Manganese in PDB 6ozl: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+, PDB code: 6ozl 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)	35.82 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.621, 72.519, 155.764, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.7

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ also contains other interesting chemical elements:

Sodium

(Na)

1 atom

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

Manganese 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 2 Min Soak in MN2+


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 in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:39.6 occ:1.00 OD1 A:ASP240 2.0 50.5 1.0 OP1 C:U12 2.1 33.8 1.0 O C:HOH205 2.2 39.7 1.0 O A:HOH420 2.3 35.4 1.0 OD2 A:ASP52 2.3 40.9 1.0 O C:HOH201 2.5 36.2 1.0 CG A:ASP240 3.0 54.4 1.0 CG A:ASP52 3.1 45.2 1.0 OD1 A:ASP52 3.3 36.1 1.0 P C:U12 3.4 36.5 1.0 CB A:ASP240 3.8 34.3 1.0 MN A:MN302 4.0 42.1 1.0 OD2 A:ASP240 4.0 49.1 1.0 O5' C:U12 4.1 45.6 1.0 OP2 C:U12 4.1 29.7 1.0 O A:HOH472 4.2 42.5 1.0 OP2 C:A13 4.3 43.2 1.0 OD2 A:ASP126 4.4 45.0 1.0 C5' C:U12 4.4 43.2 1.0 CA A:ASP240 4.4 36.8 1.0 O A:VAL53 4.5 41.5 1.0 CB A:ASP52 4.5 39.9 1.0 O3' C:A11 4.6 43.0 1.0 OG A:SER54 4.6 52.1 1.0 CG A:ASP126 4.8 42.4 1.0 O A:HOH415 4.9 37.5 1.0 NZ A:LYS155 4.9 45.7 1.0

Manganese 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 2 Min Soak in MN2+


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 in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:42.1 occ:1.00 OD1 A:ASP52 2.1 36.1 1.0 OD2 A:ASP126 2.1 45.0 1.0 O A:HOH415 2.3 37.5 1.0 O3' C:A11 2.4 43.0 1.0 OP1 C:U12 2.5 33.8 1.0 O A:HOH411 2.5 39.9 1.0 P C:U12 3.0 36.5 1.0 CG A:ASP126 3.1 42.4 1.0 CG A:ASP52 3.3 45.2 1.0 CB A:ASP126 3.5 33.4 1.0 C3' C:A11 3.6 31.9 1.0 O2' C:A11 3.9 39.4 1.0 OD2 A:ASP52 3.9 40.9 1.0 MN A:MN301 4.0 39.6 1.0 C4' C:A11 4.0 33.1 1.0 O A:VAL53 4.0 41.5 1.0 O5' C:U12 4.0 45.6 1.0 OP2 C:U12 4.1 29.7 1.0 C5' C:U12 4.1 43.2 1.0 O A:ASP126 4.2 49.5 1.0 OD1 A:ASP126 4.2 49.1 1.0 N A:VAL53 4.2 35.7 1.0 O C:HOH205 4.3 39.7 1.0 OE1 A:GLU100 4.3 55.8 1.0 C2' C:A11 4.3 33.3 1.0 OE2 A:GLU100 4.4 68.7 1.0 CB A:ASP52 4.5 39.9 1.0 CA A:ASP52 4.5 33.1 1.0 C5' C:A11 4.6 37.7 1.0 O A:HOH420 4.7 35.4 1.0 C A:ASP126 4.8 44.8 1.0 CA A:ASP126 4.8 36.5 1.0 CD A:GLU100 4.8 66.2 1.0 NZ A:LYS155 4.9 45.7 1.0 C A:ASP52 4.9 33.9 1.0 C A:VAL53 4.9 36.1 1.0

Manganese 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 2 Min Soak in MN2+


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 in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:43.4 occ:1.00 OD1 B:ASP240 2.1 48.2 1.0 OP1 D:U12 2.2 44.7 1.0 OD2 B:ASP52 2.2 47.4 1.0 O D:HOH206 2.3 42.4 1.0 O B:HOH412 2.3 36.3 1.0 O D:HOH207 2.5 45.7 1.0 CG B:ASP52 3.1 39.2 1.0 CG B:ASP240 3.2 40.4 1.0 OD1 B:ASP52 3.3 35.3 1.0 P D:U12 3.5 45.8 1.0 CB B:ASP240 3.8 33.5 1.0 MN B:MN302 4.0 42.4 1.0 OD2 B:ASP126 4.0 48.7 1.0 O5' D:U12 4.1 49.0 1.0 OD2 B:ASP240 4.2 47.2 1.0 OP2 D:U12 4.2 46.0 1.0 O B:HOH441 4.2 57.4 1.0 C5' D:U12 4.4 46.7 1.0 CA B:ASP240 4.4 37.3 1.0 O B:VAL53 4.4 34.2 1.0 OP2 D:A13 4.4 47.1 1.0 CB B:ASP52 4.5 35.0 1.0 OG B:SER54 4.6 55.4 1.0 O3' D:A11 4.7 46.1 1.0 O B:HOH401 4.7 36.8 1.0 CG B:ASP126 5.0 49.7 1.0

Manganese 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 2 Min Soak in MN2+


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 in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:42.4 occ:1.00 OD2 B:ASP126 2.1 48.7 1.0 OD1 B:ASP52 2.1 35.3 1.0 O B:HOH401 2.3 36.8 1.0 O B:HOH406 2.4 39.0 1.0 O3' D:A11 2.6 46.1 1.0 OP1 D:U12 2.6 44.7 1.0 CG B:ASP126 3.1 49.7 1.0 P D:U12 3.2 45.8 1.0 CG B:ASP52 3.3 39.2 1.0 CB B:ASP126 3.5 37.7 1.0 C3' D:A11 3.8 44.1 1.0 OD2 B:ASP52 4.0 47.4 1.0 MN B:MN301 4.0 43.4 1.0 O2' D:A11 4.0 45.9 1.0 O B:VAL53 4.1 34.2 1.0 OE2 B:GLU100 4.1 67.3 1.0 O D:HOH206 4.2 42.4 1.0 C5' D:U12 4.2 46.7 1.0 O B:ASP126 4.2 53.6 1.0 C4' D:A11 4.2 44.2 1.0 OE1 B:GLU100 4.2 67.5 1.0 O5' D:U12 4.2 49.0 1.0 OD1 B:ASP126 4.2 51.1 1.0 N B:VAL53 4.2 36.9 1.0 OP2 D:U12 4.2 46.0 1.0 CB B:ASP52 4.5 35.0 1.0 C2' D:A11 4.5 47.3 1.0 CA B:ASP52 4.6 34.6 1.0 CD B:GLU100 4.6 69.6 1.0 O B:HOH412 4.8 36.3 1.0 C5' D:A11 4.8 43.1 1.0 CA B:ASP126 4.8 35.7 1.0 C B:ASP126 4.8 47.0 1.0 C B:ASP52 5.0 31.2 1.0 C B:VAL53 5.0 35.5 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