Zinc in PDB 3r0d: Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site

All present enzymatic activity of Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site:
3.5.4.1;

The structure of Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site, PDB code: 3r0d was solved by A.A.Fedorov, E.V.Fedorov, S.Kamat, D.Hitchcock, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.13 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	145.492, 145.492, 199.704, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site (pdb code 3r0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site, PDB code: 3r0d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn428 b:22.2 occ:0.99 O A:HOH434 2.0 21.5 1.0 NE2 A:HIS63 2.0 19.5 1.0 NE2 A:HIS214 2.1 25.1 1.0 NE2 A:HIS61 2.1 21.8 1.0 CE1 A:HIS63 3.0 23.8 1.0 OD2 A:ASP313 3.0 23.6 1.0 CE1 A:HIS61 3.0 24.1 1.0 CD2 A:HIS63 3.1 22.2 1.0 CE1 A:HIS214 3.1 19.9 1.0 CD2 A:HIS214 3.1 22.4 1.0 CD2 A:HIS61 3.2 20.1 1.0 O A:HOH433 3.4 22.9 1.0 ZN A:ZN429 3.4 25.5 0.6 O A:HOH436 3.7 27.8 1.0 CG A:ASP313 3.9 25.0 1.0 NE2 A:HIS246 3.9 19.3 1.0 ND1 A:HIS63 4.1 22.7 1.0 ND1 A:HIS61 4.2 24.0 1.0 CG A:HIS63 4.2 22.7 1.0 ND1 A:HIS214 4.2 22.7 1.0 OD1 A:ASP313 4.2 23.1 1.0 O A:HOH619 4.2 38.6 1.0 CG A:HIS214 4.2 22.1 1.0 CG A:HIS61 4.3 19.2 1.0 CD2 A:HIS246 4.6 21.6 1.0 CD2 A:HIS122 4.7 22.9 1.0 CG A:HIS122 4.8 23.4 1.0 CE1 A:HIS246 4.9 22.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn429 b:25.5 occ:0.61 O A:HOH433 1.9 22.9 1.0 O A:HOH434 2.0 21.5 1.0 O A:HOH435 2.1 26.3 1.0 O A:HOH436 2.1 27.8 1.0 OD1 A:ASP313 2.2 23.1 1.0 OD2 A:ASP313 2.5 23.6 1.0 CG A:ASP313 2.6 25.0 1.0 OD1 A:ASP314 2.7 28.7 1.0 ZN A:ZN428 3.4 22.2 1.0 O A:HOH619 3.4 38.6 1.0 CG A:ASP314 3.7 29.2 1.0 NE2 A:HIS246 3.8 19.3 1.0 OD2 A:ASP314 4.0 30.0 1.0 CB A:ASP313 4.1 23.3 1.0 NE2 A:HIS63 4.1 19.5 1.0 CE1 A:HIS246 4.2 22.6 1.0 CG1 A:VAL278 4.2 19.6 1.0 OE1 A:GLU217 4.2 23.9 1.0 CD2 A:HIS63 4.3 22.2 1.0 NE2 A:HIS61 4.7 21.8 1.0 OE2 A:GLU217 4.7 25.1 1.0 CG A:TRP319 4.8 35.8 1.0 CB A:TRP319 4.8 30.9 1.0 CD A:GLU217 4.9 23.1 1.0 C A:ASP313 4.9 23.4 1.0 CA A:ASP313 5.0 23.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn430 b:31.5 occ:0.50 NE2 A:HIS97 2.1 32.7 1.0 OE2 A:GLU138 2.2 33.5 1.0 OE1 A:GLU138 2.4 33.0 1.0 CD A:GLU138 2.6 29.0 1.0 CD2 A:HIS97 3.0 32.3 1.0 CE1 A:HIS97 3.1 31.6 1.0 O A:HOH585 3.9 38.0 1.0 CG A:GLU138 4.1 30.4 1.0 CG A:HIS97 4.2 31.1 1.0 ND1 A:HIS97 4.2 33.0 1.0 NZ A:LYS101 4.5 33.0 1.0 O A:HOH631 4.7 45.5 1.0 CD A:LYS101 4.9 32.5 1.0 CB A:GLU138 5.0 28.4 1.0

A.A.Fedorov, E.V.Fedorov, S.Kamat, D.Hitchcock, F.M.Raushel, S.C.Almo. Crystal Structure of Cytosine Deaminase From Escherichia Coli Complexed with Two Zinc Atoms in the Active Site To Be Published.