Zinc in PDB 5a0t: Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family

The structure of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family, PDB code: 5a0t was solved by X.Y.Pei, P.Bralley, G.H.Jones, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.340 / 2.28
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	186.187, 186.187, 113.382, 90.00, 90.00, 90.00
R / Rfree (%)	14.46 / 17.69

The binding sites of Zinc atom in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family (pdb code 5a0t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family, PDB code: 5a0t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1457 b:49.8 occ:0.66 OD2 A:ASP173 2.1 39.1 0.9 OP2 E:G1 2.2 56.9 0.7 O A:HOH2069 2.2 38.6 0.5 OD2 A:ASP88 2.3 41.6 0.7 NE2 A:HIS399 2.4 45.9 0.7 NE2 A:HIS89 2.5 42.5 0.9 CD2 A:HIS89 3.0 37.9 1.0 CG A:ASP173 3.2 38.6 0.7 CE1 A:HIS399 3.3 40.7 1.0 CG A:ASP88 3.3 38.3 0.8 ZN A:ZN1458 3.3 62.0 0.9 CD2 A:HIS399 3.4 44.8 0.8 P E:G1 3.4 57.9 0.7 OD1 A:ASP88 3.5 40.9 0.7 OD1 A:ASP173 3.6 37.9 0.6 CE1 A:HIS89 3.7 34.8 0.6 ND2 A:ASN33 3.9 42.5 1.0 OP1 E:G1 3.9 49.8 1.0 O5' E:G1 4.0 65.0 0.6 NE2 A:HIS84 4.2 36.4 0.7 CG A:HIS89 4.3 37.1 0.7 ND1 A:HIS399 4.4 44.2 0.6 CE1 A:HIS377 4.4 39.8 0.8 CG A:HIS399 4.5 43.4 0.9 CB A:ASP173 4.5 41.1 1.0 CE1 A:HIS84 4.6 37.9 1.0 ND1 A:HIS89 4.6 35.9 0.6 CB A:ASP88 4.6 39.6 0.9 O3' E:C0 4.6 86.5 0.5 O2' E:C0 4.7 63.0 0.6 CG A:ASN33 4.9 39.7 0.5

Zinc binding site 2 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1458 b:62.0 occ:0.93 O A:HOH2069 2.2 38.6 0.5 NE2 A:HIS151 2.4 38.4 0.9 ND1 A:HIS86 2.5 38.2 0.8 NE2 A:HIS84 2.6 36.4 0.7 OD2 A:ASP173 2.7 39.1 0.9 OP1 E:G1 2.8 49.8 1.0 CD2 A:HIS84 3.2 33.6 1.0 ZN A:ZN1457 3.3 49.8 0.7 CE1 A:HIS151 3.3 37.9 0.9 CE1 A:HIS86 3.3 37.1 1.0 CD2 A:HIS151 3.4 38.6 0.9 P E:G1 3.5 57.9 0.7 CG A:HIS86 3.5 41.2 0.8 O5' E:G1 3.5 65.0 0.6 CG A:ASP173 3.5 38.6 0.7 OP2 E:G1 3.6 56.9 0.7 CE1 A:HIS84 3.7 37.9 1.0 CB A:ASP173 3.7 41.1 1.0 CB A:HIS86 3.8 39.7 1.0 C5' E:G1 4.1 59.2 1.0 CD2 A:HIS89 4.4 37.9 1.0 NE2 A:HIS89 4.4 42.5 0.9 CE1 A:HIS377 4.5 39.8 0.8 CG A:HIS84 4.5 35.0 0.8 ND1 A:HIS151 4.5 38.2 1.0 NE2 A:HIS86 4.5 33.9 0.6 OD1 A:ASP88 4.6 40.9 0.7 CG A:HIS151 4.6 34.9 0.7 CD2 A:HIS86 4.6 37.4 0.6 ND1 A:HIS84 4.6 36.0 0.7 O A:HOH2130 4.7 53.7 0.9 OD1 A:ASP173 4.7 37.9 0.6 NE2 A:HIS377 4.8 38.1 0.8 OG A:SER152 4.9 39.7 0.8 OD2 A:ASP88 4.9 41.6 0.7

Zinc binding site 3 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1454 b:53.5 occ:0.70 OP2 F:G1 2.2 62.0 1.0 O B:HOH2056 2.2 43.5 0.5 OD2 B:ASP173 2.3 42.6 0.7 OD2 B:ASP88 2.3 48.2 0.6 NE2 B:HIS399 2.4 50.8 0.7 NE2 B:HIS89 2.4 49.6 0.9 CD2 B:HIS89 3.0 40.2 1.0 CG B:ASP173 3.2 41.8 0.9 CG B:ASP88 3.3 45.1 0.8 CD2 B:HIS399 3.3 48.8 1.0 CE1 B:HIS399 3.3 42.2 1.0 ZN B:ZN1455 3.4 59.3 0.9 OD1 B:ASP173 3.4 43.1 0.7 OD1 B:ASP88 3.5 54.0 0.8 P F:G1 3.6 64.3 0.6 CE1 B:HIS89 3.6 45.0 0.7 ND2 B:ASN33 3.9 45.7 1.0 CG B:HIS89 4.3 45.0 0.6 NE2 B:HIS84 4.3 42.0 0.8 OP1 F:G1 4.4 56.6 1.0 CE1 B:HIS377 4.4 44.3 0.8 O5' F:G1 4.4 77.1 0.8 CG B:HIS399 4.4 48.7 0.8 ND1 B:HIS399 4.4 46.3 0.6 O3' F:C0 4.5 84.5 0.4 CB B:ASP173 4.5 38.3 0.9 ND1 B:HIS89 4.5 41.8 0.8 CE1 B:HIS84 4.6 43.3 0.9 CB B:ASP88 4.6 43.9 0.9 O2' F:C0 4.6 80.4 0.5 NE2 B:HIS377 4.8 40.3 0.6 CG B:ASN33 4.8 49.8 0.7

Zinc binding site 4 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1455 b:59.3 occ:0.90 O B:HOH2056 2.0 43.5 0.5 ND1 B:HIS86 2.3 52.0 1.0 NE2 B:HIS151 2.4 46.9 1.0 OD2 B:ASP173 2.5 42.6 0.7 NE2 B:HIS84 2.6 42.0 0.8 OP1 F:G1 3.0 56.6 1.0 OP2 F:G1 3.2 62.0 1.0 CE1 B:HIS86 3.2 44.9 0.8 P F:G1 3.3 64.3 0.6 CD2 B:HIS84 3.3 37.2 1.0 CE1 B:HIS151 3.4 41.7 1.0 ZN B:ZN1454 3.4 53.5 0.7 CG B:HIS86 3.4 47.5 0.7 CD2 B:HIS151 3.4 47.0 0.8 CG B:ASP173 3.4 41.8 0.9 O5' F:G1 3.5 77.1 0.8 CE1 B:HIS84 3.6 43.3 0.9 CB B:ASP173 3.7 38.3 0.9 CB B:HIS86 3.8 48.0 1.0 NE2 B:HIS86 4.4 53.9 0.7 C5' F:G1 4.4 74.7 0.9 CE1 B:HIS377 4.4 44.3 0.8 NE2 B:HIS89 4.4 49.6 0.9 CD2 B:HIS89 4.4 40.2 1.0 CD2 B:HIS86 4.5 44.7 1.0 ND1 B:HIS151 4.5 45.2 0.8 NE2 B:HIS377 4.5 40.3 0.6 CG B:HIS84 4.5 37.2 0.7 OD1 B:ASP173 4.5 43.1 0.7 O B:HOH2120 4.6 49.3 0.8 CG B:HIS151 4.6 42.8 0.9 OD1 B:ASP88 4.6 54.0 0.8 ND1 B:HIS84 4.6 37.5 0.7 OG B:SER152 4.9 42.3 0.8 O3' F:C0 4.9 84.5 0.4 OD2 B:ASP88 5.0 48.2 0.6

X.Y.Pei, P.Bralley, G.H.Jones, B.F.Luisi. Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J Nucleic Acids Res. V. 43 8066 2015.
ISSN: ISSN 0305-1048
PubMed: 26253740
DOI: 10.1093/NAR/GKV732