Atomistry » Cobalt » PDB 1e31-1hgw » 1gid
Atomistry »
  Cobalt »
    PDB 1e31-1hgw »
      1gid »

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

Protein crystallography data

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

Other elements in 1gid:

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

Cobalt Binding Sites:

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 1gid

Go back to Cobalt Binding Sites List in 1gid
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 1gid

Go back to Cobalt Binding Sites List in 1gid
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 1gid

Go back to Cobalt Binding Sites List in 1gid
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 1gid

Go back to Cobalt Binding Sites List in 1gid
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

Reference:

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
Page generated: Sun Dec 13 10:34:54 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy