Zinc in PDB 6rz0: Crystal Structure of Escherichia Coli Glyoxalase II

All present enzymatic activity of Crystal Structure of Escherichia Coli Glyoxalase II:
3.1.2.6;

The structure of Crystal Structure of Escherichia Coli Glyoxalase II, PDB code: 6rz0 was solved by A.Skorupskaite, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.382, 63.383, 72.726, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 12.8

The structure of Crystal Structure of Escherichia Coli Glyoxalase II also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Glyoxalase II (pdb code 6rz0). 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 Escherichia Coli Glyoxalase II, PDB code: 6rz0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Glyoxalase II


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 Escherichia Coli Glyoxalase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:6.4 occ:1.00 NE2 A:HIS56 2.0 6.5 1.0 O A:HOH713 2.1 8.8 1.0 CL A:CL306 2.2 6.2 1.0 CE1 A:HIS56 2.9 7.2 1.0 HE1 A:HIS56 3.1 8.7 1.0 CD2 A:HIS56 3.1 6.4 1.0 HD2 A:HIS56 3.3 7.7 1.0 ND1 A:HIS56 4.1 7.0 1.0 CG A:HIS56 4.2 5.9 1.0 HD1 A:HIS56 4.9 8.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Glyoxalase II


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 Escherichia Coli Glyoxalase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:5.0 occ:1.00 O A:HOH430 1.9 5.3 1.0 NE2 A:HIS53 2.1 4.6 1.0 NE2 A:HIS110 2.1 5.0 1.0 ND1 A:HIS55 2.2 4.4 1.0 OD2 A:ASP127 2.4 5.5 1.0 CD2 A:HIS110 3.0 5.0 1.0 CD2 A:HIS53 3.0 4.3 1.0 CE1 A:HIS55 3.1 4.9 1.0 CE1 A:HIS53 3.1 4.5 1.0 CE1 A:HIS110 3.1 4.8 1.0 HB2 A:HIS55 3.1 6.0 1.0 HD2 A:HIS110 3.2 6.0 1.0 HD2 A:HIS53 3.2 5.1 1.0 HE1 A:HIS55 3.2 5.9 1.0 CG A:HIS55 3.2 4.7 1.0 ZN A:ZN304 3.2 5.1 1.0 HE1 A:HIS53 3.3 5.5 1.0 HE1 A:HIS110 3.3 5.8 1.0 CG A:ASP127 3.4 5.1 1.0 HB2 A:ASP127 3.5 6.2 1.0 CB A:HIS55 3.6 5.0 1.0 NE2 A:HIS58 3.8 5.2 1.0 HB3 A:HIS55 3.8 6.0 1.0 HD2 A:HIS58 3.9 5.2 1.0 CB A:ASP127 3.9 5.2 1.0 O A:HOH710 3.9 15.5 1.0 HB3 A:ASP127 4.0 6.2 1.0 CD2 A:HIS58 4.0 4.3 1.0 ND1 A:HIS53 4.2 4.5 1.0 CG A:HIS110 4.2 5.0 1.0 CG A:HIS53 4.2 4.5 1.0 ND1 A:HIS110 4.2 5.2 1.0 NE2 A:HIS55 4.2 5.4 1.0 CD2 A:HIS55 4.3 5.1 1.0 OD1 A:ASP57 4.4 5.2 1.0 OD1 A:ASP127 4.4 5.8 1.0 CE1 A:HIS58 4.7 5.2 1.0 H A:HIS55 4.7 5.8 1.0 HG23 A:THR111 4.7 6.5 1.0 OD2 A:ASP57 4.8 5.5 1.0 HD1 A:HIS53 5.0 5.3 1.0 HE2 A:HIS55 5.0 6.5 1.0 HD2 A:PHE138 5.0 8.2 1.0 HD1 A:HIS110 5.0 6.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Glyoxalase II


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 Escherichia Coli Glyoxalase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:5.1 occ:1.00 O A:HOH430 2.0 5.3 1.0 NE2 A:HIS165 2.0 5.4 1.0 NE2 A:HIS58 2.0 5.2 1.0 OD2 A:ASP127 2.1 5.5 1.0 OD2 A:ASP57 2.3 5.5 1.0 CG A:ASP127 3.0 5.1 1.0 CD2 A:HIS58 3.0 4.3 1.0 CE1 A:HIS165 3.0 5.5 1.0 CD2 A:HIS165 3.1 5.2 1.0 CE1 A:HIS58 3.1 5.2 1.0 HD2 A:HIS58 3.1 5.2 1.0 OD1 A:ASP127 3.2 5.8 1.0 HE1 A:HIS165 3.2 6.7 1.0 ZN A:ZN303 3.2 5.0 1.0 HD2 A:HIS165 3.2 6.3 1.0 CG A:ASP57 3.3 4.9 1.0 HE1 A:HIS58 3.3 6.2 1.0 O A:HOH710 3.5 15.5 1.0 HD21 A:ASN12 3.5 7.2 1.0 OD1 A:ASP57 3.5 5.2 1.0 HE1 A:HIS53 3.7 5.5 1.0 ND1 A:HIS165 4.1 5.5 1.0 NE2 A:HIS53 4.2 4.6 1.0 CG A:HIS58 4.2 5.0 1.0 ND1 A:HIS58 4.2 5.1 1.0 CG A:HIS165 4.2 5.3 1.0 ND2 A:ASN12 4.2 6.0 1.0 CE1 A:HIS53 4.3 4.5 1.0 HB3 A:ALA164 4.3 7.3 1.0 CB A:ASP127 4.4 5.2 1.0 HB2 A:HIS55 4.5 6.0 1.0 HD22 A:ASN12 4.5 7.2 1.0 CB A:ASP57 4.6 5.5 1.0 HB2 A:ASP57 4.7 6.7 1.0 HB2 A:ASP127 4.7 6.2 1.0 HB3 A:ASP127 4.7 6.2 1.0 NE2 A:HIS110 4.7 5.0 1.0 HB1 A:ALA164 4.7 7.3 1.0 HB3 A:HIS55 4.9 6.0 1.0 HZ A:PHE130 4.9 9.1 1.0 HD1 A:HIS165 4.9 6.6 1.0 HD1 A:HIS58 5.0 6.1 1.0 ND1 A:HIS55 5.0 4.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Glyoxalase II


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 Escherichia Coli Glyoxalase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:79.2 occ:1.00 NE2 A:HIS100 2.3 15.4 1.0 CE1 A:HIS100 3.2 13.6 1.0 HE1 A:HIS100 3.3 16.3 1.0 CD2 A:HIS100 3.4 13.1 1.0 O A:HOH614 3.4 27.8 1.0 HD2 A:HIS100 3.5 15.7 1.0 H3 A:MET1 4.2 18.6 1.0 HE2 A:MET1 4.3 17.6 1.0 ND1 A:HIS100 4.4 11.6 1.0 H1 A:MET1 4.5 18.6 1.0 CG A:HIS100 4.5 10.6 1.0 HG3 A:MET1 4.5 16.5 1.0 O A:HOH433 4.5 12.6 0.5 N A:MET1 4.8 15.5 1.0 O A:HOH433 4.8 15.3 0.5

A.Skorupskaite, M.A.Mcdonough, J.Brem, C.J.Schofield. Crystal Structure of Escherichia Coli Glyoxalase II To Be Published.