Zinc in PDB 1z2l: Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate

The structure of Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate, PDB code: 1z2l was solved by R.Agarwal, S.Swaminathan, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.532, 186.579, 49.218, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.3

The binding sites of Zinc atom in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate (pdb code 1z2l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate, PDB code: 1z2l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate


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 Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:33.1 occ:1.00 OD2 A:ASP94 2.2 22.7 1.0 NE2 A:HIS83 2.3 19.1 1.0 O A:HOH629 2.3 35.9 1.0 NE2 A:HIS192 2.3 19.1 1.0 O A:HOH631 2.6 35.9 1.0 CE1 A:HIS83 3.2 18.5 1.0 CE1 A:HIS192 3.2 17.0 1.0 CG A:ASP94 3.3 23.3 1.0 CD2 A:HIS83 3.3 17.2 1.0 CD2 A:HIS192 3.4 16.5 1.0 ZN A:ZN512 3.4 39.8 1.0 OD1 A:ASP94 3.7 25.7 1.0 OE1 A:GLU128 3.7 41.8 1.0 N A:GLY95 4.2 22.0 1.0 ND1 A:HIS360 4.2 23.8 1.0 ND1 A:HIS83 4.3 20.7 1.0 CD A:GLU128 4.3 41.5 1.0 ND1 A:HIS192 4.4 18.9 1.0 CG A:HIS83 4.4 20.6 1.0 CG A:HIS192 4.5 19.7 1.0 CA A:GLY95 4.5 21.2 1.0 C A:ASP94 4.5 20.8 1.0 O A:HOH523 4.5 29.7 1.0 OE2 A:GLU129 4.6 45.6 1.0 CE1 A:HIS360 4.6 25.9 1.0 OE2 A:GLU128 4.6 45.5 1.0 CB A:ASP94 4.6 23.6 1.0 CA A:ASP94 4.8 21.1 1.0 NE2 A:GLN195 4.9 24.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate


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 Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:39.8 occ:1.00 OD1 A:ASP94 2.1 25.7 1.0 NE2 A:HIS384 2.3 36.5 1.0 OE2 A:GLU129 2.4 45.6 1.0 O A:HOH631 2.5 35.9 1.0 OE1 A:GLU129 2.9 40.3 1.0 CD A:GLU129 2.9 41.8 1.0 CG A:ASP94 3.0 23.3 1.0 OD2 A:ASP94 3.2 22.7 1.0 CD2 A:HIS384 3.2 36.6 1.0 CE1 A:HIS384 3.3 36.0 1.0 ZN A:ZN511 3.4 33.1 1.0 O A:HOH596 3.6 32.6 1.0 NE2 A:GLN195 3.8 24.6 1.0 O A:HOH588 4.1 32.8 1.0 OE1 A:GLU128 4.2 41.8 1.0 CE1 A:HIS83 4.3 18.5 1.0 CB A:ASP94 4.3 23.6 1.0 CG A:HIS384 4.3 36.5 1.0 ND1 A:HIS384 4.4 36.8 1.0 CG A:GLU129 4.4 40.1 1.0 NE2 A:HIS83 4.4 19.1 1.0 O A:HOH629 4.9 35.9 1.0 CD A:GLN195 4.9 26.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate


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 Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn513 b:37.0 occ:1.00 OD1 B:ASP94 2.1 30.5 1.0 NE2 B:HIS83 2.2 22.1 1.0 O B:HOH590 2.3 35.9 1.0 NE2 B:HIS192 2.4 31.9 1.0 O B:HOH591 2.6 35.9 1.0 CE1 B:HIS192 2.9 32.6 1.0 CG B:ASP94 3.0 32.4 1.0 CE1 B:HIS83 3.1 24.5 1.0 CD2 B:HIS83 3.2 23.2 1.0 OD2 B:ASP94 3.2 34.0 1.0 ZN B:ZN514 3.3 48.3 1.0 CD2 B:HIS192 3.6 32.9 1.0 OE2 B:GLU128 3.9 38.9 1.0 N B:GLY95 4.0 32.2 1.0 ND1 B:HIS192 4.2 33.5 1.0 OE1 B:GLU129 4.2 42.2 1.0 ND1 B:HIS83 4.3 23.9 1.0 CD B:GLU128 4.3 39.3 1.0 CA B:GLY95 4.3 30.5 1.0 CG B:HIS83 4.4 25.3 1.0 CB B:ASP94 4.4 33.7 1.0 ND1 B:HIS360 4.4 32.3 1.0 C B:ASP94 4.4 32.1 1.0 CG B:HIS192 4.5 35.0 1.0 OE1 B:GLU128 4.6 38.4 1.0 NE2 B:GLN195 4.7 37.8 1.0 CA B:ASP94 4.7 33.5 1.0 O B:HOH561 4.8 37.1 1.0 CD B:GLU129 4.8 40.8 1.0 CE1 B:HIS360 4.8 31.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Allantoate-Amidohydrolase From E.Coli K12 in Complex with Substrate Allantoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn514 b:48.3 occ:1.00 OD2 B:ASP94 2.2 34.0 1.0 NE2 B:HIS384 2.2 54.1 1.0 OE1 B:GLU129 2.4 42.2 1.0 OE2 B:GLU129 2.6 37.0 1.0 O B:HOH591 2.8 35.9 1.0 CD B:GLU129 2.8 40.8 1.0 CG B:ASP94 3.0 32.4 1.0 CE1 B:HIS384 3.2 53.5 1.0 OD1 B:ASP94 3.2 30.5 1.0 CD2 B:HIS384 3.2 52.6 1.0 ZN B:ZN513 3.3 37.0 1.0 O B:HOH550 3.5 24.8 1.0 NE2 B:GLN195 3.5 37.8 1.0 O B:HOH574 4.0 48.3 1.0 OE2 B:GLU128 4.1 38.9 1.0 CG B:GLU129 4.2 41.3 1.0 CB B:ASP94 4.3 33.7 1.0 ND1 B:HIS384 4.3 54.4 1.0 CG B:HIS384 4.3 53.4 1.0 NE2 B:HIS83 4.4 22.1 1.0 CE1 B:HIS83 4.4 24.5 1.0 CD B:GLN195 4.7 39.3 1.0 O B:HOH590 4.8 35.9 1.0 CD B:GLU128 4.9 39.3 1.0

R.Agarwal, S.K.Burley, S.Swaminathan. Structural Analysis of A Ternary Complex of Allantoate Amidohydrolase From Escherichia Coli Reveals Its Mechanics. J.Mol.Biol. V. 368 450 2007.
ISSN: ISSN 0022-2836
PubMed: 17362992
DOI: 10.1016/J.JMB.2007.02.028