Potassium in PDB 5tf6: Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core

The structure of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core, PDB code: 5tf6 was solved by E.J.Montemayor, D.A.Brow, S.E.Butcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.10 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.921, 84.446, 255.142, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.2

The structure of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Potassium atom in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core (pdb code 5tf6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core, PDB code: 5tf6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core within 5.0Å range: probe atom residue distance (Å) B Occ A:K501 b:39.3 occ:0.58 O B:HOH370 2.5 51.1 1.0 O A:HOH898 2.6 54.1 1.0 O B:HOH325 2.6 37.8 1.0 OD1 A:ASN37 2.8 44.6 1.0 O A:HOH836 2.8 69.3 1.0 O A:HOH857 3.0 53.1 1.0 O A:HOH856 3.2 56.7 1.0 O A:HOH849 3.6 58.9 1.0 CG A:ASN37 3.6 41.0 1.0 CL A:CL503 4.1 46.3 1.0 ND2 A:ASN37 4.3 41.1 1.0 O A:HOH816 4.4 62.8 1.0 CA A:ASN37 4.4 37.6 1.0 N A:ARG38 4.4 36.9 1.0 O A:HOH641 4.5 46.5 1.0 CB A:ASN37 4.5 36.2 1.0 O B:HOH352 4.7 39.5 1.0 C A:ASN37 4.8 39.6 1.0 N1 B:G52 4.8 35.0 1.0 O6 B:G52 4.9 35.3 1.0 O B:HOH407 4.9 54.6 1.0 CD A:GLU39 4.9 55.4 1.0

Potassium binding site 2 out of 5 in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core within 5.0Å range: probe atom residue distance (Å) B Occ B:K201 b:55.1 occ:1.00 O B:HOH354 2.5 48.2 1.0 O4 B:U87 2.7 59.5 1.0 O6 B:G60 2.8 55.3 1.0 O6 B:G86 2.8 53.0 1.0 N6 B:A59 3.2 48.0 1.0 O B:HOH416 3.3 77.0 1.0 O B:HOH376 3.3 62.0 1.0 O B:HOH362 3.6 61.4 1.0 C4 B:U87 3.6 58.9 1.0 C6 B:G86 3.8 52.0 1.0 N3 B:U87 3.8 55.6 1.0 C6 B:G60 3.9 50.9 1.0 N4 B:C61 3.9 55.8 1.0 C6 B:A59 4.0 49.0 1.0 O B:HOH330 4.3 69.9 1.0 N7 B:G60 4.3 53.8 1.0 C5 B:G60 4.5 53.4 1.0 C5 B:G86 4.5 49.2 1.0 C5 B:A59 4.5 51.8 1.0 N7 B:G86 4.6 55.1 1.0 O4 B:U88 4.7 57.4 1.0 N1 B:A59 4.7 53.4 1.0 N7 B:A59 4.7 56.5 1.0 N1 B:G86 4.8 52.2 1.0 O B:HOH386 4.8 68.3 1.0 C4 B:C61 4.9 56.2 1.0 C5 B:U87 5.0 59.7 1.0

Potassium binding site 3 out of 5 in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core within 5.0Å range: probe atom residue distance (Å) B Occ C:K501 b:60.7 occ:1.00 O C:ASN373 2.7 45.3 1.0 O C:ILE371 2.9 60.3 1.0 O C:MET370 3.0 62.9 1.0 C C:ILE371 3.5 55.3 1.0 CA C:ILE371 3.8 58.0 1.0 C C:ASN373 3.9 48.2 1.0 C C:MET370 4.1 58.9 1.0 N C:ASN373 4.4 51.2 1.0 N C:ILE371 4.4 55.8 1.0 N C:LEU372 4.5 52.0 1.0 CA C:ASN373 4.6 49.5 1.0 C C:LEU372 4.7 52.8 1.0 CB C:ASN373 4.9 46.7 1.0 N C:GLY374 4.9 50.0 1.0

Potassium binding site 4 out of 5 in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core within 5.0Å range: probe atom residue distance (Å) B Occ C:K502 b:59.8 occ:1.00 OD1 C:ASN37 2.8 42.7 1.0 O D:HOH363 2.8 53.0 1.0 O D:HOH309 2.9 42.5 1.0 O C:HOH833 3.0 45.5 1.0 O C:HOH727 3.0 51.3 1.0 O C:HOH817 3.0 53.5 1.0 O C:HOH792 3.0 69.0 1.0 CG C:ASN37 3.6 43.2 1.0 O C:HOH831 3.7 53.5 1.0 O C:HOH839 4.0 71.4 1.0 O C:HOH803 4.0 71.2 1.0 CL C:CL503 4.1 45.5 1.0 O C:HOH624 4.3 44.1 1.0 ND2 C:ASN37 4.3 39.1 1.0 N C:ARG38 4.4 40.5 1.0 CA C:ASN37 4.5 38.0 1.0 CB C:ASN37 4.6 39.6 1.0 O C:HOH678 4.6 64.7 1.0 C C:ASN37 4.7 40.3 1.0 CD C:GLU39 4.8 49.5 1.0 O D:HOH333 4.8 42.3 1.0 OE1 C:GLU39 4.8 51.5 1.0 N C:GLU39 4.9 35.8 1.0

Potassium binding site 5 out of 5 in the Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core within 5.0Å range: probe atom residue distance (Å) B Occ D:K201 b:93.8 occ:1.00 O6 D:G60 3.2 97.8 1.0 N6 D:A59 3.5 68.4 1.0 O6 D:G86 3.6 0.0 1.0 N7 D:G60 3.8 84.1 1.0 C6 D:A59 4.0 69.5 1.0 N4 D:C61 4.0 0.2 1.0 C6 D:G60 4.1 93.2 1.0 C5 D:G60 4.3 85.3 1.0 C5 D:A59 4.3 67.6 1.0 N7 D:A59 4.4 64.4 1.0 O4 D:U87 4.5 0.5 1.0 N3 D:U87 4.7 0.6 1.0 N1 D:A59 4.7 69.0 1.0 C6 D:G86 4.8 0.3 1.0 C8 D:G60 5.0 85.7 1.0

E.J.Montemayor, A.L.Didychuk, H.Liao, P.Hu, D.A.Brow, S.E.Butcher. Structure and Conformational Plasticity of the U6 Small Nuclear Ribonucleoprotein Core. Acta Crystallogr D Struct V. 73 1 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045380
DOI: 10.1107/S2059798316018222