Zinc in PDB 6ohc: E. Coli Guanine Deaminase

All present enzymatic activity of E. Coli Guanine Deaminase:
3.5.4.3;

The structure of E. Coli Guanine Deaminase, PDB code: 6ohc was solved by R.S.Shek, J.B.French, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.628, 80.588, 101.427, 104.80, 105.72, 105.83
R / Rfree (%)	20.9 / 25.8

The binding sites of Zinc atom in the E. Coli Guanine Deaminase (pdb code 6ohc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the E. Coli Guanine Deaminase, PDB code: 6ohc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the E. Coli Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Guanine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:37.7 occ:1.00 O A:HOH643 2.0 29.7 1.0 NE2 A:HIS82 2.0 45.0 1.0 NE2 A:HIS84 2.0 46.8 1.0 NE2 A:HIS237 2.1 49.1 1.0 OD1 A:ASP327 2.3 44.7 1.0 CD2 A:HIS84 3.0 45.4 1.0 CD2 A:HIS82 3.0 44.0 1.0 CE1 A:HIS82 3.0 44.5 1.0 CE1 A:HIS84 3.1 46.7 1.0 CE1 A:HIS237 3.1 47.9 1.0 CD2 A:HIS237 3.1 47.7 1.0 CG A:ASP327 3.3 39.5 1.0 OD2 A:ASP327 3.8 40.6 1.0 O A:HOH681 3.9 33.4 1.0 ND1 A:HIS82 4.1 42.4 1.0 NE2 A:HIS276 4.1 40.0 1.0 CG A:HIS82 4.1 41.9 1.0 CG A:HIS84 4.1 42.9 1.0 ND1 A:HIS84 4.1 44.5 1.0 ND1 A:HIS237 4.2 45.9 1.0 CG A:HIS237 4.3 47.0 1.0 CB A:ASP327 4.5 38.4 1.0 O A:HOH699 4.7 46.7 1.0 CE1 A:HIS276 4.9 40.0 1.0 CA A:ASP327 5.0 37.1 1.0 CD2 A:HIS276 5.0 40.3 1.0 CB A:ALA275 5.0 41.3 1.0

Zinc binding site 2 out of 4 in the E. Coli Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Guanine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:40.1 occ:1.00 NE2 B:HIS82 2.0 50.4 1.0 O B:HOH620 2.0 33.3 1.0 NE2 B:HIS237 2.0 48.3 1.0 NE2 B:HIS84 2.0 47.9 1.0 OD1 B:ASP327 2.7 38.2 1.0 CE1 B:HIS82 2.9 49.4 1.0 CE1 B:HIS237 3.0 47.4 1.0 CE1 B:HIS84 3.0 47.1 1.0 CD2 B:HIS82 3.0 47.6 1.0 CD2 B:HIS237 3.0 47.1 1.0 CD2 B:HIS84 3.0 45.5 1.0 CG B:ASP327 3.6 38.0 1.0 O B:HOH622 3.9 41.3 1.0 O B:HOH724 4.0 49.0 1.0 ND1 B:HIS82 4.0 46.6 1.0 OD2 B:ASP327 4.0 38.0 1.0 ND1 B:HIS84 4.1 43.8 1.0 NE2 B:HIS276 4.1 41.5 1.0 ND1 B:HIS237 4.1 44.6 1.0 CG B:HIS82 4.1 45.4 1.0 O B:HOH686 4.1 44.1 1.0 CG B:HIS84 4.1 43.1 1.0 CG B:HIS237 4.1 46.4 1.0 O B:HOH720 4.5 43.2 1.0 CB B:ASP327 4.8 37.4 1.0 CD2 B:HIS276 4.9 41.8 1.0 CB B:ALA275 4.9 43.0 1.0 CE1 B:HIS276 5.0 41.0 1.0

Zinc binding site 3 out of 4 in the E. Coli Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Guanine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:73.5 occ:1.00 O C:HOH601 1.9 56.1 1.0 NE2 C:HIS237 2.0 0.7 1.0 NE2 C:HIS82 2.0 74.1 1.0 NE2 C:HIS84 2.1 85.2 1.0 OD1 C:ASP327 2.6 79.5 1.0 CD2 C:HIS237 3.0 0.8 1.0 CE1 C:HIS82 3.0 75.4 1.0 CE1 C:HIS237 3.0 0.8 1.0 CD2 C:HIS82 3.0 73.3 1.0 CD2 C:HIS84 3.0 76.9 1.0 CE1 C:HIS84 3.0 83.1 1.0 CG C:ASP327 3.6 77.6 1.0 OD2 C:ASP327 4.0 75.0 1.0 ND1 C:HIS237 4.1 0.9 1.0 NE2 C:HIS276 4.1 79.4 1.0 ND1 C:HIS82 4.1 72.7 1.0 CG C:HIS237 4.1 99.5 1.0 CG C:HIS82 4.2 72.8 1.0 ND1 C:HIS84 4.2 74.7 1.0 CG C:HIS84 4.2 75.6 1.0 CB C:ASP327 4.8 76.2 1.0 CD2 C:HIS276 4.9 83.5 1.0 CB C:ALA275 4.9 89.7 1.0

Zinc binding site 4 out of 4 in the E. Coli Guanine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Guanine Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:67.6 occ:1.00 O D:HOH601 1.8 37.7 1.0 NE2 D:HIS237 1.9 94.6 1.0 NE2 D:HIS82 2.0 84.1 1.0 NE2 D:HIS84 2.1 85.9 1.0 OD1 D:ASP327 2.7 79.7 1.0 CE1 D:HIS237 2.9 94.0 1.0 CE1 D:HIS82 2.9 79.1 1.0 CD2 D:HIS237 2.9 93.3 1.0 CD2 D:HIS82 3.0 77.6 1.0 CE1 D:HIS84 3.0 85.8 1.0 CD2 D:HIS84 3.1 83.6 1.0 CG D:ASP327 3.6 77.9 1.0 ND1 D:HIS237 4.0 93.8 1.0 ND1 D:HIS82 4.0 73.5 1.0 CG D:HIS237 4.0 94.8 1.0 OD2 D:ASP327 4.1 74.9 1.0 CG D:HIS82 4.1 74.5 1.0 NE2 D:HIS276 4.1 81.8 1.0 ND1 D:HIS84 4.1 81.0 1.0 CG D:HIS84 4.2 79.7 1.0 CB D:ASP327 4.8 73.2 1.0 CB D:ALA275 4.9 77.0 1.0 CD2 D:HIS276 4.9 84.0 1.0

R.Shek, T.Hilaire, J.Sim, J.B.French. Structural Determinants For Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Biochemistry V. 58 3280 2019.
ISSN: ISSN 0006-2960
PubMed: 31283204
DOI: 10.1021/ACS.BIOCHEM.9B00341