Zinc in PDB 2dxn: Glycerophosphodiesterase From Enterobacter Aerogenes

All present enzymatic activity of Glycerophosphodiesterase From Enterobacter Aerogenes:
3.1.4.46;

The structure of Glycerophosphodiesterase From Enterobacter Aerogenes, PDB code: 2dxn was solved by C.J.Jackson, P.D.Carr, D.L.Ollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.92
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	164.274, 164.274, 164.274, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.5

The binding sites of Zinc atom in the Glycerophosphodiesterase From Enterobacter Aerogenes (pdb code 2dxn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Glycerophosphodiesterase From Enterobacter Aerogenes, PDB code: 2dxn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Glycerophosphodiesterase From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:82.0 occ:0.75 OD1 A:ASP8 2.0 76.8 1.0 NE2 A:HIS197 2.2 78.4 1.0 OD2 A:ASP50 2.3 79.1 1.0 NE2 A:HIS10 2.3 79.0 1.0 CE1 A:HIS197 3.1 78.7 1.0 CD2 A:HIS197 3.2 78.3 1.0 CG A:ASP8 3.2 76.0 1.0 CE1 A:HIS10 3.2 78.0 1.0 CD2 A:HIS10 3.4 77.9 1.0 CG A:ASP50 3.5 77.7 1.0 ZN A:ZN1002 3.6 76.3 0.6 CB A:ASP8 3.9 75.1 1.0 CB A:ASP50 4.1 78.1 1.0 OD2 A:ASP8 4.1 75.0 1.0 O A:HIS195 4.2 82.3 1.0 ND1 A:HIS197 4.2 77.8 1.0 CG A:HIS197 4.3 77.9 1.0 ND1 A:HIS10 4.4 76.4 1.0 OD1 A:ASP50 4.5 75.5 1.0 CG A:HIS10 4.5 76.3 1.0 CD2 A:HIS81 4.5 74.9 1.0 CE1 A:HIS156 4.5 78.1 1.0 CA A:HIS195 4.7 82.5 1.0 NE2 A:HIS81 4.7 75.3 1.0 NE2 A:HIS156 4.8 77.4 1.0 CA A:ASP8 4.8 75.2 1.0 C A:HIS195 4.8 82.0 1.0

Zinc binding site 2 out of 4 in the Glycerophosphodiesterase From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:76.3 occ:0.60 OD1 A:ASN80 2.3 80.7 1.0 NE2 A:HIS156 2.3 77.4 1.0 ND1 A:HIS195 2.3 85.6 1.0 OD2 A:ASP50 2.5 79.1 1.0 CE1 A:HIS195 3.0 86.1 1.0 OD1 A:ASP50 3.0 75.5 1.0 CE1 A:HIS156 3.2 78.1 1.0 CG A:ASP50 3.2 77.7 1.0 CG A:ASN80 3.2 77.0 1.0 CD2 A:HIS156 3.4 77.7 1.0 CG A:HIS195 3.5 84.4 1.0 ND2 A:ASN80 3.5 78.1 1.0 ZN A:ZN1001 3.6 82.0 0.8 CA A:HIS195 3.7 82.5 1.0 CD2 A:HIS81 4.0 74.9 1.0 CB A:HIS195 4.0 82.8 1.0 NE2 A:HIS195 4.2 86.0 1.0 OD1 A:ASP8 4.2 76.8 1.0 O A:HIS195 4.3 82.3 1.0 ND1 A:HIS156 4.3 77.3 1.0 CD2 A:HIS195 4.4 85.7 1.0 CG A:HIS156 4.5 77.9 1.0 N A:ASN80 4.5 75.0 1.0 N A:HIS195 4.5 82.5 1.0 C A:HIS195 4.5 82.0 1.0 CB A:ASN80 4.6 75.1 1.0 NE2 A:HIS81 4.6 75.3 1.0 CB A:ASP50 4.6 78.1 1.0

Zinc binding site 3 out of 4 in the Glycerophosphodiesterase From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:79.3 occ:0.75 NE2 B:HIS197 2.0 78.3 1.0 NE2 B:HIS10 2.3 75.5 1.0 OD1 B:ASP8 2.3 81.1 1.0 OD2 B:ASP50 2.4 80.3 1.0 CE1 B:HIS197 3.0 78.7 1.0 CD2 B:HIS197 3.0 78.0 1.0 CE1 B:HIS10 3.1 74.2 1.0 CG B:ASP8 3.2 78.2 1.0 CD2 B:HIS10 3.3 75.2 1.0 CG B:ASP50 3.5 79.1 1.0 ZN B:ZN1004 3.5 73.3 0.6 CB B:ASP8 3.7 76.2 1.0 CB B:ASP50 3.9 78.8 1.0 ND1 B:HIS197 4.1 78.2 1.0 CG B:HIS197 4.2 77.4 1.0 OD2 B:ASP8 4.3 78.2 1.0 ND1 B:HIS10 4.3 73.4 1.0 O B:HIS195 4.3 81.2 1.0 CE1 B:HIS156 4.4 76.7 1.0 CG B:HIS10 4.4 73.3 1.0 CA B:HIS195 4.5 81.2 1.0 CA B:ASP8 4.6 76.0 1.0 CD2 B:HIS81 4.6 74.3 1.0 OD1 B:ASP50 4.6 78.2 1.0 NE2 B:HIS156 4.7 76.1 1.0 C B:HIS195 4.8 80.7 1.0 N B:HIS195 4.9 81.0 1.0 NE2 B:HIS81 4.9 75.4 1.0 N B:ASP50 4.9 79.2 1.0

Zinc binding site 4 out of 4 in the Glycerophosphodiesterase From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:73.3 occ:0.60 OD1 B:ASN80 2.1 77.9 1.0 NE2 B:HIS156 2.3 76.1 1.0 OD2 B:ASP50 2.3 80.3 1.0 ND1 B:HIS195 2.4 85.7 1.0 CG B:ASN80 3.0 75.3 1.0 CE1 B:HIS156 3.1 76.7 1.0 CG B:ASP50 3.2 79.1 1.0 CE1 B:HIS195 3.2 86.5 1.0 OD1 B:ASP50 3.3 78.2 1.0 ND2 B:ASN80 3.3 76.6 1.0 CD2 B:HIS156 3.4 76.5 1.0 CG B:HIS195 3.4 83.6 1.0 ZN B:ZN1003 3.5 79.3 0.8 CA B:HIS195 3.6 81.2 1.0 CB B:HIS195 3.8 81.5 1.0 OD1 B:ASP8 4.0 81.1 1.0 CD2 B:HIS81 4.1 74.3 1.0 O B:HIS195 4.3 81.2 1.0 ND1 B:HIS156 4.3 76.4 1.0 NE2 B:HIS195 4.4 86.3 1.0 CG B:HIS156 4.4 77.2 1.0 C B:HIS195 4.5 80.7 1.0 CB B:ASN80 4.5 73.0 1.0 CD2 B:HIS195 4.5 85.8 1.0 N B:HIS195 4.5 81.0 1.0 N B:ASN80 4.6 72.7 1.0 CB B:ASP50 4.6 78.8 1.0 NE2 B:HIS81 4.7 75.4 1.0

C.J.Jackson, P.D.Carr, J.W.Liu, S.J.Watt, J.L.Beck, D.L.Ollis. The Structure and Function of A Novel Glycerophosphodiesterase From Enterobacter Aerogenes J.Mol.Biol. V. 367 1047 2007.
ISSN: ISSN 0022-2836
PubMed: 17306828
DOI: 10.1016/J.JMB.2007.01.032