Potassium in PDB 3iin: Plasticity of the Kink Turn Structural Motif

The structure of Plasticity of the Kink Turn Structural Motif, PDB code: 3iin was solved by S.V.Lipchock, S.A.Strobel, A.H.Antonioli, J.C.Cochrane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 4.18
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.826, 109.826, 250.218, 90.00, 90.00, 90.00
R / Rfree (%)	29 / 32.3

The structure of Plasticity of the Kink Turn Structural Motif also contains other interesting chemical elements:

Magnesium

(Mg)

13 atoms

The binding sites of Potassium atom in the Plasticity of the Kink Turn Structural Motif (pdb code 3iin). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Plasticity of the Kink Turn Structural Motif, PDB code: 3iin:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Plasticity of the Kink Turn Structural Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:K2 b:0.9 occ:1.00 O C:HOH101 2.3 12.9 1.0 OP2 B:A172 2.5 86.9 1.0 OP1 B:G128 2.7 0.6 1.0 OP2 C:DA207 3.0 94.0 1.0 O3' B:C171 3.2 86.1 1.0 O3' C:DG206 3.2 97.0 1.0 OP2 B:C88 3.2 84.6 1.0 O3' B:A127 3.3 0.4 1.0 P B:A172 3.3 86.8 1.0 P C:DA207 3.6 96.1 1.0 P B:G128 3.6 0.6 1.0 O2' B:C171 3.6 87.0 1.0 O5' C:DA207 3.8 96.8 1.0 OP1 B:A87 3.9 81.2 1.0 O5' B:A87 3.9 81.5 1.0 MG B:MG1 4.0 87.6 1.0 C5' B:A87 4.1 82.8 1.0 OP1 B:A172 4.2 86.5 1.0 C3' B:C171 4.3 87.0 1.0 P B:C88 4.4 84.9 1.0 C3' C:DG206 4.5 99.6 1.0 P B:A87 4.5 82.3 1.0 O3' B:A87 4.5 85.3 1.0 C2' B:C171 4.6 87.3 1.0 C3' B:A127 4.6 98.2 1.0 OP2 B:G128 4.6 0.7 1.0 O5' B:A172 4.6 86.9 1.0 C4' B:A127 4.7 97.9 1.0 C2' C:DG206 4.8 0.1 1.0 O5' B:G128 4.8 0.1 1.0 C5' B:G128 4.9 0.8 1.0 C4' B:A87 4.9 84.4 1.0 C3' B:A87 4.9 85.0 1.0 OP1 B:C88 4.9 84.9 1.0

Potassium binding site 2 out of 5 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Plasticity of the Kink Turn Structural Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:K1015 b:86.3 occ:1.00 OP2 B:A150 2.9 0.5 1.0 O2' B:A149 3.3 0.7 1.0 O6 B:G152 3.3 0.9 1.0 N7 B:G151 3.4 0.6 1.0 O5' B:A150 3.5 0.6 1.0 O6 B:G151 3.5 0.9 1.0 P B:A150 3.7 0.2 1.0 O3' B:A149 4.0 0.2 1.0 C5 B:G151 4.1 0.8 1.0 C6 B:G151 4.2 0.6 1.0 N4 B:C159 4.3 0.5 1.0 OP2 B:G151 4.3 0.8 1.0 C6 B:G152 4.3 0.8 1.0 C2' B:A149 4.4 0.8 1.0 C8 B:G151 4.4 1.0 1.0 N7 B:G152 4.5 0.2 1.0 O4 B:U160 4.6 0.1 1.0 C8 B:A150 4.7 0.2 1.0 C3' B:A149 4.7 0.5 1.0 C5 B:G152 4.8 1.0 1.0 C5' B:A150 4.8 0.4 1.0 N7 B:A150 5.0 0.1 1.0 N4 B:C153 5.0 0.0 1.0 C3' B:A150 5.0 0.8 1.0

Potassium binding site 3 out of 5 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Plasticity of the Kink Turn Structural Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:K1016 b:0.7 occ:1.00 O2 B:U126 3.3 98.6 1.0 O5' B:C171 3.4 90.8 1.0 OP2 B:C171 3.4 92.6 1.0 OP2 B:U124 3.6 0.8 1.0 P B:C171 3.7 91.0 1.0 OP1 B:C171 3.8 91.0 1.0 O2' B:U126 3.8 96.2 1.0 OP1 B:U124 3.9 0.8 1.0 P B:U124 4.3 0.6 1.0 MG B:MG1023 4.3 96.7 1.0 C2 B:U126 4.4 97.1 1.0 C5' B:C171 4.4 89.7 1.0 O4' B:C171 4.5 87.8 1.0 OP2 B:A127 4.7 97.2 1.0

Potassium binding site 4 out of 5 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Plasticity of the Kink Turn Structural Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:K1017 b:0.3 occ:1.00 O6 B:G8 4.1 95.9 1.0 N7 B:G8 4.2 95.6 1.0 O4 B:U9 4.5 95.3 1.0 C6 B:G8 4.7 95.2 1.0 C5 B:G8 4.8 95.6 1.0

Potassium binding site 5 out of 5 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Plasticity of the Kink Turn Structural Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:K1018 b:0.5 occ:1.00 O6 B:G24 3.4 0.8 1.0 N7 B:G22 4.0 0.2 1.0 O6 B:G22 4.2 0.3 1.0 O6 B:G23 4.2 0.4 1.0 C5 B:G22 4.4 0.0 1.0 OP2 B:G22 4.4 0.2 1.0 C6 B:G22 4.5 0.1 1.0 C6 B:G24 4.5 0.5 1.0 N7 B:G23 4.8 1.0 1.0 C8 B:G22 4.8 0.4 1.0

A.H.Antonioli, J.C.Cochrane, S.V.Lipchock, S.A.Strobel. Plasticity of the Rna Kink Turn Structural Motif. Rna V. 16 762 2010.
ISSN: ISSN 1355-8382
PubMed: 20145044
DOI: 10.1261/RNA.1883810