Cobalt in PDB 2pxv: Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxv 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 (°)	129.262, 78.039, 32.333, 90.00, 94.14, 90.00
R / Rfree (%)	27.7 / 31.4

The binding sites of Cobalt atom in the Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxv). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxv:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:55.6 occ:0.93 CO B:NCO201 0.0 55.6 0.9 N5 B:NCO201 2.0 55.0 0.9 N2 B:NCO201 2.0 54.4 0.9 N3 B:NCO201 2.0 54.0 0.9 N1 B:NCO201 2.0 54.0 0.9 N4 B:NCO201 2.0 54.2 0.9 N6 B:NCO201 2.0 54.9 0.9 O4 B:U137 4.4 16.3 1.0 N7 B:G170 4.4 22.9 1.0 O6 B:G170 4.7 18.6 1.0

Cobalt binding site 2 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:78.1 occ:0.94 CO B:NCO202 0.0 78.1 0.9 N1 B:NCO202 2.0 77.2 0.9 N2 B:NCO202 2.0 77.5 0.9 N6 B:NCO202 2.0 76.6 0.9 N3 B:NCO202 2.0 77.0 0.9 N4 B:NCO202 2.0 76.6 0.9 N5 B:NCO202 2.0 77.0 0.9 OP1 B:C163 3.9 33.4 1.0 OP2 B:C142 4.5 56.9 1.0 O6 B:G145 4.6 16.0 1.0 O4 B:U146 4.6 24.8 1.0 N7 B:G144 4.7 36.5 1.0 OP1 B:C142 4.7 54.9 1.0 OP2 B:A164 4.7 37.6 1.0 P B:C163 4.8 34.9 1.0 OP2 B:C163 4.8 28.4 1.0 OP1 B:C141 4.8 42.1 1.0 N7 B:G145 4.9 17.7 1.0

Cobalt binding site 3 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:81.9 occ:0.92 CO B:NCO203 0.0 81.9 0.9 N5 B:NCO203 2.0 80.6 0.9 N2 B:NCO203 2.0 81.3 0.9 N1 B:NCO203 2.0 81.0 0.9 N6 B:NCO203 2.0 81.0 0.9 N4 B:NCO203 2.0 80.4 0.9 N3 B:NCO203 2.0 80.1 0.9 OP2 B:G149 3.6 47.9 1.0 N7 B:G150 4.0 38.9 1.0 O6 B:G150 4.1 36.8 1.0 OP1 B:A148 4.3 48.8 1.0 O4 B:U151 4.5 36.3 1.0 OP2 B:A148 4.5 48.3 1.0 P B:A148 4.8 56.2 1.0 C5 B:G150 4.8 37.1 1.0 C6 B:G150 4.8 35.7 1.0

Cobalt binding site 4 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:65.7 occ:0.88 CO B:NCO204 0.0 65.7 0.9 N6 B:NCO204 2.0 64.1 0.9 N4 B:NCO204 2.0 64.0 0.9 N5 B:NCO204 2.0 64.4 0.9 N2 B:NCO204 2.0 65.6 0.9 N1 B:NCO204 2.0 65.7 0.9 N3 B:NCO204 2.0 64.4 0.9 O6 B:G154 4.1 29.2 1.0 N7 B:G154 4.7 21.6 1.0 C6 B:G154 5.0 22.3 1.0

Cobalt binding site 5 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:77.7 occ:0.67 CO B:NCO205 0.0 77.7 0.7 N4 B:NCO205 2.0 77.2 0.7 N3 B:NCO205 2.0 77.4 0.7 N1 B:NCO205 2.0 77.7 0.7 N6 B:NCO205 2.0 77.4 0.7 N5 B:NCO205 2.0 77.6 0.7 N2 B:NCO205 2.0 77.4 0.7 N7 B:G158 3.6 33.0 1.0 O6 B:G158 4.1 32.7 1.0 C5 B:G158 4.4 30.6 1.0 C8 B:G158 4.6 34.2 1.0 C6 B:G158 4.6 30.6 1.0

Cobalt binding site 6 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:95.6 occ:0.89 CO B:NCO206 0.0 95.6 0.9 N4 B:NCO206 2.0 95.1 0.9 N6 B:NCO206 2.0 95.5 0.9 N2 B:NCO206 2.0 94.8 0.9 N5 B:NCO206 2.0 95.3 0.9 N1 B:NCO206 2.0 95.1 0.9 N3 B:NCO206 2.0 95.4 0.9 OP2 B:C147 3.6 47.6 1.0 N7 B:G162 4.3 33.2 1.0 OP2 B:A161 4.4 46.3 1.0 O6 B:G162 4.5 38.5 1.0 OP2 B:U146 4.9 49.3 1.0

Cobalt binding site 7 out of 8 in the Variant 6 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 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:89.1 occ:0.64 CO B:NCO207 0.0 89.1 0.6 N4 B:NCO207 2.0 88.8 0.6 N2 B:NCO207 2.0 88.8 0.6 N1 B:NCO207 2.0 88.8 0.6 N5 B:NCO207 2.0 88.8 0.6 N3 B:NCO207 2.0 88.5 0.6 N6 B:NCO207 2.0 88.8 0.6 O6 B:G134 3.9 27.2 1.0 N7 B:G134 4.2 24.1 1.0 N7 B:G133 4.4 22.3 1.0 O4 B:U135 4.4 25.4 1.0 O6 B:G133 4.6 22.0 1.0 N6 B:A173 4.6 26.4 1.0 C6 B:G134 4.8 24.2 1.0 C5 B:G134 4.9 21.1 1.0

Cobalt binding site 8 out of 8 in the Variant 6 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 8 of Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co208 b:86.4 occ:0.73 CO B:NCO208 0.0 86.4 0.7 N1 B:NCO208 2.0 85.7 0.7 N6 B:NCO208 2.0 86.1 0.7 N5 B:NCO208 2.0 86.0 0.7 N4 B:NCO208 2.0 85.7 0.7 N3 B:NCO208 2.0 85.7 0.7 N2 B:NCO208 2.0 85.6 0.7 O4 B:U175 3.7 28.3 1.0 O6 B:G131 4.0 29.6 1.0 O4 B:U132 4.1 34.8 1.0 O6 B:G130 4.1 30.0 1.0 N7 B:G130 4.4 28.2 1.0 C4 B:U175 4.7 25.2 1.0 N4 B:C177 4.7 38.7 1.0 C6 B:G130 4.7 25.1 1.0 N7 B:G131 4.8 25.7 1.0 C5 B:G130 4.8 25.9 1.0 C6 B:G131 5.0 24.9 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