Zinc in PDB 3lu2: Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase

The structure of Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase, PDB code: 3lu2 was solved by S.M.Anderson, Z.Wawrzak, O.Onopriyenko, J.Hasseman, A.Edwards, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.60 / 2.20
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	179.088, 179.088, 46.412, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 18.5

The binding sites of Zinc atom in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase (pdb code 3lu2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase, PDB code: 3lu2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:0.5 occ:1.00 O A:HOH395 2.7 61.6 1.0 ZN A:ZN310 2.9 0.4 1.0 O A:HOH393 3.0 72.5 1.0 O A:HOH329 3.1 67.9 1.0 OE2 A:GLU105 3.1 66.7 1.0 NE2 A:HIS172 3.3 48.8 1.0 CE1 A:HIS172 3.5 45.1 1.0 NE2 A:HIS192 3.5 37.1 1.0 OD2 A:ASP261 3.7 56.0 1.0 NE1 A:TRP132 3.9 48.6 1.0 OD1 A:ASP261 4.1 57.5 1.0 CD2 A:HIS192 4.1 36.5 1.0 CG A:ASP261 4.2 53.1 1.0 O A:HOH396 4.2 52.8 1.0 CD A:GLU105 4.4 63.8 1.0 CD1 A:TRP132 4.5 48.4 1.0 NE2 A:HIS7 4.5 42.7 1.0 NH2 A:ARG203 4.6 46.4 1.0 CE1 A:HIS192 4.6 37.3 1.0 CD2 A:HIS172 4.7 41.5 1.0 ND1 A:HIS172 4.8 44.7 1.0

Zinc binding site 2 out of 4 in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn310 b:0.4 occ:1.00 OD1 A:ASP9 2.7 62.5 1.0 ZN A:ZN309 2.9 0.5 1.0 OE2 A:GLU105 3.1 66.7 1.0 OD2 A:ASP9 3.2 71.5 1.0 CG A:ASP9 3.2 63.7 1.0 O A:HOH329 3.3 67.9 1.0 O A:HOH393 3.3 72.5 1.0 NE2 A:HIS7 3.3 42.7 1.0 OD1 A:ASP261 3.8 57.5 1.0 CD A:GLU105 4.0 63.8 1.0 CD2 A:HIS7 4.2 43.0 1.0 CE1 A:HIS7 4.3 43.4 1.0 CG A:PHE49 4.4 49.9 1.0 CG A:GLU105 4.5 54.3 1.0 CD2 A:PHE49 4.5 49.4 1.0 CB A:ASP9 4.6 55.4 1.0 CB A:PHE49 4.6 47.3 1.0 CD1 A:PHE49 4.7 48.9 1.0 CG A:ASP261 4.7 53.1 1.0 OD2 A:ASP261 4.8 56.0 1.0 NE2 A:HIS192 4.9 37.1 1.0 CE2 A:PHE49 4.9 48.4 1.0 OE1 A:GLU105 5.0 71.7 1.0

Zinc binding site 3 out of 4 in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:0.6 occ:1.00 O B:HOH431 2.7 47.0 1.0 O B:HOH420 2.9 46.2 1.0 ZN B:ZN310 3.1 0.2 1.0 O B:HOH494 3.2 67.3 1.0 NE2 B:HIS172 3.4 40.2 1.0 OE2 B:GLU105 3.4 64.2 1.0 NE2 B:HIS192 3.5 24.9 1.0 CE1 B:HIS172 3.7 38.6 1.0 NE1 B:TRP132 3.8 35.6 1.0 OD2 B:ASP261 3.9 41.4 1.0 OD1 B:ASP261 4.0 42.4 1.0 CD2 B:HIS192 4.1 24.7 1.0 CD1 B:TRP132 4.3 35.6 1.0 CG B:ASP261 4.3 35.9 1.0 O B:HOH489 4.5 39.5 1.0 NE2 B:HIS7 4.6 38.0 1.0 CE1 B:HIS192 4.6 28.0 1.0 CD B:GLU105 4.6 54.3 1.0 CD2 B:HIS172 4.6 32.7 1.0 ND1 B:HIS172 4.9 36.7 1.0 CE2 B:TRP132 4.9 37.5 1.0

Zinc binding site 4 out of 4 in the Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn310 b:0.2 occ:1.00 O B:HOH431 2.5 47.0 1.0 OD1 B:ASP9 3.0 41.1 1.0 ZN B:ZN309 3.1 0.6 1.0 OD2 B:ASP9 3.2 54.3 1.0 O B:HOH420 3.4 46.2 1.0 NE2 B:HIS7 3.4 38.0 1.0 CG B:ASP9 3.5 43.8 1.0 OE2 B:GLU105 3.6 64.2 1.0 CG B:GLU105 3.9 36.6 1.0 CG B:PHE49 4.0 28.3 1.0 CD B:GLU105 4.0 54.3 1.0 CD2 B:PHE49 4.2 31.6 1.0 CB B:PHE49 4.2 26.2 1.0 CE1 B:HIS7 4.3 36.7 1.0 OD1 B:ASP261 4.3 42.4 1.0 CD1 B:PHE49 4.3 26.6 1.0 CD2 B:HIS7 4.4 33.5 1.0 CB B:GLU105 4.6 25.6 1.0 CE2 B:PHE49 4.7 37.7 1.0 CE1 B:PHE49 4.8 29.9 1.0 CB B:ALA47 4.9 24.9 1.0 NE2 B:HIS192 4.9 24.9 1.0 CB B:ASP9 4.9 35.5 1.0 CZ B:PHE49 5.0 33.5 1.0

S.M.Anderson, Z.Wawrzak, O.Onopriyenko, J.Hasseman, A.Edwards, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of LMO2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase To Be Published.