Manganese in PDB 6ozq: Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+, PDB code: 6ozq 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)	42.72 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.205, 73.807, 154.659, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.9

The binding sites of Manganese atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ (pdb code 6ozq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+, PDB code: 6ozq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:48.9 occ:1.00 OD1 A:ASP240 2.2 72.3 1.0 OP1 C:U12 2.2 48.8 1.0 OD2 A:ASP126 2.3 48.8 1.0 O A:HOH422 2.4 24.6 0.5 OD1 A:ASP52 2.4 50.8 1.0 O A:HOH406 2.5 46.9 1.0 CG A:ASP240 3.0 63.5 1.0 CG A:ASP52 3.1 46.4 1.0 OD2 A:ASP240 3.3 56.3 1.0 CG A:ASP126 3.3 52.9 1.0 O A:HOH426 3.5 37.6 1.0 CB A:ASP52 3.6 30.1 1.0 P C:U12 3.7 42.2 1.0 O A:HOH405 3.9 32.6 1.0 CB A:ASP126 3.9 43.2 1.0 OD2 A:ASP52 3.9 62.9 1.0 CA A:ASP52 4.2 33.0 1.0 O3' C:A11 4.2 43.3 1.0 OD1 A:ASP126 4.3 56.7 1.0 CB A:ASP240 4.4 42.6 1.0 CG2 A:ILE236 4.4 36.4 1.0 O A:VAL51 4.5 31.9 1.0 O5' C:U12 4.6 37.7 1.0 C5' C:U12 4.6 46.6 1.0 OP2 C:U12 4.6 44.0 1.0 O A:ILE236 4.7 31.9 1.0 CA A:ASP240 4.8 39.9 1.0 N A:VAL53 5.0 38.8 1.0

Manganese binding site 2 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:49.0 occ:1.00 OD1 B:ASP52 2.1 39.1 1.0 OP1 D:U12 2.2 45.3 1.0 O B:HOH413 2.2 41.2 1.0 OD1 B:ASP240 2.3 79.6 1.0 OD2 B:ASP126 2.5 71.5 1.0 O B:HOH420 2.5 69.5 1.0 CG B:ASP240 3.1 68.0 1.0 CG B:ASP52 3.1 47.4 1.0 OD2 B:ASP240 3.3 71.9 1.0 O B:HOH403 3.3 39.7 1.0 CG B:ASP126 3.4 68.2 1.0 CB B:ASP52 3.6 28.8 1.0 P D:U12 3.6 45.0 1.0 O B:HOH402 3.8 38.1 1.0 CB B:ASP126 3.8 44.8 1.0 O3' D:A11 4.1 41.8 1.0 OD2 B:ASP52 4.1 55.0 1.0 CA B:ASP52 4.1 28.4 1.0 O B:HOH441 4.2 45.1 0.5 OD1 B:ASP126 4.4 72.0 1.0 O B:VAL51 4.4 40.4 1.0 CB B:ASP240 4.5 55.1 1.0 OP2 D:U12 4.5 40.0 1.0 CG2 B:ILE236 4.6 45.6 1.0 O5' D:U12 4.6 38.3 1.0 C5' D:U12 4.6 41.5 1.0 O B:ILE236 4.7 34.4 1.0 CA B:ASP240 4.8 41.5 1.0 N B:VAL53 4.9 32.7 1.0 N B:ASP240 5.0 38.5 1.0

Manganese binding site 3 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:52.9 occ:0.60 O C:HOH211 2.5 39.1 1.0 O4 C:U18 2.5 39.2 1.0 C4 C:U18 3.5 43.0 1.0 C5 C:U18 3.9 37.0 1.0 N7 C:A17 3.9 42.4 1.0 N6 C:A17 4.3 34.1 1.0 C5 C:A17 4.5 43.5 1.0 N6 D:A17 4.7 31.9 1.0 O6 C:G19 4.7 38.7 1.0 N3 C:U18 4.7 37.0 1.0 C6 C:A17 4.7 37.8 1.0 C8 C:A17 4.7 42.2 1.0

Manganese binding site 4 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn102 b:45.5 occ:0.50 O C:HOH210 2.1 43.6 1.0 OP2 C:A13 2.1 53.9 1.0 O A:HOH426 2.8 37.6 1.0 P C:A13 3.4 47.6 1.0 OP1 C:A13 3.8 48.6 1.0 O C:HOH203 3.8 54.9 1.0 OP1 C:U12 4.3 48.8 1.0 O3' C:U12 4.3 42.8 1.0 NH2 A:ARG244 4.4 87.7 1.0 O5' C:U12 4.4 37.7 1.0 O5' C:A13 4.5 45.4 1.0 OD1 A:ASP240 4.6 72.3 1.0 C3' C:U12 4.6 39.2 1.0 OP2 C:U12 4.7 44.0 1.0 P C:U12 4.7 42.2 1.0 CG A:ASP240 4.8 63.5 1.0 O C:HOH207 4.9 81.7 1.0 C5' C:U12 4.9 46.6 1.0

Manganese binding site 5 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn101 b:52.6 occ:0.50 MN D:MN101 0.0 52.6 0.5 MN D:MN101 2.4 51.2 0.5 O4 D:U18 2.7 38.1 1.0 C4 D:U18 3.5 36.6 1.0 C5 D:U18 3.8 33.6 1.0 N7 D:A17 3.9 43.7 1.0 N6 D:A17 4.3 31.9 1.0 C5 D:A17 4.5 40.4 1.0 O6 D:G19 4.6 43.8 1.0 C8 D:A17 4.7 40.6 1.0 C6 D:A17 4.7 41.5 1.0 N6 C:A17 4.8 34.1 1.0 N3 D:U18 4.8 31.8 1.0

Manganese binding site 6 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn101 b:51.2 occ:0.50 MN D:MN101 0.0 51.2 0.5 MN D:MN101 2.4 52.6 0.5 O4 D:U18 3.8 38.1 1.0 C5 D:U18 4.3 33.6 1.0 C4 D:U18 4.3 36.6 1.0 O6 D:G19 4.4 43.8 1.0 O D:HOH205 4.5 43.7 1.0 N7 D:G19 4.6 42.0 1.0

Manganese binding site 7 out of 7 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Mus Musculus (Mm) Endonuclease V (K155M) in Complex with A 23MER Rna Oligo Containing An Inosine After A 100 Min Soak in 10 Mm MN2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn102 b:49.3 occ:0.50 OP2 D:A13 1.9 54.4 1.0 O B:HOH401 2.0 56.4 0.5 O D:HOH210 2.0 53.2 0.5 O D:HOH213 2.1 48.9 1.0 O B:HOH441 2.2 45.1 0.5 O B:HOH403 2.8 39.7 1.0 P D:A13 3.2 46.1 1.0 O D:HOH203 3.4 52.5 1.0 OP1 D:A13 3.8 53.2 1.0 NH1 B:ARG244 3.8 97.0 1.0 O3' D:U12 4.0 41.9 1.0 O5' D:U12 4.1 38.3 1.0 OP1 D:U12 4.2 45.3 1.0 C3' D:U12 4.2 39.8 1.0 OP2 D:U12 4.4 40.0 1.0 O5' D:A13 4.4 52.5 1.0 P D:U12 4.4 45.0 1.0 OD1 B:ASP240 4.5 79.6 1.0 C5' D:U12 4.5 41.5 1.0 CG B:ASP240 4.8 68.0 1.0 C4' D:U12 5.0 48.1 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