Cobalt in PDB 2pxt: Variant 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxt 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 (°)	134.380, 78.520, 32.600, 90.00, 94.99, 90.00
R / Rfree (%)	22.3 / 24.5

The binding sites of Cobalt atom in the Variant 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle (pdb code 2pxt). 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxt:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:64.0 occ:1.00 CO B:NCO201 0.0 64.0 1.0 N5 B:NCO201 2.0 58.6 1.0 N2 B:NCO201 2.0 59.0 1.0 N1 B:NCO201 2.0 59.3 1.0 N3 B:NCO201 2.0 58.9 1.0 N4 B:NCO201 2.0 59.6 1.0 N6 B:NCO201 2.0 59.2 1.0 O4 B:U137 4.2 36.8 1.0 N7 B:G170 4.4 41.2 1.0 O6 B:G170 4.4 40.3 1.0 O6 B:G171 4.6 35.2 1.0

Cobalt binding site 2 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:83.4 occ:0.95 CO B:NCO202 0.0 83.4 0.9 N3 B:NCO202 2.0 82.6 0.9 N5 B:NCO202 2.0 82.8 0.9 N4 B:NCO202 2.0 83.5 0.9 N6 B:NCO202 2.0 81.9 0.9 N1 B:NCO202 2.0 82.4 0.9 N2 B:NCO202 2.0 81.3 0.9 OP1 B:C163 3.9 45.5 1.0 O6 B:G145 4.0 47.9 1.0 OP2 B:A164 4.4 40.0 1.0 O4 B:U146 4.6 42.9 1.0 OP2 B:C163 4.6 43.8 1.0 N7 B:G144 4.6 57.9 1.0 O6 B:G144 4.7 55.4 1.0 P B:C163 4.7 46.6 1.0 N7 B:G145 5.0 45.8 1.0

Cobalt binding site 3 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:78.1 occ:0.90 CO B:NCO203 0.0 78.1 0.9 N1 B:NCO203 2.0 76.8 0.9 N4 B:NCO203 2.0 76.5 0.9 N2 B:NCO203 2.0 77.2 0.9 N6 B:NCO203 2.0 77.1 0.9 N3 B:NCO203 2.0 77.1 0.9 N5 B:NCO203 2.0 76.8 0.9 OP2 B:G149 3.7 51.6 1.0 OP1 B:A148 4.1 71.0 1.0 N7 B:G150 4.2 40.3 1.0 O6 B:G150 4.3 42.5 1.0 O4 B:U151 4.4 46.8 1.0 OP2 B:A148 4.8 67.7 1.0 P B:A148 4.9 70.3 1.0 C5 B:G150 5.0 40.9 1.0 C6 B:G150 5.0 40.4 1.0

Cobalt binding site 4 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:87.5 occ:0.97 CO B:NCO204 0.0 87.5 1.0 N6 B:NCO204 2.0 87.1 1.0 N2 B:NCO204 2.0 87.4 1.0 N4 B:NCO204 2.0 86.3 1.0 N5 B:NCO204 2.0 86.7 1.0 N1 B:NCO204 2.0 87.1 1.0 N3 B:NCO204 2.0 87.0 1.0 O6 B:G154 4.2 51.1 1.0 N7 B:G154 4.3 45.8 1.0 C6 B:G154 4.9 47.9 1.0 C5 B:G154 4.9 46.9 1.0

Cobalt binding site 5 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:0.2 occ:0.87 CO B:NCO205 0.0 0.2 0.9 N2 B:NCO205 2.0 0.3 0.9 N6 B:NCO205 2.0 0.7 0.9 N3 B:NCO205 2.0 1.0 0.9 N1 B:NCO205 2.0 0.3 0.9 N5 B:NCO205 2.0 1.0 0.9 N4 B:NCO205 2.0 0.8 0.9 N7 B:G158 3.8 53.8 1.0 O6 B:G158 4.2 51.0 1.0 C5 B:G158 4.7 52.3 1.0 C6 B:G158 4.8 50.8 1.0 C8 B:G158 4.8 52.9 1.0 O6 B:G159 4.9 45.1 1.0

Cobalt binding site 6 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:97.3 occ:0.85 CO B:NCO206 0.0 97.3 0.8 N6 B:NCO206 2.0 97.1 0.8 N1 B:NCO206 2.0 96.3 0.8 N2 B:NCO206 2.0 96.3 0.8 N4 B:NCO206 2.0 96.7 0.8 N3 B:NCO206 2.0 97.2 0.8 N5 B:NCO206 2.0 96.5 0.8 OP2 B:C147 4.0 60.3 1.0 OP2 B:A161 4.4 58.9 1.0 N7 B:G162 4.4 40.0 1.0 OP2 B:U146 4.5 57.5 1.0 O6 B:G162 4.7 45.1 1.0

Cobalt binding site 7 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:73.4 occ:0.87 CO B:NCO207 0.0 73.4 0.9 N6 B:NCO207 2.0 72.5 0.9 N2 B:NCO207 2.0 72.4 0.9 N5 B:NCO207 2.0 72.0 0.9 N3 B:NCO207 2.0 71.3 0.9 N4 B:NCO207 2.0 72.7 0.9 N1 B:NCO207 2.0 72.3 0.9 N7 B:G176 4.3 49.9 1.0 O6 B:G177 4.4 45.2 1.0 O6 B:G176 4.5 51.2 1.0 N4 B:C175 4.9 43.1 1.0 O6 B:G130 5.0 51.4 1.0

Cobalt binding site 8 out of 8 in the Variant 15 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 15 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co208 b:85.7 occ:0.88 CO B:NCO208 0.0 85.7 0.9 N5 B:NCO208 2.0 86.3 0.9 N3 B:NCO208 2.0 86.0 0.9 N6 B:NCO208 2.0 85.8 0.9 N1 B:NCO208 2.0 85.9 0.9 N2 B:NCO208 2.0 86.1 0.9 N4 B:NCO208 2.0 85.1 0.9 OP2 B:U132 4.2 52.6 1.0 OP2 B:G171 4.4 48.7 1.0 OP1 B:G170 4.5 51.7 1.0 OP2 B:C131 5.0 62.7 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