Cobalt in PDB 2pxd: Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxd 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 (°)	131.881, 77.867, 32.428, 90.00, 94.04, 90.00
R / Rfree (%)	25.1 / 28.3

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

Cobalt binding site 1 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:40.3 occ:1.00 CO B:NCO201 0.0 40.3 1.0 N2 B:NCO201 2.0 38.5 1.0 N5 B:NCO201 2.0 37.5 1.0 N1 B:NCO201 2.0 37.6 1.0 N3 B:NCO201 2.0 38.3 1.0 N6 B:NCO201 2.0 36.6 1.0 N4 B:NCO201 2.0 37.2 1.0 N7 B:G170 4.2 12.2 1.0 O4 B:U137 4.3 14.3 1.0 O6 B:G170 4.4 8.4 1.0 O6 B:G171 4.8 11.7 1.0

Cobalt binding site 2 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:57.2 occ:1.00 CO B:NCO202 0.0 57.2 1.0 N3 B:NCO202 2.0 57.1 1.0 N5 B:NCO202 2.0 57.4 1.0 N6 B:NCO202 2.0 56.6 1.0 N1 B:NCO202 2.0 56.4 1.0 N4 B:NCO202 2.0 56.6 1.0 N2 B:NCO202 2.0 55.2 1.0 O6 B:G145 3.8 11.5 1.0 OP1 B:C163 3.9 27.6 1.0 O4 B:U146 4.1 20.7 1.0 O6 B:G144 4.3 32.0 1.0 OP2 B:C163 4.4 26.1 1.0 N7 B:G144 4.4 36.9 1.0 N7 B:G145 4.6 12.1 1.0 OP2 B:A164 4.6 23.4 1.0 P B:C163 4.6 28.0 1.0 C6 B:G145 4.8 11.1 1.0 C6 B:G144 4.8 33.6 1.0 C5 B:G144 4.8 34.9 1.0

Cobalt binding site 3 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:63.3 occ:0.93 CO B:NCO203 0.0 63.3 0.9 N5 B:NCO203 2.0 63.7 0.9 N3 B:NCO203 2.0 63.3 0.9 N6 B:NCO203 2.0 63.0 0.9 N2 B:NCO203 2.0 63.3 0.9 N1 B:NCO203 2.0 63.6 0.9 N4 B:NCO203 2.0 63.3 0.9 OP2 B:G149 3.1 34.5 1.0 OP1 B:A148 3.9 51.6 1.0 O6 B:G150 4.2 20.0 1.0 N7 B:G150 4.3 20.6 1.0 P B:G149 4.5 43.6 1.0 P B:A148 4.7 71.5 1.0 OP2 B:A148 4.7 51.1 1.0 O4 B:U151 4.9 28.9 1.0 O5' B:A148 5.0 64.8 1.0 C6 B:G150 5.0 18.7 1.0

Cobalt binding site 4 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:71.6 occ:0.92 CO B:NCO204 0.0 71.6 0.9 N5 B:NCO204 2.0 71.5 0.9 N4 B:NCO204 2.0 70.8 0.9 N3 B:NCO204 2.0 71.7 0.9 N1 B:NCO204 2.0 71.4 0.9 N6 B:NCO204 2.0 71.3 0.9 N2 B:NCO204 2.0 71.4 0.9 O6 B:G154 4.2 24.2 1.0 N7 B:G154 4.7 18.6 1.0

Cobalt binding site 5 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:87.3 occ:0.73 CO B:NCO205 0.0 87.3 0.7 N6 B:NCO205 2.0 86.7 0.7 N5 B:NCO205 2.0 86.5 0.7 N2 B:NCO205 2.0 86.6 0.7 N3 B:NCO205 2.0 86.2 0.7 N1 B:NCO205 2.0 86.3 0.7 N4 B:NCO205 2.0 86.4 0.7 N7 B:G158 4.2 25.7 1.0 O6 B:G158 4.7 24.1 1.0

Cobalt binding site 6 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:75.0 occ:0.78 CO B:NCO206 0.0 75.0 0.8 N4 B:NCO206 2.0 74.1 0.8 N6 B:NCO206 2.0 74.0 0.8 N3 B:NCO206 2.0 73.3 0.8 N5 B:NCO206 2.0 73.7 0.8 N1 B:NCO206 2.0 73.6 0.8 N2 B:NCO206 2.0 73.5 0.8 OP2 B:U146 4.2 36.9 1.0 OP2 B:C147 4.2 37.2 1.0 N7 B:G162 4.5 20.3 1.0 OP2 B:A161 4.7 38.7 1.0 OP1 B:U146 4.8 38.0 1.0 P B:U146 4.9 44.8 1.0

Cobalt binding site 7 out of 7 in the Variant 1 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 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:74.4 occ:0.98 CO B:NCO207 0.0 74.4 1.0 N3 B:NCO207 2.0 73.6 1.0 N5 B:NCO207 2.0 73.0 1.0 N6 B:NCO207 2.0 73.4 1.0 N2 B:NCO207 2.0 72.0 1.0 N4 B:NCO207 2.0 73.3 1.0 N1 B:NCO207 2.0 72.5 1.0 N7 B:G132 3.7 34.5 1.0 O6 B:G132 3.9 33.8 1.0 O6 B:G131 4.1 25.9 1.0 O4 B:U175 4.1 17.5 1.0 N7 B:G131 4.2 25.4 1.0 O6 B:G133 4.2 19.5 1.0 C5 B:G132 4.5 33.8 1.0 C6 B:G131 4.5 23.1 1.0 C5 B:G131 4.6 23.6 1.0 C6 B:G132 4.6 33.5 1.0 C8 B:G132 4.8 35.1 1.0 O4 B:U176 4.8 24.4 1.0 N7 B:G133 4.8 20.5 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