Cobalt in PDB 2pxf: Variant 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

The structure of Variant 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxf 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)	40.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.320, 77.450, 32.690, 90.00, 94.15, 90.00
R / Rfree (%)	26.8 / 31.2

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

Cobalt binding site 1 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:61.3 occ:1.00 CO B:NCO201 0.0 61.3 1.0 N2 B:NCO201 2.0 59.2 1.0 N1 B:NCO201 2.0 58.9 1.0 N3 B:NCO201 2.0 58.6 1.0 N6 B:NCO201 2.0 60.0 1.0 N4 B:NCO201 2.0 59.8 1.0 N5 B:NCO201 2.0 59.1 1.0 O4 B:U137 4.2 16.6 1.0 N7 B:G170 4.3 24.3 1.0 O6 B:G170 4.5 20.4 1.0 O6 B:G171 4.8 12.0 1.0

Cobalt binding site 2 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:76.5 occ:1.00 CO B:NCO202 0.0 76.5 1.0 N5 B:NCO202 2.0 75.7 1.0 N6 B:NCO202 2.0 75.4 1.0 N4 B:NCO202 2.0 74.5 1.0 N2 B:NCO202 2.0 74.6 1.0 N3 B:NCO202 2.0 74.5 1.0 N1 B:NCO202 2.0 75.4 1.0 OP1 B:C163 3.9 37.0 1.0 O6 B:G145 4.0 28.4 1.0 O4 B:U146 4.2 23.6 1.0 OP2 B:C163 4.3 34.5 1.0 OP2 B:A164 4.6 28.4 1.0 P B:C163 4.6 38.3 1.0 N7 B:G145 4.8 31.1 1.0 N7 B:G144 4.9 50.0 1.0 C6 B:G145 4.9 29.2 1.0 O6 B:G144 5.0 47.4 1.0

Cobalt binding site 3 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:81.6 occ:0.93 CO B:NCO203 0.0 81.6 0.9 N3 B:NCO203 2.0 81.2 0.9 N1 B:NCO203 2.0 81.1 0.9 N5 B:NCO203 2.0 81.1 0.9 N6 B:NCO203 2.0 81.2 0.9 N4 B:NCO203 2.0 80.3 0.9 N2 B:NCO203 2.0 80.8 0.9 OP2 B:G149 3.3 48.7 1.0 OP1 B:A148 3.9 56.8 1.0 O6 B:G150 4.2 28.2 1.0 N7 B:G150 4.2 32.1 1.0 P B:G149 4.6 61.6 1.0 P B:A148 4.9 62.0 1.0 OP2 B:A148 4.9 55.4 1.0 O4 B:U151 4.9 42.9 1.0 C6 B:G150 4.9 28.7 1.0 C5 B:G150 4.9 30.2 1.0

Cobalt binding site 4 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:84.8 occ:0.92 CO B:NCO204 0.0 84.8 0.9 N4 B:NCO204 2.0 83.8 0.9 N5 B:NCO204 2.0 84.2 0.9 N2 B:NCO204 2.0 84.5 0.9 N1 B:NCO204 2.0 83.9 0.9 N6 B:NCO204 2.0 84.0 0.9 N3 B:NCO204 2.0 83.8 0.9 N7 B:G154 4.4 30.4 1.0 O6 B:G154 4.4 36.2 1.0

Cobalt binding site 5 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co205 b:97.9 occ:0.73 CO B:NCO205 0.0 97.9 0.7 N3 B:NCO205 2.0 97.1 0.7 N6 B:NCO205 2.0 97.1 0.7 N2 B:NCO205 2.0 97.2 0.7 N1 B:NCO205 2.0 97.1 0.7 N4 B:NCO205 2.0 97.6 0.7 N5 B:NCO205 2.0 97.2 0.7 N7 B:G158 3.3 39.0 1.0 C8 B:G158 4.2 39.3 1.0 O6 B:G158 4.3 38.7 1.0 C5 B:G158 4.4 37.4 1.0 C6 B:G158 4.7 36.9 1.0

Cobalt binding site 6 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co206 b:81.7 occ:0.78 CO B:NCO206 0.0 81.7 0.8 N6 B:NCO206 2.0 81.6 0.8 N2 B:NCO206 2.0 81.3 0.8 N4 B:NCO206 2.0 81.9 0.8 N3 B:NCO206 2.0 81.6 0.8 N1 B:NCO206 2.0 81.6 0.8 N5 B:NCO206 2.0 81.7 0.8 OP2 B:C147 4.1 48.6 1.0 N7 B:G162 4.2 28.0 1.0 OP2 B:A161 4.2 47.6 1.0 O6 B:G162 4.2 30.9 1.0 OP2 B:U146 4.9 50.0 1.0 C5 B:G162 5.0 27.3 1.0

Cobalt binding site 7 out of 7 in the Variant 5 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 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Co207 b:73.0 occ:0.98 CO B:NCO207 0.0 73.0 1.0 N5 B:NCO207 2.0 73.2 1.0 N4 B:NCO207 2.0 72.9 1.0 N1 B:NCO207 2.0 73.1 1.0 N2 B:NCO207 2.0 72.1 1.0 N6 B:NCO207 2.0 73.7 1.0 N3 B:NCO207 2.0 72.8 1.0 N7 B:G132 3.9 37.8 1.0 O6 B:G132 4.2 35.1 1.0 O6 B:G133 4.3 25.4 1.0 O6 B:G131 4.4 33.9 1.0 N7 B:G133 4.5 26.8 1.0 N7 B:G131 4.6 32.2 1.0 O4 B:U175 4.6 21.6 1.0 C5 B:G132 4.7 36.0 1.0 C6 B:G131 4.8 30.7 1.0 C8 B:G132 4.8 37.8 1.0 C6 B:G132 4.8 35.7 1.0 C5 B:G131 4.8 30.9 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