Potassium in PDB 6ozr: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+, PDB code: 6ozr was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.37 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.078, 72.663, 154.574, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.4

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Potassium atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+ (pdb code 6ozr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+, PDB code: 6ozr:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+


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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K302 b:40.3 occ:0.60 O A:HOH417 2.7 34.1 1.0 N A:VAL53 3.0 27.0 1.0 OP1 C:U12 3.0 36.9 1.0 OD1 A:ASP52 3.1 39.2 1.0 O3' C:A11 3.2 26.9 1.0 CB A:ASP126 3.3 35.9 1.0 OD2 A:ASP126 3.4 48.8 0.7 CA A:ASP52 3.5 24.2 1.0 CG A:ASP126 3.6 47.2 0.7 O A:VAL53 3.7 34.6 1.0 P C:U12 3.7 31.6 1.0 C5' C:U12 3.7 27.3 1.0 O2' C:A11 3.7 29.8 1.0 C A:ASP52 3.8 24.6 1.0 CG A:ASP52 3.8 40.3 1.0 MG A:MG301 4.0 39.0 0.9 CA A:VAL53 4.0 29.3 1.0 C A:VAL53 4.1 32.5 1.0 O A:HOH409 4.1 34.7 1.0 CB A:ASP52 4.1 25.5 1.0 O5' C:U12 4.2 26.9 1.0 C3' C:A11 4.3 25.3 1.0 CB A:VAL53 4.4 29.9 1.0 O A:ASP126 4.4 32.1 1.0 C2' C:A11 4.5 29.9 1.0 OD1 A:ASP126 4.6 52.6 0.7 OD2 A:ASP52 4.6 54.9 1.0 OE2 A:GLU100 4.6 27.4 0.7 O A:VAL51 4.7 25.2 1.0 OE1 A:GLU100 4.7 27.6 0.7 CA A:ASP126 4.7 31.1 1.0 N A:ASP52 4.7 27.9 1.0 CG2 A:VAL53 4.8 28.6 1.0 O A:ASP52 5.0 24.2 1.0 C4' C:A11 5.0 28.1 1.0 C A:ASP126 5.0 31.1 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+


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 Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 15 Min Soak in 10 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:K302 b:43.5 occ:0.60 OD2 B:ASP126 2.7 53.8 0.4 O B:HOH414 2.7 55.6 1.0 CG B:ASP126 3.0 50.3 0.5 OP1 D:U12 3.0 43.8 1.0 N B:VAL53 3.1 24.0 1.0 OD1 B:ASP126 3.2 51.7 0.7 O3' D:A11 3.2 37.2 1.0 OD1 B:ASP52 3.2 44.4 1.0 O B:VAL53 3.5 31.0 1.0 CA B:ASP52 3.7 22.5 1.0 P D:U12 3.7 36.3 1.0 C5' D:U12 3.8 35.1 1.0 O2' D:A11 3.8 40.3 1.0 C B:ASP52 3.9 27.6 1.0 MG B:MG301 3.9 54.6 1.0 CB B:ASP126 4.0 41.8 1.0 CG B:ASP52 4.0 42.2 1.0 CA B:VAL53 4.0 24.2 1.0 C B:VAL53 4.1 24.9 1.0 O5' D:U12 4.3 31.4 1.0 CB B:ASP52 4.3 26.5 1.0 CB B:VAL53 4.3 22.8 1.0 C3' D:A11 4.3 29.1 1.0 OE1 B:GLU100 4.4 43.8 1.0 O B:ASP126 4.5 40.7 1.0 OE2 B:GLU100 4.5 51.4 1.0 C2' D:A11 4.6 32.4 1.0 CG2 B:VAL53 4.8 22.2 1.0 OD2 B:ASP52 4.8 42.6 1.0 N B:ASP52 4.9 31.1 1.0 CD B:GLU100 4.9 45.4 1.0 O B:VAL51 4.9 35.2 1.0 C4' D:A11 4.9 31.9 1.0 O D:HOH209 4.9 44.2 1.0

J.Wu, N.L.Samara, I.Kuraoka, W.Yang. Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046