Cobalt in PDB 1gid: Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing

The structure of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing, PDB code: 1gid was solved by J.H.Cate, A.R.Gooding, E.Podell, K.Zhou, B.L.Golden, C.E.Kundrot, T.R.Cech, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.800, 128.700, 145.900, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 28.5

The structure of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing also contains other interesting chemical elements:

Magnesium

(Mg)

24 atoms

The binding sites of Cobalt atom in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing (pdb code 1gid). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing, PDB code: 1gid:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range: probe atom residue distance (Å) B Occ A:Co261 b:29.8 occ:0.64 CO A:NCO261 0.0 29.8 0.6 N1 A:NCO261 2.0 31.1 0.6 N2 A:NCO261 2.0 31.6 0.6 N5 A:NCO261 2.0 24.6 0.6 N3 A:NCO261 2.0 29.3 0.6 N6 A:NCO261 2.0 28.4 0.6 N4 A:NCO261 2.0 29.8 0.6 O6 A:G148 4.0 66.4 1.0 O4 A:U155 4.2 45.8 1.0 O6 A:G147 4.3 58.5 1.0 N7 A:G147 4.5 53.5 1.0 O6 A:G149 4.6 42.6 1.0 N7 A:G148 4.8 53.4 1.0 C6 A:G148 4.9 60.2 1.0 C6 A:G147 5.0 53.5 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range: probe atom residue distance (Å) B Occ A:Co262 b:39.6 occ:0.50 CO A:NCO262 0.0 39.6 0.5 N6 A:NCO262 2.0 39.3 0.5 N2 A:NCO262 2.0 38.7 0.5 N4 A:NCO262 2.0 38.4 0.5 N5 A:NCO262 2.0 40.6 0.5 N1 A:NCO262 2.0 38.4 0.5 N3 A:NCO262 2.0 37.7 0.5 O6 A:G176 3.8 32.9 1.0 OP2 A:G174 3.8 36.8 1.0 O4 A:U177 4.0 61.0 1.0 N7 A:G176 4.3 33.9 1.0 N7 A:G175 4.5 47.2 1.0 C6 A:G176 4.6 32.1 1.0 OP2 A:G175 4.6 36.8 1.0 C5 A:G176 4.9 33.3 1.0 C4 A:U177 4.9 58.5 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range: probe atom residue distance (Å) B Occ B:Co263 b:40.0 occ:0.67 CO B:NCO263 0.0 40.0 0.7 N1 B:NCO263 2.0 46.7 0.7 N6 B:NCO263 2.0 40.5 0.7 N2 B:NCO263 2.0 42.1 0.7 N4 B:NCO263 2.0 43.4 0.7 N3 B:NCO263 2.0 42.7 0.7 N5 B:NCO263 2.0 36.8 0.7 O6 B:G148 4.0 59.3 1.0 O4 B:U155 4.2 31.0 1.0 O6 B:G147 4.3 47.1 1.0 O6 B:G149 4.4 41.2 1.0 N7 B:G147 4.4 40.7 1.0 N7 B:G148 4.8 49.5 1.0 C6 B:G148 5.0 51.6 1.0 C6 B:G147 5.0 41.9 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range: probe atom residue distance (Å) B Occ B:Co264 b:30.0 occ:0.46 CO B:NCO264 0.0 30.0 0.5 N5 B:NCO264 2.0 30.5 0.5 N2 B:NCO264 2.0 29.5 0.5 N6 B:NCO264 2.0 29.7 0.5 N4 B:NCO264 2.0 28.1 0.5 N1 B:NCO264 2.0 29.9 0.5 N3 B:NCO264 2.0 30.6 0.5 O6 B:G176 3.7 45.0 1.0 OP2 B:G174 3.9 35.9 1.0 O4 B:U177 3.9 42.0 1.0 N7 B:G176 4.3 38.2 1.0 N7 B:G175 4.5 42.5 1.0 C6 B:G176 4.6 40.4 1.0 OP2 B:G175 4.7 37.3 1.0 C5 B:G176 4.9 36.5 1.0 C4 B:U177 4.9 37.6 1.0

J.H.Cate, A.R.Gooding, E.Podell, K.Zhou, B.L.Golden, C.E.Kundrot, T.R.Cech, J.A.Doudna. Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing. Science V. 273 1678 1996.
ISSN: ISSN 0036-8075
PubMed: 8781224