Cobalt in PDB 2pxk: Variant 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxk 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 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.607, 77.916, 32.436, 90.00, 94.53, 90.00
R / Rfree (%)	27.5 / 31.1

The binding sites of Cobalt atom in the Variant 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxk). 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxk:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:49.0 occ:0.91 CO B:NCO201 0.0 49.0 0.9 N3 B:NCO201 2.0 47.1 0.9 N2 B:NCO201 2.0 48.0 0.9 N4 B:NCO201 2.0 47.6 0.9 N1 B:NCO201 2.0 49.4 0.9 N5 B:NCO201 2.0 48.9 0.9 N6 B:NCO201 2.0 48.4 0.9 N7 B:G170 4.1 45.2 1.0 O6 B:G170 4.1 43.7 1.0 O6 B:G171 4.3 36.3 1.0 O4 B:U137 4.4 33.4 1.0 C6 B:G170 4.8 42.5 1.0 C5 B:G170 4.8 44.2 1.0 O6 B:G136 4.9 44.6 1.0

Cobalt binding site 2 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:62.6 occ:0.82 CO B:NCO202 0.0 62.6 0.8 N3 B:NCO202 2.0 62.0 0.8 N4 B:NCO202 2.0 62.0 0.8 N2 B:NCO202 2.0 62.1 0.8 N1 B:NCO202 2.0 60.3 0.8 N6 B:NCO202 2.0 61.5 0.8 N5 B:NCO202 2.0 60.7 0.8 OP1 B:C163 4.0 37.6 1.0 O6 B:G145 4.5 32.3 1.0 OP2 B:A164 4.5 33.2 1.0 OP2 B:C163 4.6 36.5 1.0 O4 B:U146 4.6 24.4 1.0 P B:C163 4.7 43.3 1.0 N7 B:G144 4.8 50.0 1.0 O6 B:G144 4.9 49.1 1.0

Cobalt binding site 3 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:80.6 occ:0.91 CO B:NCO203 0.0 80.6 0.9 N6 B:NCO203 2.0 78.8 0.9 N2 B:NCO203 2.0 78.9 0.9 N1 B:NCO203 2.0 78.7 0.9 N5 B:NCO203 2.0 78.8 0.9 N4 B:NCO203 2.0 79.4 0.9 N3 B:NCO203 2.0 79.0 0.9 OP2 B:G149 3.6 50.1 1.0 OP1 B:A148 4.0 65.7 1.0 O6 B:G150 4.1 42.5 1.0 N7 B:G150 4.1 40.9 1.0 C6 B:G150 4.8 41.0 1.0 O4 B:U151 4.8 35.8 1.0 C5 B:G150 4.9 41.1 1.0 P B:A148 4.9 92.0 1.0 P B:G149 5.0 59.8 1.0

Cobalt binding site 4 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:69.9 occ:0.90 CO B:NCO204 0.0 69.9 0.9 N5 B:NCO204 2.0 69.0 0.9 N1 B:NCO204 2.0 69.2 0.9 N3 B:NCO204 2.0 69.7 0.9 N4 B:NCO204 2.0 70.4 0.9 N2 B:NCO204 2.0 68.5 0.9 N6 B:NCO204 2.0 69.8 0.9 N7 B:G154 4.6 32.7 1.0 O6 B:G154 4.7 40.5 1.0

Cobalt binding site 5 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:86.3 occ:0.67 CO B:NCO205 0.0 86.3 0.7 N3 B:NCO205 2.0 85.5 0.7 N6 B:NCO205 2.0 85.4 0.7 N1 B:NCO205 2.0 85.6 0.7 N5 B:NCO205 2.0 85.5 0.7 N4 B:NCO205 2.0 85.0 0.7 N2 B:NCO205 2.0 84.8 0.7 N7 B:G158 3.7 34.7 1.0 O6 B:G158 4.3 40.9 1.0 C5 B:G158 4.6 36.0 1.0 C8 B:G158 4.6 34.9 1.0 C6 B:G158 4.8 37.9 1.0

Cobalt binding site 6 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:80.9 occ:0.81 CO B:NCO206 0.0 80.9 0.8 N2 B:NCO206 2.0 79.6 0.8 N1 B:NCO206 2.0 79.6 0.8 N5 B:NCO206 2.0 79.4 0.8 N4 B:NCO206 2.0 79.5 0.8 N3 B:NCO206 2.0 79.0 0.8 N6 B:NCO206 2.0 79.3 0.8 OP2 B:C147 4.2 52.6 1.0 OP2 B:U146 4.4 51.1 1.0 N7 B:G162 4.5 25.1 1.0 OP2 B:A161 4.6 45.3 1.0 OP1 B:U146 4.8 52.8 1.0

Cobalt binding site 7 out of 7 in the Variant 8 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 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:55.9 occ:0.95 CO B:NCO207 0.0 55.9 0.9 N5 B:NCO207 2.0 54.3 0.9 N4 B:NCO207 2.0 54.9 0.9 N2 B:NCO207 2.0 54.9 0.9 N3 B:NCO207 2.0 55.0 0.9 N6 B:NCO207 2.0 54.6 0.9 N1 B:NCO207 2.0 54.6 0.9 O4 B:U176 4.0 37.1 1.0 O4 B:U133 4.4 45.6 1.0 O6 B:G175 4.5 32.6 1.0 O6 B:G132 4.5 46.4 1.0 N7 B:G131 4.8 54.3 1.0 O6 B:G131 4.9 53.5 1.0 N4 B:C174 4.9 33.9 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