Manganese in PDB 4xww: Crystal Structure of Rnase J Complexed with Rna

The structure of Crystal Structure of Rnase J Complexed with Rna, PDB code: 4xww was solved by M.Lu, H.Zhang, Q.Xu, Y.Hua, Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.59 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.120, 87.860, 249.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.7

The structure of Crystal Structure of Rnase J Complexed with Rna also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of Rnase J Complexed with Rna (pdb code 4xww). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Rnase J Complexed with Rna, PDB code: 4xww:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Rnase J Complexed with Rna


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 Rnase J Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:78.9 occ:1.00 OD1 A:ASP456 2.2 33.3 1.0 O A:GLY59 2.3 43.8 1.0 CG A:ASP456 3.3 38.6 1.0 C A:GLY59 3.4 34.9 1.0 OD2 A:ASP456 3.7 33.9 1.0 OD1 A:ASP61 3.8 54.2 1.0 OE2 B:GLU477 4.1 45.2 1.0 CA A:GLY59 4.1 34.3 1.0 OE1 B:GLU477 4.3 48.4 1.0 O B:GLN476 4.3 34.8 1.0 CG A:ASP61 4.4 44.2 1.0 OD2 A:ASP61 4.4 45.3 1.0 CD B:ARG549 4.5 40.3 1.0 N A:ILE60 4.5 35.3 1.0 CD B:GLU477 4.5 45.4 1.0 CB A:ASP456 4.6 36.6 1.0 CA A:ILE60 4.6 35.0 1.0 N A:GLY457 4.6 40.9 1.0 CA A:ASP456 4.7 35.6 1.0 C A:ASP456 4.8 34.2 1.0 CG B:ARG549 4.8 48.5 1.0 C A:ILE60 4.9 32.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Rnase J Complexed with Rna


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 Rnase J Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:62.2 occ:1.00 O B:GLY59 2.0 42.7 1.0 OD1 B:ASP456 2.0 38.1 1.0 CG B:ASP456 3.0 41.0 1.0 C B:GLY59 3.1 40.4 1.0 OD2 B:ASP456 3.2 32.7 1.0 CA B:GLY59 3.8 31.0 1.0 O A:GLN476 4.1 42.0 1.0 OE1 A:GLU477 4.1 49.2 1.0 N B:ILE60 4.2 43.0 1.0 OE2 A:GLU477 4.2 55.6 1.0 CB B:ASP456 4.4 44.6 1.0 CD A:GLU477 4.4 53.4 1.0 CA B:ILE60 4.4 42.7 1.0 CD A:ARG549 4.4 52.1 1.0 O A:HOH1077 4.6 51.0 1.0 OD1 B:ASP61 4.6 57.9 1.0 OD2 B:ASP61 4.6 52.9 1.0 CA B:ASP456 4.7 43.1 1.0 NH1 B:ARG471 4.8 30.1 1.0 N B:GLY457 4.8 37.4 1.0 C B:ILE60 4.9 40.1 1.0 CG B:ASP61 4.9 49.7 1.0 C B:ASP456 4.9 41.7 1.0 NE A:ARG549 4.9 48.6 1.0

Y.Zhao, M.Lu, H.Zhang, J.Hu, C.Zhou, Q.Xu, A.M.U.H.Shah, H.Xu, L.Wang, Y.Hua. Structural Insights Into Catalysis and Dimerization Enhanced Exonuclease Activity of Rnase J Nucleic Acids Res. V. 43 5550 2015.
ISSN: ESSN 1362-4962
PubMed: 25940620
DOI: 10.1093/NAR/GKV444