Zinc 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:

Manganese

(Mn)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Rnase J Complexed with Rna, PDB code: 4xww:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Rnase J Complexed with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn601 b:21.6 occ:1.00 O D:HOH107 1.9 16.4 1.0 ND1 A:HIS86 2.1 15.7 1.0 NE2 A:HIS84 2.1 17.2 1.0 NE2 A:HIS153 2.2 18.1 1.0 CD2 A:HIS84 2.9 19.4 1.0 CE1 A:HIS86 3.0 19.0 1.0 CD2 A:HIS153 3.0 15.6 1.0 CG A:HIS86 3.2 16.2 1.0 CE1 A:HIS84 3.2 14.6 1.0 CE1 A:HIS153 3.2 16.1 1.0 ZN A:ZN602 3.5 30.6 1.0 CB A:HIS86 3.6 18.4 1.0 CB A:ASP175 3.7 18.8 1.0 OP1 D:U2 3.8 27.6 1.0 OP2 D:U2 3.9 34.0 1.0 NE2 A:HIS89 4.0 20.9 1.0 CD2 A:HIS89 4.1 17.8 1.0 CG A:HIS84 4.1 15.6 1.0 NE2 A:HIS86 4.1 17.5 1.0 P D:U2 4.2 29.9 1.0 CG A:HIS153 4.2 13.3 1.0 ND1 A:HIS84 4.2 15.7 1.0 CD2 A:HIS86 4.3 17.9 1.0 ND1 A:HIS153 4.3 17.1 1.0 OD1 A:ASP88 4.3 28.8 1.0 O5' D:U2 4.5 30.0 1.0 CE1 A:HIS381 4.6 16.7 1.0 NE2 A:HIS381 4.8 18.9 1.0 OG A:SER154 5.0 18.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Rnase J Complexed with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rnase J Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:30.6 occ:1.00 O D:HOH107 2.0 16.4 1.0 NE2 A:HIS89 2.2 20.9 1.0 NE2 A:HIS403 2.2 22.2 1.0 OD2 A:ASP88 2.2 26.0 1.0 CD2 A:HIS89 2.9 17.8 1.0 CG A:ASP88 2.9 28.3 1.0 OD1 A:ASP88 3.0 28.8 1.0 OP2 D:U2 3.0 34.0 1.0 CD2 A:HIS403 3.1 18.4 1.0 CE1 A:HIS403 3.2 19.2 1.0 CE1 A:HIS89 3.3 19.0 1.0 ZN A:ZN601 3.5 21.6 1.0 ND2 A:ASN33 3.7 22.0 1.0 CG A:HIS89 4.1 19.0 1.0 NE2 A:HIS84 4.2 17.2 1.0 ND1 A:HIS403 4.3 19.2 1.0 CG A:HIS403 4.3 16.6 1.0 ND1 A:HIS89 4.3 21.7 1.0 CB A:ASP175 4.3 18.8 1.0 P D:U2 4.3 29.9 1.0 CB A:ASP88 4.3 21.4 1.0 CE1 A:HIS84 4.4 14.6 1.0 CE1 A:HIS381 4.5 16.7 1.0 OP1 D:U2 4.7 27.6 1.0 CG A:ASN33 4.8 20.7 1.0 O A:ASP88 4.9 20.3 1.0 C A:ASP88 5.0 22.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Rnase J Complexed with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rnase J Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:35.3 occ:1.00 OD2 B:ASP88 2.2 29.0 1.0 NE2 B:HIS89 2.2 21.7 1.0 NE2 B:HIS403 2.2 22.2 1.0 CD2 B:HIS89 2.8 22.1 1.0 OD1 B:ASP88 2.8 33.9 1.0 CG B:ASP88 2.8 32.4 1.0 OP2 E:U2 3.1 49.9 1.0 CD2 B:HIS403 3.2 21.8 1.0 CE1 B:HIS403 3.2 21.9 1.0 CE1 B:HIS89 3.4 25.8 1.0 ZN B:ZN602 3.5 23.7 1.0 ND2 B:ASN33 3.7 22.9 1.0 CG B:HIS89 4.1 24.8 1.0 CB B:ASP175 4.3 19.7 1.0 NE2 B:HIS84 4.3 18.6 1.0 CB B:ASP88 4.3 24.7 1.0 ND1 B:HIS89 4.3 26.7 1.0 ND1 B:HIS403 4.3 20.4 1.0 CG B:HIS403 4.3 20.6 1.0 P E:U2 4.4 39.4 1.0 CE1 B:HIS84 4.4 18.3 1.0 CE1 B:HIS381 4.6 19.4 1.0 OP1 E:U2 4.7 34.6 1.0 CG B:ASN33 4.8 27.6 1.0 O B:ASP88 4.9 22.1 1.0 C B:ASP88 5.0 23.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Rnase J Complexed with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rnase J Complexed with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:23.7 occ:1.00 NE2 B:HIS84 2.1 18.6 1.0 NE2 B:HIS153 2.1 20.4 1.0 ND1 B:HIS86 2.1 22.8 1.0 CD2 B:HIS84 2.9 23.2 1.0 CD2 B:HIS153 2.9 19.8 1.0 CE1 B:HIS86 3.0 22.0 1.0 CE1 B:HIS84 3.1 18.3 1.0 CE1 B:HIS153 3.2 20.1 1.0 CG B:HIS86 3.2 21.2 1.0 ZN B:ZN601 3.5 35.3 1.0 CB B:HIS86 3.6 18.9 1.0 CB B:ASP175 3.7 19.7 1.0 OP2 E:U2 3.8 49.9 1.0 OP1 E:U2 3.8 34.6 1.0 CD2 B:HIS89 4.1 22.1 1.0 CG B:HIS84 4.1 20.5 1.0 NE2 B:HIS89 4.1 21.7 1.0 CG B:HIS153 4.2 21.9 1.0 P E:U2 4.2 39.4 1.0 ND1 B:HIS84 4.2 21.9 1.0 NE2 B:HIS86 4.2 21.4 1.0 ND1 B:HIS153 4.2 23.6 1.0 OD1 B:ASP88 4.2 33.9 1.0 CD2 B:HIS86 4.3 22.1 1.0 O5' E:U2 4.5 29.7 1.0 CE1 B:HIS381 4.6 19.4 1.0 NE2 B:HIS381 4.8 21.1 1.0 CA B:HIS86 5.0 21.4 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