Potassium in PDB 7qr3: Chimpanzee CPEB3 Hdv-Like Ribozyme

The structure of Chimpanzee CPEB3 Hdv-Like Ribozyme, PDB code: 7qr3 was solved by A.I.Przytula-Mally, S.Engilberge, S.Johannsen, V.Olieric, B.Masquida, R.K.O.Sigel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.65 / 2.18
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	120.254, 135.916, 83.254, 90, 90, 90
R / Rfree (%)	24.1 / 27.7

The binding sites of Potassium atom in the Chimpanzee CPEB3 Hdv-Like Ribozyme (pdb code 7qr3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Chimpanzee CPEB3 Hdv-Like Ribozyme, PDB code: 7qr3:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Chimpanzee CPEB3 Hdv-Like Ribozyme


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Chimpanzee CPEB3 Hdv-Like Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:68.8 occ:1.00 O A:HOH205 2.7 41.6 1.0 N A:GLY47 2.8 41.7 1.0 CA A:GLY47 3.6 36.7 1.0 C A:ARG46 3.8 38.5 1.0 CA A:ARG46 3.8 41.3 1.0 CB A:ARG46 4.0 38.7 1.0 CA A:GLU13 4.0 41.6 1.0 CD2 A:LEU20 4.2 39.7 1.0 CG A:ARG41 4.3 47.0 1.0 O A:SER40 4.3 44.6 1.0 O A:GLU13 4.4 41.5 1.0 N A:GLN48 4.4 44.3 1.0 C A:GLY47 4.5 43.8 1.0 O A:ASN12 4.5 40.3 1.0 NE A:ARG41 4.6 44.6 1.0 CB A:GLU13 4.6 42.6 1.0 O A:ILE15 4.6 48.5 1.0 C A:GLU13 4.6 40.8 1.0 CG A:GLU13 4.7 42.8 1.0 CA A:ARG41 4.8 42.6 1.0 CD A:ARG41 4.9 50.9 1.0 CB A:ARG41 4.9 41.6 1.0 N A:GLU13 5.0 39.0 1.0 O A:ARG46 5.0 40.3 1.0

Potassium binding site 2 out of 3 in the Chimpanzee CPEB3 Hdv-Like Ribozyme


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Chimpanzee CPEB3 Hdv-Like Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:70.1 occ:1.00 O B:SER40 2.8 45.9 1.0 O B:GLN48 2.9 39.7 1.0 CG1 B:VAL39 3.4 37.4 1.0 O B:HOH209 3.5 41.1 1.0 O B:MET45 3.5 42.1 1.0 N B:GLY47 3.5 44.4 1.0 N B:GLN48 3.6 37.8 1.0 C B:SER40 3.7 43.0 1.0 CA B:ARG46 3.8 45.4 1.0 N B:SER40 3.9 40.6 1.0 C B:GLN48 4.0 42.1 1.0 C B:ARG46 4.0 42.6 1.0 CD2 B:LEU20 4.1 42.9 1.0 CA B:GLY47 4.4 39.6 1.0 CA B:GLN48 4.4 40.9 1.0 C B:GLY47 4.4 47.7 1.0 C B:MET45 4.4 44.7 1.0 CA B:SER40 4.4 42.5 1.0 N B:ARG41 4.5 46.3 1.0 CB B:VAL39 4.5 42.0 1.0 CA B:ARG41 4.6 47.7 1.0 CG B:ARG41 4.6 43.5 1.0 N B:ARG46 4.6 35.6 1.0 CA B:VAL39 4.6 37.9 1.0 C B:VAL39 4.6 40.1 1.0 O B:HOH217 4.8 49.6 1.0 CB B:ARG46 4.8 38.4 1.0 CG2 B:VAL39 4.9 39.9 1.0 O B:ARG46 5.0 47.0 1.0

Potassium binding site 3 out of 3 in the Chimpanzee CPEB3 Hdv-Like Ribozyme


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Chimpanzee CPEB3 Hdv-Like Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:94.8 occ:1.00 O4 C:U46 2.8 55.9 1.0 OE2 B:GLU13 2.9 47.0 1.0 O B:HOH222 3.0 44.4 1.0 C4 C:U46 3.2 56.1 1.0 NZ B:LYS74 3.2 53.2 1.0 O B:HOH214 3.3 49.8 1.0 C5 C:U46 3.3 52.4 1.0 CD B:GLU13 3.5 53.3 1.0 CG B:GLU13 4.0 49.5 1.0 N3 C:U46 4.2 47.3 1.0 O4 C:U45 4.2 52.0 1.0 OE1 B:GLU13 4.3 51.4 1.0 C6 C:U46 4.3 52.1 1.0 CE B:LYS74 4.6 45.5 1.0 O B:LEU11 4.6 40.9 1.0 C4 C:U45 4.7 53.0 1.0 N1 C:G47 4.8 43.9 1.0 N3 C:U45 4.8 49.3 1.0 O B:HOH231 4.9 57.9 1.0 CB B:GLU13 4.9 46.0 1.0

A.I.Przytula-Mally, S.Engilberge, S.Johannsen, V.Olieric, B.Masquida, R.K.Sigel. Anticodon-Like Loop-Mediated Dimerization in the Crystal Structures of Hdv-Like CPEB3 Ribozymes Biorxiv 2022.
ISSN: ISSN 2692-8205
DOI: 10.1101/2022.09.22.508989