Manganese in PDB 5zo4: Inactive State of the Nuclease

The structure of Inactive State of the Nuclease, PDB code: 5zo4 was solved by Z.L.Yuan, L.C.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 2.50
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.010, 122.010, 148.808, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.8

The binding sites of Manganese atom in the Inactive State of the Nuclease (pdb code 5zo4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Inactive State of the Nuclease, PDB code: 5zo4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Inactive State of the Nuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Inactive State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:79.5 occ:1.00 OE2 A:GLU29 2.3 64.3 1.0 OE1 A:GLU29 2.6 54.7 1.0 OD2 A:ASP157 2.6 68.7 1.0 CD A:GLU29 2.8 53.5 1.0 CG A:ASP157 3.7 63.5 1.0 OD1 A:ASP157 4.2 66.8 1.0 OD1 A:ASP27 4.3 59.1 1.0 CG A:GLU29 4.3 57.4 1.0 CZ2 A:TRP141 4.5 50.5 1.0 O A:THR28 4.8 59.9 1.0 NE2 A:GLN44 4.8 55.1 1.0 CE2 A:TRP141 5.0 55.5 1.0 NE1 A:TRP141 5.0 54.4 1.0

Manganese binding site 2 out of 4 in the Inactive State of the Nuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Inactive State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:80.7 occ:1.00 OD2 A:ASP27 1.8 58.2 1.0 OD2 A:ASP86 2.5 60.3 1.0 CG A:ASP27 2.8 57.5 1.0 OD1 A:ASP27 3.2 59.1 1.0 CG A:ASP86 3.4 56.6 1.0 OD1 A:ASP86 3.5 62.0 1.0 O A:HIS81 3.9 50.4 1.0 CB A:ASP27 4.2 58.2 1.0 O A:TYR82 4.5 52.6 1.0 CA A:ASP27 4.7 55.8 1.0 N A:THR28 4.7 54.2 1.0 O A:THR28 4.8 59.9 1.0 CB A:ASP86 4.9 56.7 1.0 C A:HIS81 5.0 49.9 1.0

Manganese binding site 3 out of 4 in the Inactive State of the Nuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Inactive State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:99.7 occ:1.00 OD2 B:ASP157 2.0 74.6 1.0 OE2 B:GLU29 2.3 66.5 1.0 CG B:ASP157 3.2 69.0 1.0 CD B:GLU29 3.2 55.9 1.0 OE1 B:GLU29 3.3 58.9 1.0 OD1 B:ASP157 3.8 74.7 1.0 OD2 B:ASP27 4.0 64.7 1.0 NE2 B:GLN44 4.2 60.5 1.0 CB B:ASP157 4.3 62.2 1.0 CG B:GLU29 4.6 60.6 1.0 O B:THR28 4.7 63.0 1.0 O B:TYR153 4.7 65.6 1.0 CG B:ASP27 5.0 57.7 1.0 CZ2 B:TRP141 5.0 61.8 1.0

Manganese binding site 4 out of 4 in the Inactive State of the Nuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Inactive State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:90.4 occ:1.00 OD1 B:ASP27 2.2 59.2 1.0 OD2 B:ASP86 2.5 60.7 1.0 CG B:ASP27 3.1 57.7 1.0 OD2 B:ASP27 3.2 64.7 1.0 CG B:ASP86 3.3 57.8 1.0 OD1 B:ASP86 3.3 60.0 1.0 O B:HIS81 4.3 52.2 1.0 CB B:ASP27 4.5 53.6 1.0 O A:HOH413 4.5 74.6 1.0 O B:TYR82 4.6 51.0 1.0 O B:THR28 4.6 63.0 1.0 CD2 B:PHE85 4.6 43.6 1.0 N B:THR28 4.7 54.9 1.0 CB B:ASP86 4.7 56.8 1.0 CA B:ASP27 4.9 56.5 1.0

Z.Yuan, F.Gao, K.Yin, L.Gu. Nrnc, An Rnase D-Like Protein Fromagrobacterium, Is A Novel Octameric Nuclease That Specifically Degrades Dsdna But Leaves Dsrna Intact. Front Microbiol V. 9 3230 2018.
ISSN: ESSN 1664-302X
PubMed: 30666241
DOI: 10.3389/FMICB.2018.03230