Zinc in PDB 6ohb: 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: 6ohb 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)	55.99 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.479, 137.583, 98.581, 90.00, 102.16, 90.00
R / Rfree (%)	18.6 / 23.4

The binding sites of Zinc atom in the E. Coli Guanine Deaminase (pdb code 6ohb). 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: 6ohb:
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:Zn501 b:51.1 occ:1.00 NE2 A:HIS84 1.9 32.9 1.0 NE2 A:HIS82 2.0 47.8 1.0 NE2 A:HIS237 2.0 45.3 1.0 OD2 A:ASP327 2.2 54.8 1.0 OD1 A:ASP327 2.2 56.8 1.0 CG A:ASP327 2.6 51.9 1.0 CD2 A:HIS84 2.8 38.2 1.0 CE1 A:HIS237 2.9 46.6 1.0 CE1 A:HIS82 2.9 48.8 1.0 CE1 A:HIS84 3.0 41.2 1.0 CD2 A:HIS82 3.0 49.8 1.0 CD2 A:HIS237 3.1 42.3 1.0 NE2 A:HIS276 3.9 41.3 1.0 CG A:HIS84 4.0 40.1 1.0 O A:HOH632 4.0 47.0 1.0 ND1 A:HIS84 4.0 41.2 1.0 ND1 A:HIS82 4.1 43.2 1.0 ND1 A:HIS237 4.1 41.5 1.0 CB A:ASP327 4.1 51.4 1.0 CG A:HIS82 4.1 43.8 1.0 O A:HOH658 4.2 55.1 1.0 CG A:HIS237 4.2 44.7 1.0 CE1 A:HIS276 4.6 42.5 1.0 CA A:ASP327 4.7 50.8 1.0 CD2 A:HIS276 4.8 43.4 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:Zn501 b:46.5 occ:1.00 NE2 B:HIS84 2.0 40.6 1.0 NE2 B:HIS237 2.1 44.0 1.0 NE2 B:HIS82 2.1 41.6 1.0 O B:HOH601 2.1 48.0 1.0 OD1 B:ASP327 2.2 56.4 1.0 OD2 B:ASP327 2.3 63.9 1.0 CG B:ASP327 2.6 53.3 1.0 CD2 B:HIS84 2.9 41.8 1.0 CE1 B:HIS82 2.9 44.1 1.0 CD2 B:HIS237 3.0 45.0 1.0 CE1 B:HIS237 3.1 48.9 1.0 CE1 B:HIS84 3.1 45.5 1.0 CD2 B:HIS82 3.1 40.0 1.0 NE2 B:HIS276 4.0 46.5 1.0 CG B:HIS84 4.1 41.7 1.0 ND1 B:HIS82 4.1 44.4 1.0 ND1 B:HIS84 4.1 39.6 1.0 CG B:HIS237 4.2 43.9 1.0 ND1 B:HIS237 4.2 47.7 1.0 CB B:ASP327 4.2 50.2 1.0 CG B:HIS82 4.2 43.2 1.0 CE1 B:HIS276 4.8 41.6 1.0 CD2 B:HIS276 4.9 46.1 1.0 CA B:ASP327 4.9 50.4 1.0 CB B:ALA275 5.0 44.1 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:38.2 occ:1.00 NE2 C:HIS82 2.0 33.9 1.0 NE2 C:HIS237 2.0 40.5 1.0 NE2 C:HIS84 2.1 32.4 1.0 O C:HOH613 2.1 44.3 1.0 OD1 C:ASP327 2.2 48.0 1.0 CE1 C:HIS82 2.8 31.7 1.0 CD2 C:HIS84 2.9 35.1 1.0 CE1 C:HIS237 3.0 41.7 1.0 CD2 C:HIS237 3.0 37.7 1.0 CE1 C:HIS84 3.2 34.3 1.0 CD2 C:HIS82 3.2 33.0 1.0 CG C:ASP327 3.4 41.1 1.0 OD2 C:ASP327 3.8 47.2 1.0 ND1 C:HIS82 4.0 36.5 1.0 NE2 C:HIS276 4.0 44.2 1.0 O C:HOH636 4.1 37.0 1.0 CG C:HIS84 4.1 32.6 1.0 ND1 C:HIS237 4.1 38.2 1.0 CG C:HIS237 4.2 39.2 1.0 ND1 C:HIS84 4.2 33.5 1.0 CG C:HIS82 4.2 37.0 1.0 O C:HOH644 4.3 50.1 1.0 O C:HOH610 4.6 42.6 1.0 CB C:ASP327 4.7 36.0 1.0 O C:HOH667 4.9 50.7 1.0 CE1 C:HIS276 4.9 42.9 1.0 CD2 C:HIS276 4.9 40.9 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:54.9 occ:1.00 NE2 D:HIS84 2.0 54.3 1.0 NE2 D:HIS82 2.1 55.2 1.0 NE2 D:HIS237 2.1 61.4 1.0 O D:HOH605 2.1 53.5 1.0 OD1 D:ASP327 2.2 67.6 1.0 CE1 D:HIS82 2.7 55.9 1.0 CD2 D:HIS84 3.0 51.8 1.0 CE1 D:HIS84 3.0 55.0 1.0 CD2 D:HIS237 3.0 59.8 1.0 CE1 D:HIS237 3.1 62.6 1.0 CD2 D:HIS82 3.3 53.9 1.0 CG D:ASP327 3.3 60.3 1.0 OD2 D:ASP327 3.8 63.8 1.0 ND1 D:HIS82 4.0 53.9 1.0 NE2 D:HIS276 4.0 68.4 1.0 ND1 D:HIS84 4.1 54.5 1.0 CG D:HIS84 4.1 46.0 1.0 ND1 D:HIS237 4.2 60.5 1.0 CG D:HIS237 4.2 62.0 1.0 CG D:HIS82 4.3 53.7 1.0 CB D:ASP327 4.6 55.9 1.0 CE1 D:HIS276 4.8 66.5 1.0 CB D:ALA275 4.9 57.3 1.0 CD2 D:HIS276 4.9 62.6 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