Manganese in PDB 5zo5: Active State of the Nuclease

The structure of Active State of the Nuclease, PDB code: 5zo5 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)	47.26 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.743, 121.743, 149.971, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.5

The binding sites of Manganese atom in the Active State of the Nuclease (pdb code 5zo5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Active State of the Nuclease, PDB code: 5zo5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Active 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 Active State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:59.8 occ:1.00 OD2 A:ASP27 2.1 38.5 1.0 OD2 A:ASP157 2.4 40.5 1.0 OE2 A:GLU29 2.6 34.6 1.0 CG A:ASP27 3.2 34.6 1.0 CG A:ASP157 3.4 38.0 1.0 CD A:GLU29 3.6 32.8 1.0 OD1 A:ASP27 3.7 35.8 1.0 O A:THR28 3.7 31.0 1.0 O A:HOH509 3.8 44.4 1.0 MN A:MN302 3.9 80.9 1.0 OE1 A:GLU29 4.0 33.4 1.0 OH A:TYR153 4.0 51.4 1.0 CB A:ASP157 4.1 31.9 1.0 OD1 A:ASP157 4.3 36.9 1.0 CE2 A:TYR153 4.3 43.9 1.0 NE2 A:GLN44 4.3 30.8 1.0 CB A:ASP27 4.5 32.4 1.0 CZ A:TYR153 4.5 51.7 1.0 C A:THR28 4.8 30.3 1.0 CG A:GLU29 4.8 31.2 1.0

Manganese binding site 2 out of 4 in the Active 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 Active State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:80.9 occ:1.00 OD1 A:ASP27 2.1 35.8 1.0 CG A:ASP27 3.1 34.6 1.0 O A:HOH509 3.1 44.4 1.0 OD2 A:ASP86 3.2 35.5 1.0 OD2 A:ASP27 3.4 38.5 1.0 OD1 A:ASP86 3.5 33.8 1.0 O A:HIS81 3.7 29.3 1.0 CG A:ASP86 3.8 31.9 1.0 O A:HOH448 3.8 26.6 1.0 MN A:MN301 3.9 59.8 1.0 O A:HOH470 4.3 31.6 1.0 CB A:ASP27 4.4 32.4 1.0 O A:THR28 4.5 31.0 1.0 N A:THR28 4.7 29.8 1.0 O A:TYR82 4.7 28.8 1.0 CA A:ASP27 4.8 29.5 1.0 C A:HIS81 4.9 25.9 1.0

Manganese binding site 3 out of 4 in the Active 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 Active State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:74.5 occ:1.00 OD1 B:ASP27 2.5 35.0 1.0 OD2 B:ASP86 2.9 32.7 1.0 O B:HOH471 3.2 46.5 1.0 CG B:ASP27 3.3 34.3 1.0 OD1 B:ASP86 3.5 30.6 1.0 OD2 B:ASP27 3.5 40.4 1.0 CG B:ASP86 3.6 29.0 1.0 O B:HIS81 3.9 27.1 1.0 MN B:MN302 4.1 59.5 1.0 O B:HOH438 4.2 26.8 1.0 O B:THR28 4.5 31.6 1.0 O B:TYR82 4.7 26.1 1.0 CB B:ASP27 4.7 30.6 1.0 N B:THR28 4.8 29.4 1.0 CD2 B:PHE85 4.8 25.0 1.0

Manganese binding site 4 out of 4 in the Active 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 Active State of the Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:59.5 occ:1.00 OD2 B:ASP27 2.4 40.4 1.0 OD2 B:ASP157 2.5 42.0 1.0 OE2 B:GLU29 2.6 37.0 1.0 CG B:ASP27 3.2 34.3 1.0 O B:HOH471 3.2 46.5 1.0 CD B:GLU29 3.4 34.8 1.0 O B:THR28 3.6 31.6 1.0 OD1 B:ASP27 3.6 35.0 1.0 OE1 B:GLU29 3.6 34.6 1.0 CG B:ASP157 3.7 38.1 1.0 OH B:TYR153 3.8 54.2 1.0 MN B:MN301 4.1 74.5 1.0 CB B:ASP157 4.2 34.7 1.0 NE2 B:GLN44 4.3 34.5 1.0 CE2 B:TYR153 4.3 43.8 1.0 CB B:ASP27 4.3 30.6 1.0 CZ B:TYR153 4.4 50.1 1.0 C B:THR28 4.6 29.2 1.0 OD1 B:ASP157 4.7 39.2 1.0 CG B:GLU29 4.8 31.5 1.0 N B:THR28 4.9 29.4 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