Cobalt in PDB 2pxl: Variant 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxl 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 (°)	122.688, 78.847, 32.460, 90.00, 95.91, 90.00
R / Rfree (%)	23.8 / 26

The binding sites of Cobalt atom in the Variant 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxl). 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxl:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:71.7 occ:1.00 CO B:NCO201 0.0 71.7 1.0 N2 B:NCO201 2.0 67.9 1.0 N5 B:NCO201 2.0 67.4 1.0 N6 B:NCO201 2.0 67.0 1.0 N3 B:NCO201 2.0 67.1 1.0 N4 B:NCO201 2.0 68.3 1.0 N1 B:NCO201 2.0 67.3 1.0 O4 B:U137 4.0 37.2 1.0 O6 B:G170 4.2 35.0 1.0 O6 B:G171 4.2 36.3 1.0 N7 B:G170 4.5 39.2 1.0 O6 B:G136 4.9 48.7 1.0 C6 B:G170 4.9 36.9 1.0

Cobalt binding site 2 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:83.8 occ:1.00 CO B:NCO202 0.0 83.8 1.0 N6 B:NCO202 2.0 83.4 1.0 N1 B:NCO202 2.0 83.2 1.0 N5 B:NCO202 2.0 83.6 1.0 N3 B:NCO202 2.0 82.3 1.0 N2 B:NCO202 2.0 82.3 1.0 N4 B:NCO202 2.0 82.6 1.0 O6 B:G145 4.0 48.0 1.0 OP1 B:C163 4.1 47.2 1.0 O6 B:G144 4.6 48.0 1.0 OP2 B:A164 4.6 33.9 1.0 OP2 B:C163 4.6 42.7 1.0 O4 B:U146 4.7 38.6 1.0 N7 B:G144 4.7 49.6 1.0 P B:C163 4.8 44.3 1.0 N7 B:G145 4.8 51.0 1.0 OP2 B:C142 4.9 62.5 1.0 C6 B:G145 5.0 49.5 1.0

Cobalt binding site 3 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:91.3 occ:0.98 CO B:NCO203 0.0 91.3 1.0 N6 B:NCO203 2.0 90.5 1.0 N1 B:NCO203 2.0 90.9 1.0 N2 B:NCO203 2.0 90.8 1.0 N3 B:NCO203 2.0 91.0 1.0 N4 B:NCO203 2.0 90.3 1.0 N5 B:NCO203 2.0 90.7 1.0 OP2 B:G149 3.6 56.2 1.0 O6 B:G150 4.1 37.9 1.0 OP1 B:A148 4.2 76.3 1.0 N7 B:G150 4.3 40.1 1.0 O4 B:U151 4.6 50.3 1.0 OP2 B:A148 4.7 73.7 1.0 P B:A148 4.9 92.4 1.0 C6 B:G150 4.9 36.8 1.0 C5 B:G150 4.9 39.0 1.0

Cobalt binding site 4 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:94.2 occ:0.98 CO B:NCO204 0.0 94.2 1.0 N4 B:NCO204 2.0 92.6 1.0 N2 B:NCO204 2.0 92.9 1.0 N5 B:NCO204 2.0 93.1 1.0 N6 B:NCO204 2.0 92.2 1.0 N1 B:NCO204 2.0 93.1 1.0 N3 B:NCO204 2.0 93.2 1.0 O6 B:G154 3.8 55.6 1.0 N7 B:G154 4.5 51.8 1.0 C6 B:G154 4.6 53.0 1.0 OP1 B:A156 4.7 57.3 1.0 C5 B:G154 4.8 51.4 1.0

Cobalt binding site 5 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:0.6 occ:0.67 CO B:NCO205 0.0 0.6 0.7 N6 B:NCO205 2.0 0.4 0.7 N2 B:NCO205 2.0 0.3 0.7 N3 B:NCO205 2.0 0.1 0.7 N1 B:NCO205 2.0 0.5 0.7 N4 B:NCO205 2.0 0.2 0.7 N5 B:NCO205 2.0 0.5 0.7 N7 B:G158 4.0 56.1 1.0 O6 B:G158 4.2 52.4 1.0 C5 B:G158 4.8 55.2 1.0 C6 B:G158 4.8 54.5 1.0

Cobalt binding site 6 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:0.8 occ:0.95 CO B:NCO206 0.0 0.8 1.0 N4 B:NCO206 2.0 99.9 0.9 N1 B:NCO206 2.0 99.9 0.9 N2 B:NCO206 2.0 0.2 1.0 N6 B:NCO206 2.0 99.9 0.9 N5 B:NCO206 2.0 99.7 0.9 N3 B:NCO206 2.0 99.9 0.9 OP2 B:A161 4.1 59.3 1.0 OP2 B:C147 4.1 64.2 1.0 N7 B:G162 4.6 36.6 1.0 O6 B:G162 4.7 44.3 1.0 OP2 B:U146 5.0 60.2 1.0

Cobalt binding site 7 out of 7 in the Variant 9 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 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:0.6 occ:1.00 CO B:NCO207 0.0 0.6 1.0 N5 B:NCO207 2.0 0.2 1.0 N1 B:NCO207 2.0 0.5 1.0 N2 B:NCO207 2.0 0.0 1.0 N3 B:NCO207 2.0 0.9 1.0 N6 B:NCO207 2.0 0.3 1.0 N4 B:NCO207 2.0 0.6 1.0 O6 B:G133 4.1 40.2 1.0 N7 B:G132 4.4 38.5 1.0 O6 B:G132 4.4 38.2 1.0 O4 B:U175 4.5 45.9 1.0 N7 B:G133 4.7 41.2 1.0 C6 B:G133 5.0 41.2 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