Zinc in PDB 3bk1: Crystal Structure Analysis of Rnase J

The structure of Crystal Structure Analysis of Rnase J, PDB code: 3bk1 was solved by I.L.De La Sierra-Gallay, L.Zig, H.Putzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.75 / 2.33
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.830, 117.620, 230.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22

The binding sites of Zinc atom in the Crystal Structure Analysis of Rnase J (pdb code 3bk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure Analysis of Rnase J, PDB code: 3bk1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure Analysis of Rnase J


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Rnase J within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn948 b:39.2 occ:1.00 NE2 A:HIS150 2.3 21.4 1.0 ND1 A:HIS77 2.3 22.7 1.0 NE2 A:HIS75 2.5 21.3 1.0 OD2 A:ASP172 2.6 23.9 1.0 ZN A:ZN949 3.0 47.9 1.0 O A:HOH953 3.0 31.8 1.0 CD2 A:HIS150 3.2 20.7 1.0 CE1 A:HIS77 3.2 21.8 1.0 CD2 A:HIS75 3.3 19.1 1.0 CE1 A:HIS150 3.4 20.2 1.0 CG A:ASP172 3.4 23.9 1.0 CG A:HIS77 3.4 21.3 1.0 CE1 A:HIS75 3.5 21.5 1.0 CB A:ASP172 3.7 18.6 1.0 CB A:HIS77 3.8 19.8 1.0 CD2 A:HIS80 4.0 22.4 1.0 NE2 A:HIS80 4.0 23.1 1.0 NE2 A:HIS77 4.4 23.5 1.0 OD1 A:ASP79 4.4 29.1 1.0 CG A:HIS150 4.4 19.3 1.0 OD1 A:ASP172 4.4 25.9 1.0 ND1 A:HIS150 4.4 20.1 1.0 CD2 A:HIS77 4.5 21.1 1.0 CG A:HIS75 4.5 20.7 1.0 ND1 A:HIS75 4.6 21.6 1.0 CE1 A:HIS376 4.6 17.8 1.0 OG A:SER151 4.7 24.7 1.0 O A:HOH952 4.7 29.2 1.0 NE2 A:HIS376 4.8 21.6 1.0 OD2 A:ASP79 4.9 30.0 1.0 NE2 A:HIS398 5.0 24.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure Analysis of Rnase J


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Rnase J within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn949 b:47.9 occ:1.00 OD2 A:ASP172 2.2 23.9 1.0 NE2 A:HIS398 2.3 24.2 1.0 NE2 A:HIS80 2.5 23.1 1.0 OD2 A:ASP79 2.6 30.0 1.0 O A:HOH953 2.7 31.8 1.0 ZN A:ZN948 3.0 39.2 1.0 CD2 A:HIS80 3.1 22.4 1.0 CE1 A:HIS398 3.2 24.0 1.0 CG A:ASP172 3.3 23.9 1.0 CG A:ASP79 3.4 28.3 1.0 CD2 A:HIS398 3.4 25.3 1.0 OD1 A:ASP79 3.5 29.1 1.0 CE1 A:HIS80 3.7 24.4 1.0 OD1 A:ASP172 3.7 25.9 1.0 ND2 A:ASN24 3.9 17.7 1.0 NE2 A:HIS75 4.2 21.3 1.0 CE1 A:HIS376 4.3 17.8 1.0 ND1 A:HIS398 4.4 26.1 1.0 CG A:HIS80 4.4 21.7 1.0 CG A:HIS398 4.5 22.2 1.0 CB A:ASP172 4.5 18.6 1.0 CE1 A:HIS75 4.6 21.5 1.0 ND1 A:HIS80 4.7 23.0 1.0 NE2 A:HIS376 4.7 21.6 1.0 CB A:ASP79 4.8 25.1 1.0 ND1 A:HIS77 4.8 22.7 1.0 NE2 A:HIS150 4.8 21.4 1.0 CG A:ASN24 5.0 22.9 1.0

I.L.De La Sierra-Gallay, L.Zig, A.Jamalli, H.Putzer. Structural Insights Into the Dual Activity of Rnase J Nat.Struct.Mol.Biol. V. 15 206 2008.
ISSN: ISSN 1545-9993
PubMed: 18204464
DOI: 10.1038/NSMB.1376