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

Protein crystallography data

The structure of Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle, PDB code: 2pxb 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 (°) 130.981, 78.684, 32.274, 90.00, 94.86, 90.00
R / Rfree (%) 25.4 / 27.2

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 2pxb

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Cobalt binding site 1 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co201

b:51.2
occ:0.92
CO B:NCO201 0.0 51.2 0.9
N2 B:NCO201 2.0 47.0 0.9
N5 B:NCO201 2.0 46.1 0.9
N4 B:NCO201 2.0 47.5 0.9
N3 B:NCO201 2.0 47.1 0.9
N1 B:NCO201 2.0 44.4 0.9
N6 B:NCO201 2.0 46.0 0.9
O4 B:U137 4.3 36.3 1.0
N7 B:G170 4.3 40.7 1.0
O6 B:G170 4.4 39.5 1.0
O6 B:G171 4.5 35.2 1.0

Cobalt binding site 2 out of 8 in 2pxb

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Cobalt binding site 2 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co202

b:88.3
occ:1.00
CO B:NCO202 0.0 88.3 1.0
N3 B:NCO202 2.0 87.5 1.0
N6 B:NCO202 2.0 86.7 1.0
N1 B:NCO202 2.0 86.8 1.0
N5 B:NCO202 2.0 86.6 1.0
N2 B:NCO202 2.0 86.5 1.0
N4 B:NCO202 2.0 87.8 1.0
O6 B:G145 4.2 41.7 1.0
OP1 B:C163 4.3 38.8 1.0
O4 B:U146 4.4 44.9 1.0
OP2 B:A164 4.5 38.3 1.0
OP2 B:C163 4.6 34.5 1.0
N7 B:G144 4.6 53.7 1.0
O6 B:G144 4.8 51.5 1.0
OP1 B:G144 4.8 88.3 1.0
P B:C163 4.9 43.4 1.0
OP1 B:C141 4.9 46.5 1.0
N7 B:G145 5.0 41.4 1.0

Cobalt binding site 3 out of 8 in 2pxb

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Cobalt binding site 3 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co203

b:79.3
occ:0.95
CO B:NCO203 0.0 79.3 0.9
N3 B:NCO203 2.0 79.1 0.9
N6 B:NCO203 2.0 79.2 0.9
N5 B:NCO203 2.0 79.3 0.9
N4 B:NCO203 2.0 79.1 0.9
N1 B:NCO203 2.0 78.5 0.9
N2 B:NCO203 2.0 78.3 0.9
OP2 B:G149 3.4 56.5 1.0
OP1 B:A148 4.2 65.5 1.0
N7 B:G150 4.4 40.0 1.0
O6 B:G150 4.4 43.7 1.0
OP2 B:A148 4.7 65.2 1.0
P B:G149 4.7 62.9 1.0
O4 B:U151 4.8 39.1 1.0
P B:A148 4.8 84.9 1.0

Cobalt binding site 4 out of 8 in 2pxb

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Cobalt binding site 4 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co204

b:71.0
occ:0.87
CO B:NCO204 0.0 71.0 0.9
N5 B:NCO204 2.0 69.1 0.9
N6 B:NCO204 2.0 69.3 0.9
N3 B:NCO204 2.0 69.6 0.9
N2 B:NCO204 2.0 68.7 0.9
N1 B:NCO204 2.0 70.1 0.9
N4 B:NCO204 2.0 69.0 0.9
O6 B:G154 4.2 39.9 1.0
N7 B:G154 4.6 35.3 1.0
C6 B:G154 5.0 35.0 1.0

Cobalt binding site 5 out of 8 in 2pxb

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Cobalt binding site 5 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co205

b:98.6
occ:0.89
CO B:NCO205 0.0 98.6 0.9
N6 B:NCO205 2.0 98.0 0.9
N5 B:NCO205 2.0 98.1 0.9
N3 B:NCO205 2.0 98.3 0.9
N2 B:NCO205 2.0 97.8 0.9
N1 B:NCO205 2.0 97.9 0.9
N4 B:NCO205 2.0 97.4 0.9
N7 B:G158 4.0 48.7 1.0
O6 B:G158 4.6 48.1 1.0
C8 B:G158 4.9 49.3 1.0
C5 B:G158 4.9 48.3 1.0

Cobalt binding site 6 out of 8 in 2pxb

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Cobalt binding site 6 out of 8 in the Variant 2 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 2 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:0.89
CO B:NCO206 0.0 0.8 0.9
N2 B:NCO206 2.0 0.9 0.9
N4 B:NCO206 2.0 0.0 0.9
N3 B:NCO206 2.0 0.8 0.9
N6 B:NCO206 2.0 0.0 0.9
N1 B:NCO206 2.0 0.1 0.9
N5 B:NCO206 2.0 0.7 0.9
OP2 B:A161 4.2 56.4 1.0
OP2 B:C147 4.2 52.0 1.0
OP2 B:U146 4.4 59.9 1.0
N7 B:G162 4.5 35.5 1.0
O6 B:G162 4.9 42.5 1.0

Cobalt binding site 7 out of 8 in 2pxb

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Cobalt binding site 7 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co207

b:97.7
occ:0.87
CO B:NCO207 0.0 97.7 0.9
N3 B:NCO207 2.0 97.3 0.9
N6 B:NCO207 2.0 97.1 0.9
N2 B:NCO207 2.0 97.2 0.9
N1 B:NCO207 2.0 96.6 0.9
N5 B:NCO207 2.0 97.1 0.9
N4 B:NCO207 2.0 96.7 0.9
OP2 B:G131 4.2 64.6 1.0
OP2 B:U132 4.2 53.8 1.0
OP2 B:G171 4.4 47.2 1.0
OP1 B:G170 4.6 49.4 1.0
OP1 B:G131 4.7 63.8 1.0
P B:G131 4.9 60.4 1.0

Cobalt binding site 8 out of 8 in 2pxb

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Cobalt binding site 8 out of 8 in the Variant 2 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 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co208

b:70.9
occ:0.80
CO B:NCO208 0.0 70.9 0.8
N5 B:NCO208 2.0 68.3 0.8
N4 B:NCO208 2.0 68.8 0.8
N6 B:NCO208 2.0 68.8 0.8
N1 B:NCO208 2.0 68.2 0.8
N2 B:NCO208 2.0 68.7 0.8
N3 B:NCO208 2.0 68.5 0.8
O4 B:U175 3.5 45.0 1.0
O4 B:U132 4.1 42.1 1.0
O6 B:G131 4.5 54.5 1.0
C4 B:U175 4.5 43.5 1.0
O6 B:G133 4.6 42.5 1.0
O6 B:G176 4.8 50.5 1.0

Reference:

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
Page generated: Sun Dec 13 10:38:39 2020

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