Potassium in PDB 3bo4: A Relaxed Active Site Following Exon Ligation By A Group I Intron

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo4 was solved by S.V.Lipchock, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.71 / 3.33
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.188, 111.188, 240.300, 90.00, 90.00, 90.00
R / Rfree (%)	28 / 29.6

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Potassium atom in the A Relaxed Active Site Following Exon Ligation By A Group I Intron (pdb code 3bo4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo4:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1015 b:0.3 occ:1.00 OP2 B:A150 2.8 0.5 1.0 N7 B:G151 3.1 0.3 1.0 O2' B:A149 3.2 0.6 1.0 O6 B:G152 3.5 0.8 1.0 O5' B:A150 3.8 0.9 1.0 O6 B:G151 3.8 0.2 1.0 P B:A150 3.8 0.3 1.0 C5 B:G151 4.1 0.0 1.0 C8 B:G151 4.1 0.9 1.0 C2' B:A149 4.2 0.4 1.0 O3' B:A149 4.3 0.2 1.0 C6 B:G151 4.3 0.1 1.0 C6 B:G152 4.4 0.8 1.0 N4 B:C159 4.5 0.3 1.0 OP2 B:G151 4.5 0.5 1.0 C3' B:A149 4.6 0.8 1.0 N7 B:G152 4.7 0.6 1.0 C5 B:G152 4.9 0.7 1.0 C8 B:A150 5.0 0.3 1.0

Potassium binding site 2 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1016 b:0.2 occ:1.00 MG B:MG1022 2.1 79.7 1.0 OP2 B:C171 2.7 0.3 1.0 OP2 B:A127 2.7 0.8 1.0 OP1 B:U124 2.7 0.7 1.0 OP2 B:G125 3.1 0.8 1.0 O2' B:U126 3.5 0.7 1.0 P B:C171 3.8 0.1 1.0 P B:U124 4.0 0.8 1.0 P B:A127 4.0 0.3 1.0 O3' B:G170 4.0 0.4 1.0 O5' B:C171 4.2 0.1 1.0 O5' B:U124 4.2 0.6 1.0 C5' B:U124 4.2 0.4 1.0 P B:G125 4.3 0.9 1.0 OP1 B:A127 4.3 0.4 1.0 OP1 B:G125 4.6 0.5 1.0 C2' B:U126 4.6 0.7 1.0 OP2 B:U124 4.7 0.3 1.0 O3' B:U126 4.9 1.0 1.0

Potassium binding site 3 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1017 b:0.4 occ:1.00 O B:HOH1054 2.8 99.0 1.0 O6 B:G24 3.7 0.8 1.0 O6 B:G23 4.2 0.3 1.0 N7 B:G23 4.3 0.1 1.0 N7 B:G22 4.4 0.6 1.0 OP2 B:G22 4.6 0.5 1.0 O6 B:G22 4.6 0.5 1.0 C6 B:G24 4.7 0.7 1.0 C5 B:G22 4.9 0.6 1.0 C6 B:G22 5.0 0.5 1.0

Potassium binding site 4 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1026 b:89.9 occ:1.00 O D:HOH46 2.2 58.9 1.0 N7 B:G8 4.5 0.9 1.0 O6 B:G8 4.8 0.5 1.0 O4 D:DT3 4.8 0.6 1.0

Potassium binding site 5 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1028 b:0.4 occ:1.00 O B:HOH1041 2.9 73.4 1.0 O6 B:G123 3.8 0.5 1.0 O4 B:U124 3.9 0.0 1.0 C6 B:G123 4.9 0.3 1.0 C4 B:U124 5.0 0.9 1.0

Potassium binding site 6 out of 6 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:K1029 b:0.1 occ:1.00 O B:HOH1051 2.4 64.5 1.0 O2' B:A161 3.8 0.8 1.0 OP2 B:G163 4.0 0.8 1.0 OP2 B:U162 4.2 0.7 1.0 N7 B:G163 4.8 0.6 1.0 N7 B:G164 4.9 0.6 1.0

S.V.Lipchock, S.A.Strobel. A Relaxed Active Site After Exon Ligation By the Group I Intron Proc.Natl.Acad.Sci.Usa V. 105 5699 2008.
ISSN: ISSN 0027-8424
PubMed: 18408159
DOI: 10.1073/PNAS.0712016105