Magnesium 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:

Potassium

(K)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg301 b:39.0 occ:0.90 O A:HOH411 2.0 39.6 1.0 OP1 C:U12 2.0 36.9 1.0 OD1 A:ASP52 2.0 39.2 1.0 O A:HOH448 2.1 34.9 1.0 OD1 A:ASP240 2.2 39.2 0.7 OD2 A:ASP126 2.5 48.8 0.7 CG A:ASP240 3.0 35.5 0.7 CG A:ASP52 3.1 40.3 1.0 OD2 A:ASP240 3.2 34.4 0.7 CG A:ASP126 3.3 47.2 0.7 P C:U12 3.4 31.6 1.0 OD1 A:ASP126 3.6 52.6 0.7 CB A:ASP52 3.9 25.5 1.0 OD2 A:ASP52 3.9 54.9 1.0 K A:K302 4.0 40.3 0.6 O5' C:U12 4.0 26.9 1.0 OP2 C:U12 4.1 26.7 1.0 CB A:ASP240 4.2 29.3 1.0 C5' C:U12 4.3 27.3 1.0 CG2 A:ILE236 4.4 21.5 1.0 O3' C:A11 4.4 26.9 1.0 CB A:ASP126 4.4 35.9 1.0 NZ A:LYS155 4.4 45.8 1.0 CA A:ASP52 4.7 24.2 1.0 CA A:ASP240 4.7 26.8 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg301 b:54.6 occ:1.00 O B:HOH407 1.9 47.7 1.0 O D:HOH209 2.0 44.2 1.0 OD1 B:ASP52 2.0 44.4 1.0 OP1 D:U12 2.2 43.8 1.0 OD1 B:ASP240 2.2 42.1 0.5 OD2 B:ASP126 2.8 53.8 0.4 CG B:ASP240 2.9 38.0 0.5 CG B:ASP52 3.1 42.2 1.0 OD2 B:ASP240 3.2 41.5 0.5 P D:U12 3.6 36.3 1.0 O B:HOH423 3.7 44.7 1.0 CB B:ASP52 3.8 26.5 1.0 CG B:ASP126 3.9 50.3 0.5 K B:K302 3.9 43.5 0.6 OD2 B:ASP52 4.0 42.6 1.0 CB B:ASP240 4.1 36.5 1.0 CB B:ASP126 4.2 41.8 1.0 CG2 B:ILE236 4.2 27.8 1.0 OP2 D:U12 4.3 27.0 1.0 O5' D:U12 4.3 31.4 1.0 C5' D:U12 4.4 35.1 1.0 CA B:ASP52 4.5 22.5 1.0 O3' D:A11 4.5 37.2 1.0 CA B:ASP240 4.7 31.6 1.0 NZ B:LYS155 4.7 55.5 1.0 CE B:LYS155 4.8 52.6 1.0 OD1 B:ASP126 5.0 51.7 0.7

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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 C:Mg101 b:33.5 occ:0.70 O C:HOH231 2.1 38.1 1.0 O C:HOH228 2.1 44.2 1.0 O C:HOH204 2.2 36.7 1.0 O C:HOH227 2.2 48.3 1.0 O C:HOH207 2.3 36.5 1.0 O C:HOH218 2.4 31.4 1.0 O C:HOH216 3.6 30.1 1.0 O4 C:U18 3.8 24.6 1.0 O C:HOH220 4.1 51.1 1.0 C5 C:U18 4.2 27.7 1.0 O C:HOH215 4.2 33.4 1.0 C4 C:U18 4.3 26.3 1.0 O D:HOH206 4.7 38.1 1.0 O6 C:G19 4.7 28.2 1.0 O B:HOH466 4.8 47.7 1.0 N7 C:G19 4.8 29.2 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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 D:Mg101 b:43.9 occ:0.85 O D:HOH201 2.1 35.1 1.0 O D:HOH235 2.2 54.5 1.0 O C:HOH230 2.2 44.3 1.0 O D:HOH234 2.3 44.7 1.0 O D:HOH215 2.4 37.8 1.0 O D:HOH214 2.4 32.4 1.0 O D:HOH220 3.5 28.1 1.0 O D:HOH219 3.8 39.9 1.0 O4 D:U18 3.9 22.3 1.0 O C:HOH206 4.1 43.0 1.0 C5 D:U18 4.2 22.4 1.0 O D:HOH210 4.3 31.6 1.0 C4 D:U18 4.4 21.3 1.0 N7 D:G19 4.8 27.3 1.0 O6 D:G19 4.8 25.3 1.0 O A:HOH483 4.9 33.4 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