Cobalt in PDB 2dxl: 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: 2dxl 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 / 3.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	164.462, 164.462, 164.462, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.4

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

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:77.9 occ:1.00 OD1 A:ASP8 2.0 73.1 1.0 NE2 A:HIS197 2.2 79.3 1.0 NE2 A:HIS10 2.3 75.9 1.0 OD2 A:ASP50 2.4 74.8 1.0 CG A:ASP8 3.1 73.5 1.0 CE1 A:HIS10 3.1 74.4 1.0 CE1 A:HIS197 3.1 79.3 1.0 CD2 A:HIS197 3.1 78.6 1.0 CD2 A:HIS10 3.4 75.5 1.0 CG A:ASP50 3.5 73.7 1.0 CO A:CO1002 3.6 75.2 0.8 CB A:ASP8 3.9 73.1 1.0 CB A:ASP50 3.9 74.3 1.0 OD2 A:ASP8 4.0 71.8 1.0 O A:HIS195 4.3 79.8 1.0 ND1 A:HIS197 4.3 78.6 1.0 CG A:HIS197 4.3 78.2 1.0 ND1 A:HIS10 4.3 74.0 1.0 ND1 A:HIS81 4.4 72.7 1.0 CG A:HIS10 4.5 73.9 1.0 CE1 A:HIS156 4.5 72.4 1.0 OD1 A:ASP50 4.6 71.8 1.0 CE1 A:HIS81 4.6 72.3 1.0 CA A:HIS195 4.7 79.6 1.0 NE2 A:HIS156 4.7 71.5 1.0 CA A:ASP8 4.7 73.2 1.0 C A:HIS195 4.8 79.5 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:75.2 occ:0.80 OD1 A:ASN80 2.2 76.3 1.0 NE2 A:HIS156 2.2 71.5 1.0 ND1 A:HIS195 2.4 82.3 1.0 OD2 A:ASP50 2.4 74.8 1.0 CE1 A:HIS195 3.0 82.5 1.0 CE1 A:HIS156 3.1 72.4 1.0 CG A:ASP50 3.2 73.7 1.0 OD1 A:ASP50 3.2 71.8 1.0 CG A:ASN80 3.3 73.5 1.0 CD2 A:HIS156 3.3 72.2 1.0 CG A:HIS195 3.5 81.2 1.0 CO A:CO1001 3.6 77.9 1.0 CA A:HIS195 3.8 79.6 1.0 ND2 A:ASN80 3.8 75.3 1.0 ND1 A:HIS81 4.0 72.7 1.0 CB A:HIS195 4.0 79.7 1.0 OD1 A:ASP8 4.2 73.1 1.0 NE2 A:HIS195 4.2 82.3 1.0 ND1 A:HIS156 4.3 71.8 1.0 CG A:HIS156 4.4 72.2 1.0 N A:ASN80 4.4 70.5 1.0 O A:HIS195 4.4 79.8 1.0 CD2 A:HIS195 4.5 82.3 1.0 CE1 A:HIS81 4.5 72.3 1.0 CB A:ASN80 4.5 71.2 1.0 N A:HIS195 4.6 79.5 1.0 CB A:ASP50 4.6 74.3 1.0 C A:HIS195 4.6 79.5 1.0 N A:HIS81 5.0 70.6 1.0 CA A:ASN80 5.0 70.9 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1003 b:74.1 occ:1.00 NE2 B:HIS197 2.1 78.5 1.0 OD1 B:ASP8 2.2 78.1 1.0 NE2 B:HIS10 2.3 75.2 1.0 OD2 B:ASP50 2.6 78.0 1.0 CE1 B:HIS10 3.0 74.2 1.0 CD2 B:HIS197 3.1 77.6 1.0 CG B:ASP8 3.1 76.6 1.0 CE1 B:HIS197 3.2 78.7 1.0 CD2 B:HIS10 3.4 75.0 1.0 CO B:CO1004 3.5 72.1 0.8 CG B:ASP50 3.5 76.4 1.0 CB B:ASP50 3.6 76.0 1.0 CB B:ASP8 3.7 75.0 1.0 OD2 B:ASP8 4.1 75.3 1.0 O B:HIS195 4.2 78.7 1.0 CG B:HIS197 4.2 76.9 1.0 ND1 B:HIS10 4.2 73.1 1.0 ND1 B:HIS197 4.3 77.5 1.0 CE1 B:HIS156 4.4 71.7 1.0 CG B:HIS10 4.4 73.3 1.0 CA B:HIS195 4.5 78.0 1.0 ND1 B:HIS81 4.6 74.0 1.0 CA B:ASP8 4.6 74.9 1.0 NE2 B:HIS156 4.6 70.8 1.0 C B:HIS195 4.7 78.1 1.0 OD1 B:ASP50 4.7 75.7 1.0 CE1 B:HIS81 4.8 74.8 1.0 N B:HIS195 4.8 77.6 1.0 CA B:ASP50 4.9 75.8 1.0 N B:ASP50 4.9 76.5 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Glycerophosphodiesterase From Enterobacter Aerogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1004 b:72.1 occ:0.80 OD1 B:ASN80 2.0 73.6 1.0 OD2 B:ASP50 2.1 78.0 1.0 NE2 B:HIS156 2.3 70.8 1.0 ND1 B:HIS195 2.3 81.6 1.0 CG B:ASN80 3.0 72.2 1.0 CG B:ASP50 3.1 76.4 1.0 CE1 B:HIS156 3.1 71.7 1.0 CE1 B:HIS195 3.2 81.8 1.0 ND2 B:ASN80 3.2 72.3 1.0 CG B:HIS195 3.4 79.8 1.0 CD2 B:HIS156 3.4 71.6 1.0 CO B:CO1003 3.5 74.1 1.0 OD1 B:ASP50 3.5 75.7 1.0 CA B:HIS195 3.5 78.0 1.0 CB B:HIS195 3.7 78.2 1.0 OD1 B:ASP8 4.0 78.1 1.0 ND1 B:HIS81 4.1 74.0 1.0 O B:HIS195 4.2 78.7 1.0 ND1 B:HIS156 4.3 71.9 1.0 NE2 B:HIS195 4.3 81.5 1.0 C B:HIS195 4.4 78.1 1.0 CB B:ASN80 4.4 70.4 1.0 CB B:ASP50 4.4 76.0 1.0 N B:HIS195 4.4 77.6 1.0 CD2 B:HIS195 4.4 81.3 1.0 CG B:HIS156 4.5 72.2 1.0 CE1 B:HIS81 4.6 74.8 1.0 N B:ASN80 4.6 69.9 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