Cobalt in PDB 3lqx: Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine

The structure of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine, PDB code: 3lqx was solved by R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.818, 77.765, 32.735, 90.00, 94.08, 90.00
R / Rfree (%)	24.4 / 25.9

The structure of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Cobalt atom in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine (pdb code 3lqx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine, PDB code: 3lqx:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co179 b:24.0 occ:1.00 CO B:NCO179 0.0 24.0 1.0 N6 B:NCO179 1.9 23.5 1.0 N5 B:NCO179 1.9 23.6 1.0 N2 B:NCO179 2.0 23.6 1.0 N4 B:NCO179 2.0 23.5 1.0 N3 B:NCO179 2.0 23.6 1.0 N1 B:NCO179 2.0 23.6 1.0 O B:HOH24 3.9 25.8 1.0 O4 B:U137 3.9 23.4 1.0 O B:HOH60 4.0 31.0 1.0 CL B:CL38 4.2 30.8 1.0 O B:HOH77 4.2 27.2 1.0 O6 B:G170 4.2 24.6 1.0 O6 B:G171 4.2 25.2 1.0 N7 B:G170 4.2 25.3 1.0 O B:HOH67 4.3 31.8 1.0 O B:HOH182 4.4 21.1 1.0 O6 B:G136 4.8 23.9 1.0 C6 B:G170 4.9 25.0 1.0 C5 B:G170 4.9 25.1 1.0

Cobalt binding site 2 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co180 b:33.9 occ:1.00 CO B:NCO180 0.0 33.9 1.0 N6 B:NCO180 2.0 34.2 1.0 N2 B:NCO180 2.0 34.2 1.0 N3 B:NCO180 2.0 34.2 1.0 N4 B:NCO180 2.0 34.2 1.0 N5 B:NCO180 2.0 34.1 1.0 N1 B:NCO180 2.0 34.2 1.0 O B:HOH86 3.8 43.5 1.0 O B:HOH37 3.8 20.7 1.0 OP1 B:C141 3.8 25.2 1.0 O6 B:G144 4.0 34.3 1.0 N7 B:G144 4.1 34.7 1.0 OP2 B:C142 4.1 31.6 1.0 O B:HOH64 4.3 32.8 1.0 O B:HOH78 4.4 29.2 1.0 C6 B:G144 4.8 34.4 1.0 C5 B:G144 4.8 34.6 1.0

Cobalt binding site 3 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3 b:41.9 occ:1.00 CO B:NCO3 0.0 41.9 1.0 N2 B:NCO3 2.0 41.9 1.0 N5 B:NCO3 2.0 42.0 1.0 N1 B:NCO3 2.0 41.9 1.0 N3 B:NCO3 2.0 42.0 1.0 N6 B:NCO3 2.0 42.0 1.0 N4 B:NCO3 2.0 42.0 1.0 OP2 B:G149 3.5 29.7 1.0 OP1 B:A148 4.0 31.0 1.0 N7 B:G150 4.2 27.9 1.0 O6 B:G150 4.2 27.7 1.0 O4 B:U151 4.3 29.0 1.0 P B:A148 4.8 31.1 1.0 P B:G149 4.8 29.8 1.0 OP2 B:A148 4.9 31.1 1.0 C6 B:G150 4.9 27.8 1.0 C5 B:G150 4.9 27.8 1.0

Cobalt binding site 4 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co4 b:39.1 occ:1.00 CO B:NCO4 0.0 39.1 1.0 N1 B:NCO4 2.0 39.2 1.0 N2 B:NCO4 2.0 39.2 1.0 N4 B:NCO4 2.0 39.3 1.0 N5 B:NCO4 2.0 39.2 1.0 N3 B:NCO4 2.0 39.3 1.0 N6 B:NCO4 2.0 39.3 1.0 O B:HOH99 3.9 29.7 1.0 O6 B:G154 4.0 28.4 1.0 O B:HOH55 4.0 28.9 1.0 N7 B:G154 4.3 28.3 1.0 C6 B:G154 4.7 28.3 1.0 C5 B:G154 4.9 28.3 1.0

Cobalt binding site 5 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co5 b:50.3 occ:1.00 CO B:NCO5 0.0 50.3 1.0 N3 B:NCO5 2.0 50.2 1.0 N1 B:NCO5 2.0 50.2 1.0 N4 B:NCO5 2.0 50.2 1.0 N2 B:NCO5 2.0 50.2 1.0 N5 B:NCO5 2.0 50.2 1.0 N6 B:NCO5 2.0 50.2 1.0 N7 B:G158 3.9 31.2 1.0 O6 B:G158 4.0 30.8 1.0 O B:HOH73 4.5 32.3 1.0 C5 B:G158 4.6 31.1 1.0 C6 B:G158 4.7 31.0 1.0 C8 B:G158 4.9 31.4 1.0 N3 B:NCO3 5.0 42.0 1.0

Cobalt binding site 6 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co6 b:48.7 occ:1.00 CO B:NCO6 0.0 48.7 1.0 N5 B:NCO6 2.0 48.6 1.0 N3 B:NCO6 2.0 48.7 1.0 N1 B:NCO6 2.0 48.7 1.0 N6 B:NCO6 2.0 48.7 1.0 N4 B:NCO6 2.0 48.7 1.0 N2 B:NCO6 2.0 48.7 1.0 OP2 B:A161 3.9 30.9 1.0 OP2 B:C147 3.9 31.3 1.0 O6 B:G162 4.4 27.6 1.0 N7 B:G162 4.6 27.4 1.0

Cobalt binding site 7 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co7 b:37.3 occ:1.00 CO B:NCO7 0.0 37.3 1.0 N6 B:NCO7 2.0 37.5 1.0 N2 B:NCO7 2.0 37.5 1.0 N1 B:NCO7 2.0 37.5 1.0 N5 B:NCO7 2.0 37.5 1.0 N3 B:NCO7 2.0 37.5 1.0 N4 B:NCO7 2.0 37.5 1.0 O B:HOH94 3.9 30.5 1.0 O B:HOH17 3.9 26.6 1.0 CL B:CL38 3.9 30.8 1.0 O B:HOH29 4.2 27.2 1.0 O B:HOH26 4.2 33.6 1.0 O B:HOH51 4.3 29.1 1.0 O4 B:U133 4.4 27.8 1.0 O B:HOH67 4.9 31.8 1.0

Cobalt binding site 8 out of 8 in the Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Srp Ribonucleoprotein Core Complexed with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co8 b:51.8 occ:1.00 CO B:NCO8 0.0 51.8 1.0 N5 B:NCO8 2.0 51.7 1.0 N1 B:NCO8 2.0 51.7 1.0 N3 B:NCO8 2.0 51.7 1.0 N2 B:NCO8 2.0 51.7 1.0 N6 B:NCO8 2.0 51.7 1.0 N4 B:NCO8 2.0 51.7 1.0 O6 B:G130 4.1 32.0 1.0 N7 B:G130 4.5 32.1 1.0 O6 B:G131 4.9 31.6 1.0 C6 B:G130 5.0 32.0 1.0

R.T.Batey, J.A.Doudna. Structural and Energetic Analysis of Metal Ions Essential to Srp Signal Recognition Domain Assembly Biochemistry V. 41 11703 2002.
ISSN: ISSN 0006-2960
PubMed: 12269812