Zinc in PDB 4dzh: Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn

The structure of Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn, PDB code: 4dzh was solved by M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, S.Sojitra, S.Chamala, A.Kar, J.Lafleur, G.Villigas, B.Evans, J.Hammonds, A.Gizzi, W.D.Zencheck, B.Hillerich, J.Love, R.D.Seidel, J.B.Bonanno, F.M.Raushel, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.97 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.645, 53.150, 67.390, 90.00, 106.54, 90.00
R / Rfree (%)	20.8 / 23.3

The structure of Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn (pdb code 4dzh). 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 An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn, PDB code: 4dzh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn


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 An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:17.6 occ:1.00 NE2 A:HIS80 2.0 10.9 1.0 O A:HOH790 2.0 18.2 1.0 NE2 A:HIS78 2.1 16.2 1.0 NE2 A:HIS227 2.2 15.1 1.0 OD1 A:ASP315 2.4 19.4 1.0 CE1 A:HIS80 2.9 17.6 1.0 CD2 A:HIS227 3.0 20.2 1.0 CD2 A:HIS80 3.0 16.3 1.0 CE1 A:HIS78 3.0 12.3 1.0 CD2 A:HIS78 3.1 13.1 1.0 ZN A:ZN505 3.2 17.9 0.8 CE1 A:HIS227 3.3 18.1 1.0 O A:UNL506 3.4 32.5 0.8 CG A:ASP315 3.5 16.3 1.0 NE2 A:HIS264 3.9 17.6 1.0 OXT A:UNL506 3.9 23.6 0.8 C A:UNL506 4.0 31.4 0.8 OD2 A:ASP315 4.0 15.8 1.0 ND1 A:HIS80 4.0 17.0 1.0 O A:HOH655 4.1 25.1 1.0 CG A:HIS80 4.1 16.2 1.0 ND1 A:HIS78 4.1 14.8 1.0 CG A:HIS227 4.2 17.3 1.0 CG A:HIS78 4.2 13.2 1.0 ND1 A:HIS227 4.3 18.7 1.0 CE1 A:HIS264 4.7 17.9 1.0 CB A:ASP315 4.7 10.4 1.0 CD2 A:HIS264 4.8 19.2 1.0 O A:HOH631 4.9 23.2 1.0 O A:HOH844 4.9 16.2 0.8 CA A:ASP315 5.0 12.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn


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 An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:17.9 occ:0.80 O A:HOH790 1.9 18.2 1.0 OD2 A:ASP315 2.0 15.8 1.0 OXT A:UNL506 2.0 23.6 0.8 O A:HOH844 2.1 16.2 0.8 CG A:ASP315 2.6 16.3 1.0 OD1 A:ASP315 2.6 19.4 1.0 O A:UNL506 2.9 32.5 0.8 C A:UNL506 2.9 31.4 0.8 ZN A:ZN504 3.2 17.6 1.0 O A:HOH631 3.3 23.2 1.0 O A:HOH655 3.6 25.1 1.0 NE2 A:HIS264 3.8 17.6 1.0 OE2 A:GLU230 3.9 19.5 1.0 CB A:ASP315 4.1 10.4 1.0 OG A:SER289 4.1 18.8 1.0 CE1 A:HIS264 4.2 17.9 1.0 NE2 A:HIS80 4.3 10.9 1.0 OG A:SER319 4.3 20.4 1.0 CH3 A:UNL506 4.3 31.3 0.8 CD2 A:HIS80 4.5 16.3 1.0 NE2 A:HIS227 4.7 15.1 1.0 CD1 A:LEU293 4.7 23.2 1.0 CD A:GLU230 4.8 24.9 1.0 OE1 A:GLU230 4.8 27.1 1.0 NE2 A:HIS78 4.9 16.2 1.0 CD2 A:HIS264 4.9 19.2 1.0 CD2 A:HIS227 5.0 20.2 1.0 O A:HOH615 5.0 19.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn


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 An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:39.0 occ:0.80 NE2 A:HIS184 2.0 35.6 1.0 O A:HOH847 2.1 39.6 0.8 O A:HOH846 2.2 36.1 0.8 O A:LEU220 2.2 31.5 1.0 O A:HOH845 2.2 28.4 0.8 CE1 A:HIS184 2.9 36.4 1.0 CD2 A:HIS184 3.1 33.4 1.0 C A:LEU220 3.3 31.2 1.0 CA A:LEU220 4.0 32.9 1.0 ND1 A:HIS184 4.1 35.4 1.0 CG A:HIS184 4.2 31.9 1.0 CB A:LEU220 4.3 29.2 1.0 CB A:ASP221 4.3 39.6 1.0 O A:ASP221 4.3 32.2 1.0 N A:ASP221 4.3 32.1 1.0 O A:HOH820 4.4 43.3 1.0 CA A:ASP221 4.6 31.7 1.0 C A:ASP221 4.7 30.7 1.0

M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, S.Sojitra, S.Chamala, A.Kar, J.Lafleur, G.Villigas, B.Evans, J.Hammonds, A.Gizzi, W.D.Zencheck, B.Hillerich, J.Love, R.D.Seidel, J.B.Bonanno, F.M.Raushel, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc). Crystal Structure of An Adenosine Deaminase From Xanthomonas Campestris (Target Nysgrc-200456) with Bound Zn To Be Published.