Manganese in PDB 4xwt: Crystal Structure of Rnase J Complexed with Ump

The structure of Crystal Structure of Rnase J Complexed with Ump, PDB code: 4xwt 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)	29.47 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.590, 87.760, 253.420, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.5

The structure of Crystal Structure of Rnase J Complexed with Ump 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 Ump (pdb code 4xwt). 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 Ump, PDB code: 4xwt:
Jump to Manganese binding site number: 1; 2;

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


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:50.0 occ:1.00 O A:GLY59 2.1 45.9 1.0 OD1 A:ASP456 2.1 52.9 1.0 CG A:ASP456 3.1 54.8 1.0 C A:GLY59 3.1 49.5 1.0 OD2 A:ASP456 3.3 49.3 1.0 CA A:GLY59 3.7 49.7 1.0 O B:GLN476 3.9 55.7 1.0 OE1 B:GLU477 4.0 79.9 1.0 CD B:ARG549 4.2 53.2 1.0 N A:ILE60 4.2 47.5 1.0 CD B:GLU477 4.4 78.3 1.0 CA A:ILE60 4.4 52.8 1.0 CB A:ASP456 4.5 51.6 1.0 OE2 B:GLU477 4.5 82.6 1.0 OD1 A:ASP61 4.7 65.6 1.0 CA A:ASP456 4.8 51.0 1.0 N A:GLY457 4.8 54.4 1.0 CG B:ARG549 4.8 54.7 1.0 OD2 A:ASP61 4.8 65.4 1.0 C A:ASP456 4.9 44.5 1.0 C A:ILE60 5.0 46.9 1.0 CG A:ASP61 5.0 59.4 1.0

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


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:49.6 occ:1.00 O B:GLY59 2.1 53.6 1.0 OD1 B:ASP456 2.2 41.2 1.0 CG B:ASP456 3.2 46.9 1.0 C B:GLY59 3.2 43.4 1.0 OD2 B:ASP456 3.5 40.5 1.0 CA B:GLY59 3.9 46.9 1.0 CD A:ARG549 4.1 66.4 1.0 O A:GLN476 4.1 45.9 1.0 OE1 A:GLU477 4.1 65.1 1.0 OE2 A:GLU477 4.2 66.3 1.0 N B:ILE60 4.3 40.8 1.0 CD A:GLU477 4.4 62.3 1.0 CA B:ILE60 4.5 46.9 1.0 CB B:ASP456 4.5 51.3 1.0 OD2 B:ASP61 4.7 63.9 1.0 OD1 B:ASP61 4.7 62.4 1.0 NE A:ARG549 4.7 68.5 1.0 CA B:ASP456 4.8 50.6 1.0 N B:GLY457 4.8 46.6 1.0 C B:ASP456 4.9 48.5 1.0 CG B:ASP61 5.0 56.9 1.0 NH1 B:ARG471 5.0 50.1 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