Zinc in PDB 3bk2: Crystal Structure Analysis of the Rnase J/Ump Complex

The structure of Crystal Structure Analysis of the Rnase J/Ump Complex, PDB code: 3bk2 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)	50.00 / 2.10
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.080, 118.000, 228.320, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 23.6

The binding sites of Zinc atom in the Crystal Structure Analysis of the Rnase J/Ump Complex (pdb code 3bk2). 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 the Rnase J/Ump Complex, PDB code: 3bk2:
Jump to Zinc binding site number: 1; 2;

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


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 the Rnase J/Ump Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn948 b:37.5 occ:1.00 ND1 A:HIS77 2.2 30.1 1.0 NE2 A:HIS150 2.2 26.0 1.0 NE2 A:HIS75 2.4 26.5 1.0 OD2 A:ASP172 2.4 27.6 1.0 CD2 A:HIS150 3.0 27.1 1.0 CE1 A:HIS77 3.1 33.3 1.0 ZN A:ZN949 3.1 37.6 1.0 CD2 A:HIS75 3.1 27.5 1.0 CG A:ASP172 3.3 28.8 1.0 CG A:HIS77 3.3 31.1 1.0 CE1 A:HIS150 3.3 28.9 1.0 CE1 A:HIS75 3.4 26.1 1.0 CB A:ASP172 3.6 25.5 1.0 CB A:HIS77 3.7 31.8 1.0 O A:HOH955 3.8 40.2 1.0 CD2 A:HIS80 3.9 28.7 1.0 NE2 A:HIS80 3.9 27.8 1.0 CG A:HIS150 4.2 27.6 1.0 NE2 A:HIS77 4.3 33.7 1.0 OD1 A:ASP172 4.3 28.1 1.0 ND1 A:HIS150 4.4 27.7 1.0 CG A:HIS75 4.4 26.5 1.0 CD2 A:HIS77 4.4 30.7 1.0 OD1 A:ASP79 4.5 34.2 1.0 ND1 A:HIS75 4.5 27.3 1.0 O A:HOH957 4.6 35.1 1.0 CE1 A:HIS376 4.7 28.6 1.0 OD2 A:ASP79 4.7 34.6 1.0 OG A:SER151 4.7 33.7 1.0 NE2 A:HIS376 5.0 28.2 1.0 CE1 A:HIS80 5.0 29.3 1.0 CG A:HIS80 5.0 28.9 1.0

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


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 the Rnase J/Ump Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn949 b:37.6 occ:1.00 OD2 A:ASP172 2.2 27.6 1.0 NE2 A:HIS80 2.2 27.8 1.0 NE2 A:HIS398 2.3 31.1 1.0 OD2 A:ASP79 2.4 34.6 1.0 CD2 A:HIS80 3.0 28.7 1.0 CG A:ASP172 3.1 28.8 1.0 CE1 A:HIS398 3.1 31.2 1.0 ZN A:ZN948 3.1 37.5 1.0 OD1 A:ASP172 3.3 28.1 1.0 CD2 A:HIS398 3.3 31.2 1.0 CG A:ASP79 3.3 35.6 1.0 CE1 A:HIS80 3.4 29.3 1.0 O A:HOH955 3.6 40.2 1.0 OD1 A:ASP79 3.6 34.2 1.0 ND2 A:ASN24 3.7 29.4 1.0 NE2 A:HIS75 4.1 26.5 1.0 CG A:HIS80 4.2 28.9 1.0 ND1 A:HIS398 4.3 30.2 1.0 ND1 A:HIS80 4.4 26.6 1.0 CG A:HIS398 4.4 27.1 1.0 CE1 A:HIS75 4.4 26.1 1.0 CB A:ASP172 4.5 25.5 1.0 CE1 A:HIS376 4.5 28.6 1.0 CB A:ASP79 4.6 30.2 1.0 CG A:ASN24 4.8 29.9 1.0 ND1 A:HIS77 4.8 30.1 1.0 NE2 A:HIS150 4.8 26.0 1.0 NE2 A:HIS376 4.9 28.2 1.0 O A:ASP79 4.9 29.2 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