Zinc in PDB 8ewo: Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa

The structure of Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa, PDB code: 8ewo was solved by P.J.Stogios, T.Skarina, M.Endres, A.Savchenko, A.Joachimiak, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.71 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.723, 76.608, 75.43, 90, 94.63, 90
R / Rfree (%)	17.9 / 21.9

The structure of Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa (pdb code 8ewo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa, PDB code: 8ewo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


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 Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.3 occ:0.76 OD2 A:ASP132 2.2 27.8 1.0 NE2 A:HIS56 2.2 27.7 1.0 ND1 A:HIS58 2.3 29.9 1.0 NE2 A:HIS112 2.3 29.3 1.0 ZN A:ZN303 3.0 26.3 0.7 CE1 A:HIS56 3.2 21.8 1.0 CD2 A:HIS112 3.2 28.4 1.0 CD2 A:HIS56 3.2 27.8 1.0 CG A:ASP132 3.2 27.4 1.0 CE1 A:HIS58 3.2 31.1 1.0 CG A:HIS58 3.2 26.3 1.0 CE1 A:HIS112 3.3 29.7 1.0 CB A:HIS58 3.5 26.9 1.0 NE2 A:HIS61 3.7 27.7 1.0 CB A:ASP132 3.7 24.2 1.0 CD2 A:HIS61 4.1 28.4 1.0 OD1 A:ASP132 4.3 28.4 1.0 ND1 A:HIS56 4.3 26.4 1.0 CG A:HIS112 4.3 29.9 1.0 CG A:HIS56 4.3 29.1 1.0 NE2 A:HIS58 4.3 31.9 1.0 ND1 A:HIS112 4.3 31.6 1.0 CD2 A:HIS58 4.3 27.0 1.0 OD1 A:ASP60 4.5 32.8 1.0 CE1 A:HIS61 4.7 25.6 1.0 OD2 A:ASP60 4.7 27.9 1.0 CA A:HIS58 5.0 29.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


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 Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:26.3 occ:0.73 OD2 A:ASP132 2.1 27.8 1.0 OD2 A:ASP60 2.2 27.9 1.0 NE2 A:HIS61 2.3 27.7 1.0 NE2 A:HIS170 2.3 24.8 1.0 ZN A:ZN302 3.0 30.3 0.8 CG A:ASP132 3.0 27.4 1.0 CG A:ASP60 3.2 31.6 1.0 CD2 A:HIS61 3.2 28.4 1.0 CE1 A:HIS170 3.2 26.8 1.0 OD1 A:ASP132 3.2 28.4 1.0 CE1 A:HIS61 3.3 25.6 1.0 CD2 A:HIS170 3.3 25.7 1.0 OD1 A:ASP60 3.4 32.8 1.0 NE2 A:HIS56 4.1 27.7 1.0 CE1 A:HIS56 4.3 21.8 1.0 ND1 A:HIS170 4.4 27.5 1.0 CG A:HIS61 4.4 29.1 1.0 ND1 A:HIS61 4.4 24.2 1.0 CB A:ASP132 4.4 24.2 1.0 CG A:HIS170 4.5 28.8 1.0 CB A:ASP60 4.6 28.9 1.0 OD1 A:ASN13 4.6 30.7 1.0 ND1 A:HIS58 4.8 29.9 1.0 CB A:HIS58 4.9 26.9 1.0 NE2 A:HIS112 4.9 29.3 1.0 CG2 A:THR169 5.0 26.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


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 Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:27.9 occ:0.87 OD2 B:ASP132 2.1 25.3 1.0 ND1 B:HIS58 2.3 26.2 1.0 NE2 B:HIS112 2.3 24.0 1.0 NE2 B:HIS56 2.3 26.6 1.0 CD2 B:HIS112 3.0 26.8 1.0 ZN B:ZN302 3.1 27.6 0.9 CG B:ASP132 3.2 26.1 1.0 CE1 B:HIS56 3.2 25.4 1.0 CD2 B:HIS56 3.2 26.9 1.0 CE1 B:HIS58 3.3 27.1 1.0 CG B:HIS58 3.3 25.3 1.0 CE1 B:HIS112 3.4 24.4 1.0 CB B:HIS58 3.5 24.6 1.0 CB B:ASP132 3.7 26.0 1.0 NE2 B:HIS61 3.9 24.3 1.0 CD2 B:HIS61 4.2 25.0 1.0 OD1 B:ASP132 4.2 26.4 1.0 CG B:HIS112 4.2 25.4 1.0 ND1 B:HIS56 4.3 29.0 1.0 CG B:HIS56 4.3 29.8 1.0 ND1 B:HIS112 4.3 23.8 1.0 NE2 B:HIS58 4.4 24.1 1.0 CD2 B:HIS58 4.4 24.9 1.0 OD1 B:ASP60 4.5 27.1 1.0 OD2 B:ASP60 4.6 28.5 1.0 CE1 B:HIS61 5.0 27.1 1.0 CA B:HIS58 5.0 25.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


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 Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.6 occ:0.87 OD2 B:ASP60 2.1 28.5 1.0 OD2 B:ASP132 2.2 25.3 1.0 NE2 B:HIS61 2.3 24.3 1.0 NE2 B:HIS170 2.3 26.7 1.0 CG B:ASP132 3.0 26.1 1.0 CD2 B:HIS61 3.1 25.0 1.0 OD1 B:ASP132 3.1 26.4 1.0 ZN B:ZN301 3.1 27.9 0.9 CG B:ASP60 3.2 25.8 1.0 CD2 B:HIS170 3.2 27.8 1.0 CE1 B:HIS170 3.3 27.8 1.0 CE1 B:HIS61 3.4 27.1 1.0 OD1 B:ASP60 3.5 27.1 1.0 NE2 B:HIS56 4.1 26.6 1.0 CE1 B:HIS56 4.2 25.4 1.0 CG B:HIS61 4.3 27.1 1.0 ND2 B:ASN13 4.4 22.6 1.0 CG B:HIS170 4.4 26.9 1.0 ND1 B:HIS170 4.4 23.7 1.0 ND1 B:HIS61 4.4 28.4 1.0 CB B:ASP132 4.4 26.0 1.0 CB B:ASP60 4.5 24.9 1.0 NE2 B:HIS112 5.0 24.0 1.0 CB B:HIS58 5.0 24.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:29.7 occ:0.86 OE2 B:GLU124 2.2 34.0 1.0 OD2 C:ASP132 2.3 26.9 1.0 ND1 C:HIS58 2.3 27.5 1.0 NE2 C:HIS56 2.3 32.3 1.0 NE2 C:HIS112 2.3 32.3 1.0 CD B:GLU124 3.1 30.4 1.0 CD2 C:HIS112 3.1 27.8 1.0 CE1 C:HIS56 3.1 27.6 1.0 CE1 C:HIS58 3.1 28.8 1.0 ZN C:ZN302 3.2 27.0 0.8 CE1 C:HIS112 3.3 29.6 1.0 CG C:ASP132 3.3 27.8 1.0 CD2 C:HIS56 3.3 30.9 1.0 OE1 B:GLU124 3.3 37.5 1.0 CG C:HIS58 3.4 25.9 1.0 CB C:ASP132 3.7 26.1 1.0 CB C:HIS58 3.8 24.9 1.0 NE2 C:HIS61 3.9 27.7 1.0 CG C:HIS112 4.2 27.6 1.0 ND1 C:HIS56 4.2 27.5 1.0 CD2 C:HIS61 4.3 28.8 1.0 ND1 C:HIS112 4.3 29.7 1.0 NE2 C:HIS58 4.3 24.6 1.0 O C:HOH487 4.3 25.0 1.0 CG C:HIS56 4.4 30.7 1.0 CG B:GLU124 4.4 33.2 1.0 OD1 C:ASP132 4.4 29.1 1.0 CD2 C:HIS58 4.4 25.9 1.0 OD2 C:ASP60 4.5 26.9 1.0 OD1 C:ASP60 4.6 28.8 1.0 CE1 C:HIS61 4.8 27.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Putative Glyoxylase II From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:27.0 occ:0.81 OE2 B:GLU124 2.0 34.0 1.0 OD2 C:ASP132 2.1 26.9 1.0 OD2 C:ASP60 2.1 26.9 1.0 NE2 C:HIS61 2.3 27.7 1.0 NE2 C:HIS170 2.3 26.1 1.0 CD B:GLU124 2.9 30.4 1.0 CD2 C:HIS170 2.9 25.9 1.0 CG C:ASP132 3.0 27.8 1.0 ZN C:ZN301 3.2 29.7 0.9 CG B:GLU124 3.2 33.2 1.0 CD2 C:HIS61 3.2 28.8 1.0 CG C:ASP60 3.2 25.6 1.0 OD1 C:ASP132 3.3 29.1 1.0 CE1 C:HIS61 3.3 27.0 1.0 CE1 C:HIS170 3.5 31.2 1.0 OD1 C:ASP60 3.7 28.8 1.0 O C:HOH487 3.9 25.0 1.0 OE1 B:GLU124 4.1 37.5 1.0 CE1 C:HIS56 4.2 27.6 1.0 CG C:HIS170 4.2 27.1 1.0 NE2 C:HIS56 4.2 32.3 1.0 ND2 C:ASN13 4.4 24.7 1.0 CG C:HIS61 4.4 27.2 1.0 CB C:ASP132 4.4 26.1 1.0 ND1 C:HIS61 4.4 26.2 1.0 ND1 C:HIS170 4.4 26.9 1.0 CB C:ASP60 4.5 24.2 1.0 CB B:GLU124 4.6 27.7 1.0 ND1 C:HIS58 4.9 27.5 1.0 CG2 C:THR169 5.0 25.5 1.0

P.J.Stogios, P.J.Stogios, T.Skarina, M.Endres, A.Savchenko, A.Joachimiak, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). N/A N/A.