Zinc 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:

Manganese

(Mn)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Rnase J Complexed with Ump, PDB code: 4xwt:
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 Ump


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:36.6 occ:1.00 ND1 A:HIS86 2.1 25.5 1.0 NE2 A:HIS153 2.3 26.6 1.0 NE2 A:HIS84 2.4 25.4 1.0 OD2 A:ASP175 2.4 24.5 1.0 CE1 A:HIS86 2.9 32.1 1.0 CD2 A:HIS84 3.1 25.6 1.0 O A:HOH865 3.1 44.5 1.0 CD2 A:HIS153 3.2 28.9 1.0 CG A:HIS86 3.2 26.4 1.0 ZN A:ZN602 3.3 32.8 1.0 CE1 A:HIS153 3.3 30.5 1.0 CG A:ASP175 3.3 32.2 1.0 CE1 A:HIS84 3.5 28.5 1.0 CB A:HIS86 3.6 27.2 1.0 CB A:ASP175 3.8 31.9 1.0 NE2 A:HIS89 4.0 25.7 1.0 NE2 A:HIS86 4.1 30.5 1.0 CD2 A:HIS89 4.2 28.4 1.0 CD2 A:HIS86 4.2 28.7 1.0 CG A:HIS84 4.3 28.3 1.0 CG A:HIS153 4.3 33.3 1.0 OD1 A:ASP175 4.4 26.8 1.0 ND1 A:HIS153 4.4 30.6 1.0 ND1 A:HIS84 4.5 30.5 1.0 OD1 A:ASP88 4.5 34.9 1.0 NE2 A:HIS381 4.7 38.9 1.0 CE1 A:HIS381 4.7 37.5 1.0 OD2 A:ASP88 4.9 30.0 1.0 OG A:SER154 4.9 34.2 1.0

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


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:32.8 occ:1.00 NE2 A:HIS403 2.1 24.7 1.0 NE2 A:HIS89 2.1 25.7 1.0 OD2 A:ASP175 2.2 24.5 1.0 OD2 A:ASP88 2.3 30.0 1.0 CE1 A:HIS403 2.9 35.4 1.0 CD2 A:HIS89 3.0 28.4 1.0 CG A:ASP175 3.0 32.2 1.0 CD2 A:HIS403 3.1 28.6 1.0 CE1 A:HIS89 3.1 26.1 1.0 OD1 A:ASP175 3.2 26.8 1.0 CG A:ASP88 3.2 34.6 1.0 ZN A:ZN601 3.3 36.6 1.0 OD1 A:ASP88 3.5 34.9 1.0 O A:HOH865 3.6 44.5 1.0 ND2 A:ASN33 3.8 28.9 1.0 NE2 A:HIS84 4.0 25.4 1.0 ND1 A:HIS403 4.1 28.8 1.0 CG A:HIS403 4.2 27.1 1.0 CG A:HIS89 4.2 27.7 1.0 ND1 A:HIS89 4.2 26.8 1.0 CE1 A:HIS84 4.2 28.5 1.0 CB A:ASP175 4.5 31.9 1.0 CE1 A:HIS381 4.5 37.5 1.0 CB A:ASP88 4.6 27.8 1.0 CG A:ASN33 4.9 34.4 1.0 ND1 A:HIS86 4.9 25.5 1.0 NE2 A:HIS381 4.9 38.9 1.0

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


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:37.4 occ:1.00 NE2 B:HIS403 2.0 28.2 1.0 NE2 B:HIS89 2.1 30.2 1.0 OD2 B:ASP175 2.1 29.3 1.0 OD2 B:ASP88 2.3 39.1 1.0 CE1 B:HIS403 2.9 38.5 1.0 CD2 B:HIS89 2.9 30.0 1.0 CG B:ASP175 3.0 32.3 1.0 CD2 B:HIS403 3.1 36.4 1.0 OD1 B:ASP175 3.1 36.1 1.0 O B:HOH854 3.2 37.9 1.0 CE1 B:HIS89 3.2 30.1 1.0 CG B:ASP88 3.2 39.8 1.0 ZN B:ZN602 3.3 34.2 1.0 OD1 B:ASP88 3.5 37.0 1.0 ND2 B:ASN33 3.9 29.9 1.0 NE2 B:HIS84 4.1 29.2 1.0 ND1 B:HIS403 4.1 30.1 1.0 CG B:HIS89 4.1 30.5 1.0 CG B:HIS403 4.2 28.6 1.0 ND1 B:HIS89 4.2 30.8 1.0 CE1 B:HIS84 4.2 29.8 1.0 CB B:ASP175 4.4 34.4 1.0 CE1 B:HIS381 4.4 32.7 1.0 CB B:ASP88 4.6 33.3 1.0 CG B:ASN33 4.8 40.6 1.0 NE2 B:HIS381 4.9 33.5 1.0 NE2 B:HIS153 5.0 27.7 1.0

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


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 Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:34.2 occ:1.00 NE2 B:HIS153 2.2 27.7 1.0 ND1 B:HIS86 2.3 30.4 1.0 NE2 B:HIS84 2.3 29.2 1.0 OD2 B:ASP175 2.5 29.3 1.0 CD2 B:HIS153 3.1 28.3 1.0 CD2 B:HIS84 3.1 29.4 1.0 CE1 B:HIS86 3.1 27.5 1.0 CE1 B:HIS153 3.2 39.7 1.0 CG B:HIS86 3.3 28.2 1.0 ZN B:ZN601 3.3 37.4 1.0 CG B:ASP175 3.4 32.3 1.0 CE1 B:HIS84 3.4 29.8 1.0 O B:HOH854 3.5 37.9 1.0 CB B:HIS86 3.7 31.4 1.0 CB B:ASP175 3.7 34.4 1.0 NE2 B:HIS89 4.2 30.2 1.0 CD2 B:HIS89 4.2 30.0 1.0 CG B:HIS153 4.3 31.4 1.0 ND1 B:HIS153 4.3 31.7 1.0 NE2 B:HIS86 4.3 34.6 1.0 CG B:HIS84 4.3 30.2 1.0 OD1 B:ASP175 4.4 36.1 1.0 OD1 B:ASP88 4.4 37.0 1.0 CD2 B:HIS86 4.4 31.6 1.0 ND1 B:HIS84 4.4 30.4 1.0 CE1 B:HIS381 4.6 32.7 1.0 NE2 B:HIS381 4.7 33.5 1.0 O2P B:U5P604 4.8 0.9 1.0 OD2 B:ASP88 4.9 39.1 1.0 OG B:SER154 5.0 36.7 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