Potassium in PDB 3ftm: Class II Ligase Ribozyme Product-Template Duplex, Structure 1

The structure of Class II Ligase Ribozyme Product-Template Duplex, Structure 1, PDB code: 3ftm was solved by J.N.Pitt, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 2.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	31.550, 31.550, 171.066, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.8

The structure of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Potassium atom in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1 (pdb code 3ftm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1, PDB code: 3ftm:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:K202 b:59.6 occ:1.00 OP2 D:A3 2.4 51.8 1.0 P D:A3 3.7 53.6 1.0 N7 D:A4 3.9 47.5 1.0 O5' D:A3 4.0 54.2 1.0 N6 D:A4 4.1 48.8 1.0 OP2 D:G2 4.2 53.6 1.0 N7 D:A3 4.2 51.2 1.0 C8 D:A3 4.4 51.3 1.0 O5' D:G2 4.4 50.2 1.0 OP1 D:A3 4.5 54.0 1.0 OP2 D:A4 4.6 54.2 1.0 P D:G2 4.7 53.2 1.0 C5 D:A4 4.8 48.1 1.0 OP1 D:G2 4.8 52.4 1.0 O3' D:G2 4.9 51.1 1.0 C6 D:A4 4.9 47.8 1.0 C8 D:A4 4.9 47.8 1.0

Potassium binding site 2 out of 2 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:K319 b:46.7 occ:1.00 OP2 D:C-1 2.3 51.6 1.0 P D:C-1 2.5 51.5 1.0 OP1 D:C-1 2.5 51.6 1.0 O3' D:U-2 2.7 47.7 1.0 C3' D:U-2 3.5 42.9 1.0 C5' D:U-2 3.9 40.2 1.0 O5' D:C-1 4.0 52.5 1.0 C4' D:U-2 4.1 41.4 1.0 C2' D:U-2 4.9 42.4 1.0 C5' D:C-1 5.0 53.6 1.0

J.N.Pitt, A.R.Ferre-D'amare. Structure-Guided Engineering of the Regioselectivity of Rna Ligase Ribozymes. J.Am.Chem.Soc. V. 131 3532 2009.
ISSN: ISSN 0002-7863
PubMed: 19220054
DOI: 10.1021/JA8067325