Potassium in PDB 1u6b: Crystal Structure of A Self-Splicing Group I Intron with Both Exons

The structure of Crystal Structure of A Self-Splicing Group I Intron with Both Exons, PDB code: 1u6b was solved by P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 3.10
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.541, 108.541, 249.158, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 27.9

The structure of Crystal Structure of A Self-Splicing Group I Intron with Both Exons also contains other interesting chemical elements:

Magnesium

(Mg)

13 atoms

The binding sites of Potassium atom in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons (pdb code 1u6b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons, PDB code: 1u6b:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:K2 b:57.1 occ:1.00 OP1 B:G128 2.6 64.0 1.0 O C:HOH101 2.7 33.0 1.0 O2' C:G206 2.7 2.0 0.0 OP1 B:A87 2.7 26.1 1.0 O3' B:A127 2.7 63.5 1.0 O B:HOH1030 3.0 2.3 1.0 P B:G128 3.1 63.1 1.0 OP2 B:A172 3.1 41.9 1.0 O5' B:G128 3.5 63.9 1.0 C5' B:G128 3.7 64.0 1.0 O2' B:A127 3.8 67.4 1.0 C3' B:A127 3.9 64.2 1.0 C4' B:A127 4.1 62.7 1.0 P B:A87 4.2 33.1 1.0 O2' B:C171 4.4 44.4 1.0 P B:A172 4.5 40.0 1.0 C2' B:A127 4.5 64.8 1.0 C1' C:G206 4.5 41.9 1.0 OP2 B:G128 4.5 63.9 1.0 O3' C:G206 4.5 36.1 1.0 C2' C:G206 4.6 41.9 1.0 O3' B:C171 4.6 40.8 1.0 O4' C:G206 4.7 43.1 1.0 C4' C:G206 4.8 43.6 1.0 C5' B:A87 4.8 26.8 1.0 O5' B:A87 4.8 28.9 1.0 OP2 C:A1 4.9 30.3 1.0 C3' C:G206 4.9 41.2 1.0 C5' B:A127 5.0 58.5 1.0 O3' B:A86 5.0 30.2 1.0

Potassium binding site 2 out of 5 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:K4 b:53.4 occ:1.00 OP2 B:A150 2.5 52.2 1.0 O2' B:A149 2.7 53.0 1.0 N7 B:G151 2.9 20.7 1.0 O6 B:G152 3.0 39.1 1.0 O6 B:G151 3.4 15.6 1.0 P B:A150 3.5 49.5 1.0 O3' B:A149 3.6 49.2 1.0 N4 B:C159 3.7 50.9 1.0 C5 B:G151 3.8 18.4 1.0 O5' B:A150 3.8 46.6 1.0 C2' B:A149 3.9 48.6 1.0 C6 B:G151 4.0 17.0 1.0 C8 B:G151 4.0 23.4 1.0 C6 B:G152 4.0 39.8 1.0 C3' B:A149 4.2 48.3 1.0 OP2 B:G151 4.2 36.7 1.0 O4 B:U160 4.6 26.9 1.0 C5 B:G152 4.7 40.3 1.0 C8 B:A150 4.7 34.0 1.0 N7 B:G152 4.7 41.0 1.0 N7 B:A150 4.7 33.2 1.0 OP1 B:A150 4.9 49.3 1.0 C1' B:A149 4.9 44.1 1.0 N1 B:G152 4.9 39.4 1.0

Potassium binding site 3 out of 5 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:K1015 b:92.2 occ:1.00 OP2 B:C171 2.8 40.1 1.0 O5' B:C171 2.9 37.8 1.0 O2' B:U126 3.0 43.9 1.0 OP1 B:U124 3.3 41.0 1.0 P B:C171 3.4 38.2 1.0 OP2 B:A127 3.4 52.1 1.0 O B:HOH1035 3.6 38.5 1.0 O2 B:U126 3.7 46.9 1.0 O4' B:C171 3.7 42.4 1.0 OP2 B:U124 3.8 40.1 1.0 MG B:MG1023 3.9 54.0 1.0 P B:U124 3.9 40.0 1.0 C2' B:U126 4.0 41.6 1.0 C5' B:C171 4.1 39.4 1.0 OP1 B:C171 4.2 39.4 1.0 OP2 B:G125 4.2 50.6 1.0 C4' B:C171 4.3 41.4 1.0 O5' B:U124 4.5 41.3 1.0 C2 B:U126 4.6 44.4 1.0 O3' B:G170 4.7 39.5 1.0 P B:A127 4.8 49.4 1.0 C1' B:U126 4.9 42.6 1.0 C1' B:C171 5.0 43.2 1.0

Potassium binding site 4 out of 5 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:K1016 b:55.3 occ:1.00 O4 B:U9 2.8 17.8 1.0 N6 D:A2 3.0 19.2 1.0 O4 D:5MU1 3.0 20.8 1.0 O B:HOH1032 3.1 35.5 1.0 O6 B:G10 3.2 14.0 1.0 N6 C:A1 3.6 9.2 1.0 C4 B:U9 3.7 14.8 1.0 N7 B:G10 3.9 10.9 1.0 C4 D:5MU1 4.1 19.0 1.0 C6 B:G10 4.1 11.9 1.0 C6 D:A2 4.1 17.7 1.0 O4 B:U11 4.1 8.4 1.0 O D:HOH155 4.3 25.5 1.0 N3 D:5MU1 4.3 16.8 1.0 C5 B:G10 4.4 10.9 1.0 C5 B:U9 4.4 13.5 1.0 N3 B:U9 4.5 11.7 1.0 C6 C:A1 4.5 7.4 1.0 N1 C:A1 4.8 8.1 1.0 C5 D:A2 4.8 17.7 1.0 N1 D:A2 4.9 15.9 1.0 N7 D:A2 4.9 19.8 1.0 C4 B:U11 4.9 9.4 1.0

Potassium binding site 5 out of 5 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:K1017 b:92.4 occ:1.00 O6 B:G24 3.0 40.9 1.0 O6 B:G23 3.4 44.9 1.0 N7 B:G23 3.6 46.8 1.0 C6 B:G24 3.8 40.1 1.0 N7 B:G22 4.1 42.1 1.0 O6 B:G22 4.1 41.5 1.0 C5 B:G22 4.1 42.3 1.0 C6 B:G22 4.2 41.6 1.0 C6 B:G23 4.2 45.9 1.0 C5 B:G23 4.3 46.6 1.0 C5 B:G24 4.3 40.7 1.0 N7 B:G24 4.4 42.0 1.0 N1 B:G24 4.7 39.0 1.0 C8 B:G22 4.7 44.4 1.0 C8 B:G23 4.8 47.5 1.0 C4 B:G22 4.9 43.6 1.0 N1 B:G22 5.0 42.5 1.0

P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, S.A.Strobel. Crystal Structure of A Self-Splicing Group I Intron with Both Exons. Nature V. 430 45 2004.
ISSN: ISSN 0028-0836
PubMed: 15175762
DOI: 10.1038/NATURE02642