Zinc in PDB 5a0v: 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: 5a0v 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)	32.719 / 2.80
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.130, 184.130, 112.680, 90.00, 90.00, 90.00
R / Rfree (%)	15.42 / 20.84

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 5a0v). 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: 5a0v:
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:Zn1456 b:0.9 occ:1.00 OD2 A:ASP173 2.4 33.4 0.5 OD2 A:ASP88 2.4 41.1 0.0 NE2 A:HIS399 2.5 42.1 0.5 OP2 E:G1 2.7 79.8 0.0 NE2 A:HIS89 2.9 38.8 0.7 CD2 A:HIS89 2.9 42.6 1.0 CG A:ASP88 3.3 39.8 0.9 OD1 A:ASP88 3.4 39.8 0.6 CE1 A:HIS399 3.4 49.1 1.0 CD2 A:HIS399 3.4 35.5 0.8 CG A:ASP173 3.5 37.8 1.0 ZN A:ZN1457 3.6 85.5 1.0 P E:G1 3.6 84.9 1.0 OP1 E:G1 3.6 90.0 1.0 ND2 A:ASN33 3.9 39.3 1.0 OD1 A:ASP173 4.0 36.7 0.4 CE1 A:HIS89 4.1 39.0 0.6 O2' E:C0 4.2 44.9 0.3 CG A:HIS89 4.2 45.1 1.0 NE2 A:HIS84 4.4 31.3 0.4 ND1 A:HIS399 4.5 41.8 0.7 CG A:HIS399 4.6 36.9 0.8 CB A:ASP88 4.7 43.1 0.5 NE2 A:HIS377 4.7 31.1 0.7 CE1 A:HIS84 4.7 32.4 1.0 O3' E:C0 4.7 66.7 0.4 O5' E:G1 4.7 59.8 0.2 CB A:ASP173 4.8 33.4 1.0 ND1 A:HIS89 4.8 44.7 0.4 O A:ASP88 4.8 43.2 0.8 CG A:ASN33 4.9 40.0 0.6

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:Zn1457 b:85.5 occ:1.00 OP1 E:G1 2.5 90.0 1.0 NE2 A:HIS84 2.6 31.3 0.4 ND1 A:HIS86 2.7 31.9 0.6 NE2 A:HIS151 2.8 29.6 0.8 OD2 A:ASP173 3.0 33.4 0.5 CD2 A:HIS84 3.3 30.6 1.0 CE1 A:HIS84 3.5 32.4 1.0 CD2 A:HIS151 3.5 29.3 1.0 CE1 A:HIS86 3.5 32.5 1.0 CG A:HIS86 3.6 36.2 0.9 ZN A:ZN1456 3.6 0.9 1.0 P E:G1 3.8 84.9 1.0 CG A:ASP173 3.8 37.8 1.0 CB A:HIS86 3.8 42.6 1.0 CB A:ASP173 3.8 33.4 1.0 CE1 A:HIS151 3.8 43.4 1.0 OP2 E:G1 4.3 79.8 0.0 CG A:HIS84 4.4 34.5 0.6 ND1 A:HIS84 4.4 39.4 1.0 C5' E:G1 4.4 61.5 1.0 OG A:SER152 4.5 34.1 0.7 O5' E:G1 4.6 59.8 0.2 NE2 A:HIS377 4.6 31.1 0.7 NE2 A:HIS86 4.6 31.8 0.6 CD2 A:HIS86 4.7 34.4 0.3 O3' E:C0 4.7 66.7 0.4 CG A:HIS151 4.8 29.0 1.0 CD2 A:HIS89 4.8 42.6 1.0 OD1 A:ASP88 4.8 39.8 0.6 ND1 A:HIS151 4.9 35.3 0.3 NE2 A:HIS89 4.9 38.8 0.7 CE1 A:HIS377 4.9 30.7 0.8 OD1 A:ASP173 5.0 36.7 0.4

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:Zn1453 b:83.5 occ:1.00 OP2 F:G1 2.2 0.4 0.5 ND1 B:HIS86 2.4 43.9 1.0 NE2 B:HIS84 2.4 46.8 0.3 OD2 B:ASP173 2.5 43.0 0.2 NE2 B:HIS151 2.5 49.8 1.0 P F:G1 2.9 79.7 0.5 OP1 F:G1 3.0 72.7 0.5 CD2 B:HIS84 3.1 40.3 1.0 CG B:ASP173 3.2 36.8 1.0 CE1 B:HIS86 3.3 40.3 0.7 CD2 B:HIS151 3.3 46.5 0.9 ZN B:ZN1454 3.4 0.1 1.0 CB B:ASP173 3.4 42.0 0.6 CG B:HIS86 3.5 41.4 0.2 CE1 B:HIS84 3.5 39.4 1.0 CE1 B:HIS151 3.6 42.5 1.0 O5' F:G1 3.8 54.1 0.5 CB B:HIS86 3.8 43.3 1.0 O3' F:C0 4.1 62.6 1.0 CG B:HIS84 4.2 47.6 1.0 OD1 B:ASP173 4.3 38.8 0.7 ND1 B:HIS84 4.4 47.2 0.6 NE2 B:HIS86 4.4 41.4 0.8 CD2 B:HIS89 4.4 51.8 1.0 CG B:HIS151 4.5 39.9 1.0 CD2 B:HIS86 4.6 45.3 1.0 NE2 B:HIS89 4.6 43.9 0.6 CE1 B:HIS377 4.6 35.3 0.8 ND1 B:HIS151 4.6 43.0 0.6 NE2 B:HIS377 4.7 35.4 0.7 OD1 B:ASP88 4.8 58.0 0.8 C5' F:G1 4.9 53.1 0.5 OG B:SER152 5.0 38.4 0.7 CA B:ASP173 5.0 42.2 1.0

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:Zn1454 b:0.1 occ:1.00 OD2 B:ASP88 2.3 46.8 0.2 OP2 F:G1 2.4 0.4 0.5 OD2 B:ASP173 2.4 43.0 0.2 NE2 B:HIS399 2.6 44.1 0.3 NE2 B:HIS89 2.6 43.9 0.6 CD2 B:HIS89 3.0 51.8 1.0 CG B:ASP173 3.2 36.8 1.0 CG B:ASP88 3.3 47.0 0.6 ZN B:ZN1453 3.4 83.5 1.0 OD1 B:ASP173 3.4 38.8 0.7 CE1 B:HIS399 3.5 40.3 1.0 CD2 B:HIS399 3.5 45.4 1.0 OD1 B:ASP88 3.6 58.0 0.8 P F:G1 3.8 79.7 0.5 ND2 B:ASN33 3.8 43.2 1.0 CE1 B:HIS89 3.9 45.4 0.6 O3' F:C0 4.0 62.6 1.0 NE2 B:HIS84 4.1 46.8 0.3 CG B:HIS89 4.3 51.7 1.0 O2' B:C5P1458 4.4 76.1 0.5 CE1 B:HIS377 4.4 35.3 0.8 ND1 B:HIS399 4.5 44.6 0.5 CE1 B:HIS84 4.5 39.4 1.0 CB B:ASP173 4.5 42.0 0.6 CG B:HIS399 4.6 44.6 0.7 CB B:ASP88 4.6 46.6 0.7 O5' F:G1 4.6 54.1 0.5 ND1 B:HIS89 4.7 51.4 0.7 OP1 F:G1 4.8 72.7 0.5 CG B:ASN33 4.9 43.4 0.8 NE2 B:HIS377 4.9 35.4 0.7

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