Potassium in PDB 6ozi: Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine

The structure of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozi 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)	30.00 / 2.30
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.079, 81.428, 166.034, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.1

The binding sites of Potassium atom in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine (pdb code 6ozi). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozi:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine


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 Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:K301 b:35.9 occ:1.00 O A:HOH567 2.7 38.9 1.0 O A:THR73 2.8 23.3 1.0 OD1 A:ASN72 2.8 30.7 1.0 O A:HOH491 3.1 31.7 1.0 O A:HOH573 3.2 31.8 1.0 CG A:ASN72 3.7 29.1 1.0 ND2 A:ASN72 3.9 29.2 1.0 C A:THR73 4.0 24.5 1.0 N A:THR73 4.2 25.7 1.0 OG1 A:THR73 4.7 27.3 1.0 CA A:THR73 4.7 25.2 1.0 CB A:ASN72 4.9 27.6 1.0 N A:THR74 5.0 25.3 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine


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 Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:47.2 occ:1.00 OP1 C:DI5 2.6 28.3 1.0 O4 D:DT17 2.7 33.0 1.0 O C:HOH231 2.8 31.6 1.0 O C:HOH239 3.0 43.5 1.0 O C:HOH236 3.0 31.8 1.0 O A:HOH582 3.2 41.4 1.0 C4 D:DT17 3.7 31.6 1.0 O A:HOH435 3.8 31.4 1.0 K D:K101 3.8 38.0 1.0 P C:DI5 3.9 27.0 1.0 C7 D:DT17 4.1 33.6 1.0 OP2 C:DI5 4.2 27.1 1.0 O C:HOH201 4.2 38.4 1.0 C5 D:DT17 4.4 32.2 1.0 OG A:SER147 4.6 32.6 1.0 OP2 C:DC4 4.6 39.4 1.0 N3 D:DT17 4.8 30.3 1.0 C3' C:DC4 4.8 26.5 1.0 C7 D:DT16 4.8 35.8 1.0 C5' C:DC4 4.9 31.7 1.0 O5' C:DI5 4.9 27.3 1.0 O3' C:DC4 4.9 25.1 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine


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 Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:55.3 occ:1.00 O D:HOH224 2.7 39.4 1.0 O C:HOH211 2.8 42.0 1.0 O2 C:DT9 2.8 38.6 1.0 O4' C:DG10 2.9 40.2 1.0 C4' C:DG10 3.4 42.2 1.0 C1' C:DG10 3.8 38.6 1.0 C5' C:DG10 4.0 43.3 1.0 C2 C:DT9 4.0 36.1 1.0 O D:HOH211 4.3 35.8 1.0 C1' C:DT9 4.3 35.8 1.0 N9 C:DG10 4.4 37.1 1.0 C2 D:DA15 4.5 35.1 1.0 N3 C:DG10 4.7 35.1 1.0 N1 C:DT9 4.7 34.9 1.0 C4 C:DG10 4.8 35.2 1.0 C3' C:DG10 4.8 44.0 1.0 O2 D:DT16 4.9 35.3 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine


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 Ciona Intestinalis (Ci) Endonuclease V (D234N) in Complex with A 23MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:38.0 occ:1.00 O C:HOH235 2.8 32.8 1.0 O C:HOH236 2.8 31.8 1.0 O4 C:DT7 2.9 30.7 1.0 O A:HOH582 2.9 41.4 1.0 O4 D:DT17 3.0 33.0 1.0 O C:HOH215 3.1 29.1 1.0 O4 D:DT16 3.1 33.0 1.0 K C:K101 3.8 47.2 1.0 C4 D:DT17 3.9 31.6 1.0 C4 C:DT7 3.9 31.0 1.0 C7 C:DT7 3.9 26.0 1.0 N3 D:DT17 4.0 30.3 1.0 N6 C:DA8 4.0 33.0 1.0 C4 D:DT16 4.1 33.5 1.0 C5 C:DT7 4.4 30.4 1.0 C7 D:DT16 4.5 35.8 1.0 OP2 C:A6 4.6 25.8 1.0 OG A:SER147 4.6 32.6 1.0 C5 D:DT16 4.8 34.3 1.0 O C:HOH231 4.8 31.6 1.0 CB A:SER147 5.0 30.2 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