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

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

The structure of E. Coli Ribonuclease Hi in Complex with One ZN2+ (HIS124 N-Delta Binding), PDB code: 7vsb 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)	48.50 / 1.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.174, 86.174, 80.112, 90, 90, 90
R / Rfree (%)	18.5 / 22.1

The binding sites of Zinc atom in the E. Coli Ribonuclease Hi in Complex with One ZN2+ (HIS124 N-Delta Binding) (pdb code 7vsb). 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 with One ZN2+ (HIS124 N-Delta Binding), PDB code: 7vsb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Ribonuclease Hi in Complex with One ZN2+ (HIS124 N-Delta 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 with One ZN2+ (HIS124 N-Delta Binding) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:45.5 occ:1.00 OD2 A:ASP70 2.3 46.1 1.0 ND1 A:HIS124 2.3 43.6 1.0 O A:HOH356 2.4 36.6 1.0 OD1 A:ASP10 2.5 32.5 1.0 OD2 A:ASP10 2.9 33.6 1.0 CG A:ASP10 2.9 32.2 1.0 OD1 A:ASP70 2.9 38.2 1.0 CG A:ASP70 3.0 37.7 1.0 CG A:HIS124 3.0 44.4 1.0 CB A:HIS124 3.2 43.2 1.0 CE1 A:HIS124 3.3 42.6 1.0 O A:HOH301 3.5 34.9 1.0 O A:HOH303 3.8 33.3 1.0 O A:HOH308 4.0 28.6 1.0 CD2 A:HIS124 4.1 46.2 1.0 CB A:ASP10 4.2 23.4 1.0 N A:HIS124 4.2 52.7 1.0 NE2 A:HIS124 4.2 47.9 1.0 CA A:HIS124 4.3 49.6 1.0 CB A:ASP70 4.4 38.2 1.0 O A:HOH305 4.4 34.1 1.0 OD1 A:ASP134 4.7 30.7 1.0 O A:HOH366 4.8 39.1 1.0 CB A:ASP134 4.9 25.6 1.0

Zinc binding site 2 out of 2 in the E. Coli Ribonuclease Hi in Complex with One ZN2+ (HIS124 N-Delta 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 with One ZN2+ (HIS124 N-Delta Binding) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:90.3 occ:1.00 OD2 B:ASP10 2.3 33.3 1.0 O B:HOH372 2.9 49.1 1.0 CG B:ASP10 3.2 31.7 1.0 O B:HOH339 3.3 32.9 1.0 O B:HOH327 3.3 27.9 1.0 OD1 B:ASP10 3.5 28.2 1.0 O B:HOH323 3.6 41.7 1.0 O B:HOH373 3.7 46.3 1.0 O B:HOH310 3.8 31.1 1.0 OD2 B:ASP70 3.9 41.4 1.0 CB B:ASP70 3.9 35.6 1.0 O B:HOH358 4.0 40.4 1.0 OD1 B:ASP134 4.2 27.3 1.0 CG B:ASP70 4.2 46.2 1.0 CB B:ASP134 4.6 21.4 1.0 CB B:ASP10 4.6 19.5 1.0 O B:HOH361 4.7 35.6 1.0 CG B:ASP134 4.7 29.5 1.0 O B:ASP70 4.8 36.5 1.0 C B:ASP70 5.0 32.0 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