Zinc in PDB 7vse: E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding)

All present enzymatic activity of E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding):
3.1.26.4;

The structure of E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding), PDB code: 7vse was solved by Z.Liao, T.Oyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.13 / 2.08
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.65, 64.586, 79.104, 90, 90, 90
R / Rfree (%)	23 / 27.6

The binding sites of Zinc atom in the E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding) (pdb code 7vse). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding), PDB code: 7vse:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:45.0 occ:1.00 NE2 A:HIS124 2.0 49.7 1.0 OD2 A:ASP10 2.1 42.9 1.0 OD2 A:ASP70 2.3 45.6 1.0 CE1 A:HIS124 2.7 49.4 1.0 CG A:ASP10 2.9 36.9 1.0 OD1 A:ASP10 2.9 31.0 1.0 CG A:ASP70 3.0 41.9 1.0 OD1 A:ASP70 3.0 45.1 1.0 CD2 A:HIS124 3.1 47.8 1.0 O A:HOH306 3.3 41.3 1.0 ND1 A:HIS124 3.8 48.5 1.0 CG A:HIS124 4.0 46.7 1.0 CB A:ASP10 4.3 34.1 1.0 CB A:ASP134 4.4 38.5 1.0 CB A:ASP70 4.4 42.6 1.0 OD1 A:ASP134 4.5 47.7 1.0 O A:HOH319 4.5 34.0 1.0 CG A:ASP134 4.7 41.8 1.0

Zinc binding site 2 out of 2 in the E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Ribonuclease Hi in Complex One ZN2+ (HIS124 N-Epsilon Binding) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:76.2 occ:1.00 OD2 B:ASP70 2.2 64.9 1.0 OD1 B:ASP10 2.7 51.9 1.0 CG B:ASP70 3.0 58.2 1.0 CG B:ASP10 3.1 49.3 1.0 OD1 B:ASP134 3.1 55.6 1.0 OD1 B:ASP70 3.2 61.0 1.0 ND1 B:HIS124 3.3 75.9 1.0 OD2 B:ASP10 3.3 53.4 1.0 CG B:ASP134 3.7 61.3 1.0 CG B:HIS124 3.8 77.0 1.0 CB B:HIS124 3.9 74.0 1.0 CE1 B:HIS124 4.2 77.0 1.0 OD2 B:ASP134 4.2 71.0 1.0 CB B:ASP10 4.2 46.5 1.0 CB B:ASP70 4.4 56.8 1.0 O3 B:GOL201 4.5 71.0 1.0 CB B:ASP134 4.5 58.3 1.0 N B:HIS124 4.8 76.7 1.0 CD2 B:HIS124 4.9 75.8 1.0 CA B:HIS124 4.9 80.4 1.0

Z.Liao, T.Oyama, Y.Kitagawa, K.Katayanagi, K.Morikawa, M.Oda. Pivotal Role of A Conserved Histidine in Escherichia Coli Ribonuclease Hi As Proposed By X-Ray Crystallography. Acta Crystallogr D Struct V. 78 390 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35234152
DOI: 10.1107/S2059798322000870