 17.5 1.0 N7 B:G144 4.7 26.4 1.0 N7 B:G145 4.9 17.2 1.0 C6 B:G144 4.9 26.8 1.0

Cobalt binding site 3 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:46.4 occ:1.00 CO B:NCO203 0.0 46.4 1.0 N1 B:NCO203 2.0 46.3 1.0 N4 B:NCO203 2.0 45.8 1.0 N5 B:NCO203 2.0 46.2 1.0 N6 B:NCO203 2.0 45.7 1.0 N2 B:NCO203 2.0 46.8 1.0 N3 B:NCO203 2.0 45.8 1.0 OP2 B:G149 3.7 22.5 1.0 OP1 B:A148 4.0 43.9 1.0 O6 B:G150 4.2 23.3 1.0 N7 B:G150 4.4 24.0 1.0 OP2 B:A148 4.6 41.6 1.0 O4 B:U151 4.7 18.2 1.0 P B:A148 4.7 45.4 1.0

Cobalt binding site 4 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:53.8 occ:1.00 CO B:NCO204 0.0 53.8 1.0 N1 B:NCO204 2.0 51.9 1.0 N4 B:NCO204 2.0 52.0 1.0 N5 B:NCO204 2.0 53.1 1.0 N3 B:NCO204 2.0 52.3 1.0 N6 B:NCO204 2.0 52.4 1.0 N2 B:NCO204 2.0 52.0 1.0 O6 B:G154 4.1 20.4 1.0 N7 B:G154 4.6 17.1 1.0 C6 B:G154 5.0 16.8 1.0

Cobalt binding site 5 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:73.3 occ:0.82 CO B:NCO205 0.0 73.3 0.8 N4 B:NCO205 2.0 71.9 0.8 N1 B:NCO205 2.0 72.3 0.8 N6 B:NCO205 2.0 71.6 0.8 N5 B:NCO205 2.0 71.5 0.8 N2 B:NCO205 2.0 71.6 0.8 N3 B:NCO205 2.0 71.5 0.8 O6 B:G158 4.2 22.5 1.0 N7 B:G158 4.4 21.4 1.0 C6 B:G158 4.9 21.9 1.0

Cobalt binding site 6 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:61.5 occ:0.92 CO B:NCO206 0.0 61.5 0.9 N1 B:NCO206 2.0 60.7 0.9 N4 B:NCO206 2.0 60.9 0.9 N5 B:NCO206 2.0 59.6 0.9 N3 B:NCO206 2.0 59.6 0.9 N2 B:NCO206 2.0 60.7 0.9 N6 B:NCO206 2.0 60.1 0.9 OP2 B:A161 4.2 22.9 1.0 N7 B:G162 4.4 24.0 1.0 OP2 B:U146 4.5 25.9 1.0 O6 B:G162 4.6 28.4 1.0 C5 B:C147 4.8 60.5 1.0

Cobalt binding site 7 out of 7 in the Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:50.5 occ:0.98 CO B:NCO207 0.0 50.5 1.0 N4 B:NCO207 2.0 50.0 1.0 N6 B:NCO207 2.0 50.5 1.0 N5 B:NCO207 2.0 50.3 1.0 N3 B:NCO207 2.0 50.2 1.0 N1 B:NCO207 2.0 48.7 1.0 N2 B:NCO207 2.0 48.8 1.0 O4 B:U133 4.1 17.6 1.0 O4 B:U176 4.2 18.1 1.0 O6 B:G131 4.2 26.6 1.0 O6 B:G132 4.6 23.6 1.0 O6 B:G175 4.6 19.2 1.0 O6 B:G174 4.8 24.3 1.0

A.Y.Keel, R.P.Rambo, R.T.Batey, J.S.Kieft. A General Strategy to Solve the Phase Problem in Rna Crystallography. Structure V. 15 761 2007.
ISSN: ISSN 0969-2126
PubMed: 17637337
DOI: 10.1016/J.STR.2007.06.003