Zinc in PDB 3zq4: Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1

The structure of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1, PDB code: 3zq4 was solved by J.A.Newman, L.Hewitt, C.Rodrigues, A.Solovyova, C.R.Harwood, R.J.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.76 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.823, 209.430, 74.106, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.8

The structure of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 (pdb code 3zq4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1, PDB code: 3zq4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1556 b:41.2 occ:1.00 OD2 A:ASP164 2.0 36.8 1.0 NE2 A:HIS79 2.1 32.9 1.0 NE2 A:HIS390 2.3 31.7 1.0 OD2 A:ASP78 2.4 53.4 1.0 CD2 A:HIS79 2.8 39.7 1.0 ZN A:ZN1557 3.0 34.2 1.0 CG A:ASP78 3.1 45.3 1.0 CG A:ASP164 3.2 43.0 1.0 OD1 A:ASP78 3.2 51.7 1.0 CE1 A:HIS390 3.2 40.9 1.0 CE1 A:HIS79 3.2 47.3 1.0 CD2 A:HIS390 3.2 43.3 1.0 OD1 A:ASP164 3.7 46.4 1.0 CE1 A:HIS74 3.9 35.7 1.0 NE2 A:HIS74 3.9 44.4 1.0 ND2 A:ASN23 3.9 52.6 1.0 CG A:HIS79 4.0 44.5 1.0 CE1 A:HIS368 4.1 47.2 1.0 ND1 A:HIS79 4.2 46.5 1.0 ND1 A:HIS390 4.3 38.3 1.0 CG A:HIS390 4.4 44.7 1.0 CB A:ASP164 4.4 44.5 1.0 NE2 A:HIS368 4.6 46.1 1.0 CB A:ASP78 4.6 35.5 1.0 NE2 A:HIS142 4.7 31.9 1.0 ND1 A:HIS76 4.8 48.5 1.0 O A:ASP78 4.9 44.8 1.0 CG A:ASN23 5.0 46.9 1.0

Zinc binding site 2 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1557 b:34.2 occ:1.00 NE2 A:HIS74 1.8 44.4 1.0 NE2 A:HIS142 2.1 31.9 1.0 ND1 A:HIS76 2.2 48.5 1.0 OD2 A:ASP164 2.7 36.8 1.0 CE1 A:HIS74 2.7 35.7 1.0 CD2 A:HIS74 2.9 42.6 1.0 ZN A:ZN1556 3.0 41.2 1.0 CE1 A:HIS76 3.0 51.0 1.0 CE1 A:HIS142 3.1 41.4 1.0 CD2 A:HIS142 3.1 41.8 1.0 CG A:HIS76 3.2 45.7 1.0 CG A:ASP164 3.6 43.0 1.0 CB A:HIS76 3.6 46.6 1.0 NE2 A:HIS79 3.7 32.9 1.0 CD2 A:HIS79 3.8 39.7 1.0 ND1 A:HIS74 3.8 40.2 1.0 CB A:ASP164 3.9 44.5 1.0 CG A:HIS74 4.0 42.7 1.0 OD1 A:ASP78 4.1 51.7 1.0 NE2 A:HIS76 4.2 48.7 1.0 ND1 A:HIS142 4.2 38.0 1.0 CG A:HIS142 4.3 41.6 1.0 CD2 A:HIS76 4.3 49.0 1.0 CE1 A:HIS368 4.4 47.2 1.0 OD1 A:ASP164 4.7 46.4 1.0 NE2 A:HIS368 4.7 46.1 1.0 CE1 A:HIS79 4.7 47.3 1.0 OD2 A:ASP78 4.8 53.4 1.0 CG A:HIS79 4.8 44.5 1.0 CG A:ASP78 4.9 45.3 1.0 NE2 A:HIS390 5.0 31.7 1.0

Zinc binding site 3 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1556 b:46.1 occ:1.00 NE2 C:HIS79 2.0 37.3 1.0 OD2 C:ASP164 2.1 36.1 1.0 NE2 C:HIS390 2.3 36.1 1.0 OD2 C:ASP78 2.3 51.2 1.0 CD2 C:HIS79 2.8 45.0 1.0 ZN C:ZN1557 3.0 39.6 1.0 CG C:ASP78 3.1 50.2 1.0 OD1 C:ASP78 3.1 51.5 1.0 CE1 C:HIS79 3.2 49.2 1.0 CG C:ASP164 3.2 45.2 1.0 CE1 C:HIS390 3.3 45.5 1.0 CD2 C:HIS390 3.3 45.9 1.0 OD1 C:ASP164 3.7 46.9 1.0 CE1 C:HIS74 3.8 40.3 1.0 NE2 C:HIS74 3.9 45.5 1.0 ND2 C:ASN23 3.9 57.4 1.0 CG C:HIS79 4.0 52.0 1.0 ND1 C:HIS79 4.2 54.0 1.0 CE1 C:HIS368 4.2 50.8 1.0 ND1 C:HIS390 4.4 41.3 1.0 CG C:HIS390 4.4 46.7 1.0 CB C:ASP164 4.5 42.4 1.0 CB C:ASP78 4.6 40.9 1.0 NE2 C:HIS368 4.6 49.9 1.0 NE2 C:HIS142 4.7 41.4 1.0 ND1 C:HIS76 4.7 43.4 1.0 O C:ASP78 4.9 46.5 1.0 CB C:HIS76 5.0 48.4 1.0

Zinc binding site 4 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1557 b:39.6 occ:1.00 ND1 C:HIS76 2.1 43.4 1.0 CE1 C:HIS74 2.1 40.3 1.0 NE2 C:HIS142 2.2 41.4 1.0 OD2 C:ASP164 2.8 36.1 1.0 CE1 C:HIS76 2.9 45.0 1.0 ZN C:ZN1556 3.0 46.1 1.0 ND1 C:HIS74 3.0 43.3 1.0 NE2 C:HIS74 3.1 45.5 1.0 CG C:HIS76 3.1 47.5 1.0 CE1 C:HIS142 3.1 44.3 1.0 CD2 C:HIS142 3.2 44.4 1.0 CB C:HIS76 3.5 48.4 1.0 CG C:ASP164 3.7 45.2 1.0 NE2 C:HIS79 3.9 37.3 1.0 CD2 C:HIS79 3.9 45.0 1.0 OD1 C:ASP78 4.0 51.5 1.0 CB C:ASP164 4.0 42.4 1.0 NE2 C:HIS76 4.1 50.5 1.0 CD2 C:HIS76 4.2 53.6 1.0 CG C:HIS74 4.2 49.8 1.0 CD2 C:HIS74 4.2 45.2 1.0 ND1 C:HIS142 4.3 43.8 1.0 CG C:HIS142 4.4 45.9 1.0 CE1 C:HIS368 4.5 50.8 1.0 NE2 C:HIS368 4.7 49.9 1.0 OD2 C:ASP78 4.7 51.2 1.0 CG C:ASP78 4.8 50.2 1.0 OD1 C:ASP164 4.8 46.9 1.0 CE1 C:HIS79 4.9 49.2 1.0 CG C:HIS79 4.9 52.0 1.0 OG C:SER143 4.9 43.7 1.0 CA C:HIS76 5.0 46.2 1.0

Zinc binding site 5 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1557 b:42.9 occ:1.00 NE2 D:HIS79 2.1 38.5 1.0 OD2 D:ASP164 2.1 36.2 1.0 NE2 D:HIS390 2.3 35.2 1.0 OD2 D:ASP78 2.3 55.3 1.0 CD2 D:HIS79 2.8 48.8 1.0 ZN D:ZN1558 3.0 40.4 1.0 CG D:ASP78 3.1 50.6 1.0 OD1 D:ASP78 3.1 53.5 1.0 CG D:ASP164 3.2 46.6 1.0 CE1 D:HIS79 3.3 51.4 1.0 CE1 D:HIS390 3.3 42.6 1.0 CD2 D:HIS390 3.3 48.3 1.0 OD1 D:ASP164 3.8 48.9 1.0 CE1 D:HIS74 3.8 37.8 1.0 ND2 D:ASN23 3.9 54.6 1.0 NE2 D:HIS74 3.9 45.2 1.0 CG D:HIS79 4.0 48.4 1.0 CE1 D:HIS368 4.2 48.3 1.0 ND1 D:HIS79 4.2 49.2 1.0 ND1 D:HIS390 4.4 42.1 1.0 CG D:HIS390 4.4 46.1 1.0 CB D:ASP164 4.5 43.4 1.0 CB D:ASP78 4.6 35.9 1.0 NE2 D:HIS368 4.6 51.4 1.0 NE2 D:HIS142 4.7 37.0 1.0 ND1 D:HIS76 4.8 48.4 1.0 O D:ASP78 4.9 45.4 1.0 CB D:HIS76 5.0 50.0 1.0

Zinc binding site 6 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1558 b:40.4 occ:1.00 CE1 D:HIS74 1.9 37.8 1.0 ND1 D:HIS76 2.1 48.4 1.0 NE2 D:HIS142 2.2 37.0 1.0 OD2 D:ASP164 2.7 36.2 1.0 ND1 D:HIS74 2.8 39.7 1.0 NE2 D:HIS74 2.9 45.2 1.0 ZN D:ZN1557 3.0 42.9 1.0 CE1 D:HIS76 3.0 49.2 1.0 CD2 D:HIS142 3.1 48.1 1.0 CE1 D:HIS142 3.1 43.7 1.0 CG D:HIS76 3.1 49.8 1.0 CB D:HIS76 3.5 50.0 1.0 CG D:ASP164 3.6 46.6 1.0 NE2 D:HIS79 3.8 38.5 1.0 CD2 D:HIS79 3.8 48.8 1.0 CB D:ASP164 3.9 43.4 1.0 CD2 D:HIS74 4.0 44.9 1.0 CG D:HIS74 4.0 47.9 1.0 OD1 D:ASP78 4.0 53.5 1.0 NE2 D:HIS76 4.1 54.9 1.0 CD2 D:HIS76 4.2 53.2 1.0 ND1 D:HIS142 4.3 44.8 1.0 CG D:HIS142 4.3 49.2 1.0 CE1 D:HIS368 4.5 48.3 1.0 OD1 D:ASP164 4.7 48.9 1.0 CE1 D:HIS79 4.7 51.4 1.0 OD2 D:ASP78 4.8 55.3 1.0 NE2 D:HIS368 4.8 51.4 1.0 CG D:HIS79 4.8 48.4 1.0 CG D:ASP78 4.8 50.6 1.0 CA D:HIS76 5.0 48.3 1.0

Zinc binding site 7 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1556 b:39.5 occ:1.00 OD2 E:ASP164 2.0 39.3 1.0 NE2 E:HIS79 2.0 39.6 1.0 NE2 E:HIS390 2.1 30.4 1.0 OD2 E:ASP78 2.4 50.9 1.0 CD2 E:HIS79 2.8 42.1 1.0 ZN E:ZN1557 3.0 36.9 1.0 CD2 E:HIS390 3.1 44.7 1.0 CE1 E:HIS390 3.1 45.7 1.0 CG E:ASP164 3.2 46.6 1.0 CE1 E:HIS79 3.2 48.0 1.0 CG E:ASP78 3.2 48.4 1.0 OD1 E:ASP78 3.3 50.7 1.0 OD1 E:ASP164 3.6 49.1 1.0 ND2 E:ASN23 3.8 53.4 1.0 CE1 E:HIS74 3.9 38.0 1.0 NE2 E:HIS74 4.0 41.9 1.0 CG E:HIS79 4.1 46.6 1.0 CE1 E:HIS368 4.2 51.5 1.0 ND1 E:HIS79 4.2 47.6 1.0 ND1 E:HIS390 4.2 48.3 1.0 CG E:HIS390 4.2 48.2 1.0 CB E:ASP164 4.4 41.5 1.0 NE2 E:HIS368 4.6 48.1 1.0 CB E:ASP78 4.6 38.2 1.0 NE2 E:HIS142 4.8 35.1 1.0 O E:ASP78 4.9 42.0 1.0 CG E:ASN23 4.9 45.8 1.0 ND1 E:HIS76 4.9 44.1 1.0

Zinc binding site 8 out of 8 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1557 b:36.9 occ:1.00 CE1 E:HIS74 2.0 38.0 1.0 NE2 E:HIS142 2.2 35.1 1.0 ND1 E:HIS76 2.3 44.1 1.0 OD2 E:ASP164 2.6 39.3 1.0 NE2 E:HIS74 2.9 41.9 1.0 ZN E:ZN1556 3.0 39.5 1.0 ND1 E:HIS74 3.0 43.9 1.0 CE1 E:HIS76 3.1 46.3 1.0 CE1 E:HIS142 3.1 39.0 1.0 CD2 E:HIS142 3.2 40.1 1.0 CG E:HIS76 3.3 46.8 1.0 CG E:ASP164 3.5 46.6 1.0 CB E:HIS76 3.6 45.4 1.0 NE2 E:HIS79 3.6 39.6 1.0 CD2 E:HIS79 3.8 42.1 1.0 CB E:ASP164 3.8 41.5 1.0 OD1 E:ASP78 4.0 50.7 1.0 CD2 E:HIS74 4.1 39.5 1.0 CG E:HIS74 4.1 45.9 1.0 ND1 E:HIS142 4.2 39.2 1.0 NE2 E:HIS76 4.3 49.4 1.0 CG E:HIS142 4.3 41.6 1.0 CD2 E:HIS76 4.4 50.5 1.0 CE1 E:HIS368 4.4 51.5 1.0 OD1 E:ASP164 4.6 49.1 1.0 OD2 E:ASP78 4.6 50.9 1.0 NE2 E:HIS368 4.7 48.1 1.0 CE1 E:HIS79 4.7 48.0 1.0 CG E:ASP78 4.8 48.4 1.0 CG E:HIS79 4.8 46.6 1.0 NE2 E:HIS390 4.9 30.4 1.0

J.A.Newman, L.Hewitt, C.Rodrigues, A.Solovyova, C.R.Harwood, R.J.Lewis. Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1. Structure V. 19 1241 2011.
ISSN: ISSN 0969-2126
PubMed: 21893285
DOI: 10.1016/J.STR.2011.06.017