Atomistry » Cobalt » PDB 3bbk-3ger » 3bbm
Atomistry »
  Cobalt »
    PDB 3bbk-3ger »
      3bbm »

Cobalt in PDB 3bbm: Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site

Protein crystallography data

The structure of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site, PDB code: 3bbm was solved by C.Macelrevey, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.65
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.650, 93.650, 133.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 21.7

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site (pdb code 3bbm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site, PDB code: 3bbm:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 3bbm

Go back to Cobalt Binding Sites List in 3bbm
Cobalt binding site 1 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co32

b:0.9
occ:1.00
CO B:NCO32 0.0 0.9 1.0
N5 B:NCO32 1.9 0.6 1.0
N4 B:NCO32 2.0 0.2 1.0
N3 B:NCO32 2.0 0.2 1.0
N2 B:NCO32 2.0 1.0 1.0
N1 B:NCO32 2.0 0.6 1.0
N6 B:NCO32 2.0 0.6 1.0
O2 A:SO414 4.0 0.7 1.0
O6 B:G13 4.5 67.4 1.0
O6 B:G12 4.5 68.6 1.0
O4 A:SO414 4.7 0.4 1.0
S A:SO414 4.8 1.0 1.0
N7 B:G12 4.9 66.4 1.0

Cobalt binding site 2 out of 3 in 3bbm

Go back to Cobalt Binding Sites List in 3bbm
Cobalt binding site 2 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1

b:1.0
occ:1.00
CO C:NCO1 0.0 1.0 1.0
N5 C:NCO1 2.0 0.3 1.0
N4 C:NCO1 2.0 0.3 1.0
N3 C:NCO1 2.0 0.1 1.0
N2 C:NCO1 2.0 0.6 1.0
N6 C:NCO1 2.0 0.9 1.0
N1 C:NCO1 2.0 99.3 1.0
OP2 C:U41 3.8 70.5 1.0
OP1 C:A40 3.9 80.9 1.0
OP2 B:A20 4.1 0.1 1.0
O6 B:G21 4.2 78.8 1.0
N7 B:G21 4.3 78.1 1.0
P C:A40 4.7 85.8 1.0
OP2 C:A40 4.8 85.2 1.0
O5' C:A40 5.0 83.6 1.0
C6 B:G21 5.0 77.6 1.0

Cobalt binding site 3 out of 3 in 3bbm

Go back to Cobalt Binding Sites List in 3bbm
Cobalt binding site 3 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co3

b:0.9
occ:1.00
CO C:NCO3 0.0 0.9 1.0
N4 C:NCO3 2.0 0.6 1.0
N5 C:NCO3 2.0 0.8 1.0
N2 C:NCO3 2.0 0.4 1.0
N3 C:NCO3 2.0 0.5 1.0
N1 C:NCO3 2.0 0.8 1.0
N6 C:NCO3 2.0 0.2 1.0
N7 C:G36 4.1 71.8 1.0
O6 C:G36 4.2 72.2 1.0
O2' C:C38 4.3 70.3 1.0
O6 A:G6 4.5 62.0 1.0
N4 B:C25 4.7 63.1 1.0
OP2 B:A23 4.7 78.4 1.0
C5 C:G36 4.7 70.0 1.0
C6 C:G36 4.7 70.4 1.0

Reference:

C.Macelrevey, J.D.Salter, J.Krucinska, J.E.Wedekind. Structural Effects of Nucleobase Variations at Key Active Site Residue ADE38 in the Hairpin Ribozyme. Rna V. 14 1600 2008.
ISSN: ISSN 1355-8382
PubMed: 18596253
DOI: 10.1261/RNA.1055308
Page generated: Sun Dec 13 10:39:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy