Zinc in PDB 6s0i: Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site

All present enzymatic activity of Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site:
3.1.2.6;

The structure of Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site, PDB code: 6s0i 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)	29.40 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.053, 43.655, 159.067, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.7

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site (pdb code 6s0i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site, PDB code: 6s0i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site


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 with L-Tartrate in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:19.0 occ:0.80 O A:HOH564 1.9 19.0 0.5 OD2 A:ASP127 2.0 24.4 1.0 NE2 A:HIS58 2.0 17.2 1.0 NE2 A:HIS165 2.1 17.6 1.0 O41 A:TLA403 2.1 18.4 0.5 HB A:TLA403 2.3 22.9 0.5 O3 A:TLA403 2.3 19.1 0.5 OD2 A:ASP57 2.8 30.9 0.5 CG A:ASP127 2.9 20.8 1.0 C4 A:TLA403 2.9 21.8 0.5 ZN A:ZN402 3.0 28.8 0.5 CE1 A:HIS58 3.0 21.2 1.0 CD2 A:HIS165 3.0 15.9 1.0 CD2 A:HIS58 3.0 21.8 1.0 CE1 A:HIS165 3.1 18.6 1.0 C3 A:TLA403 3.2 21.2 0.5 HD2 A:HIS165 3.2 19.1 1.0 OD1 A:ASP127 3.2 27.3 1.0 HE1 A:HIS58 3.2 25.4 1.0 HD2 A:HIS58 3.2 26.1 1.0 HE1 A:HIS165 3.3 22.3 1.0 ZN A:ZN402 3.6 20.6 0.5 HD21 A:ASN12 3.6 29.7 1.0 CG A:ASP57 3.8 27.2 0.5 H3 A:TLA403 3.8 25.4 0.5 O A:HOH514 3.9 23.9 1.0 HE1 A:HIS53 4.0 24.6 1.0 OD1 A:ASP57 4.0 31.7 0.5 O2 A:TLA403 4.0 18.1 0.5 O4 A:TLA403 4.1 20.4 0.5 ND1 A:HIS58 4.1 22.1 1.0 CG A:HIS58 4.2 20.3 1.0 ND1 A:HIS165 4.2 17.8 1.0 CG A:HIS165 4.2 17.6 1.0 C2 A:TLA403 4.2 18.2 0.5 NE2 A:HIS53 4.2 19.2 1.0 CB A:ASP127 4.3 16.7 1.0 ND2 A:ASN12 4.3 24.7 1.0 HB2 A:ASP57 4.4 24.2 0.5 HB3 A:ALA164 4.4 24.4 1.0 CE1 A:HIS53 4.5 20.5 1.0 HB3 A:ASP127 4.5 20.1 1.0 HB2 A:ASP127 4.5 20.1 1.0 NE2 A:HIS110 4.7 17.9 1.0 HD22 A:ASN12 4.7 29.7 1.0 HB2 A:HIS55 4.7 21.5 1.0 HA A:TLA403 4.8 21.7 0.5 HB1 A:ALA164 4.8 24.4 1.0 HD1 A:HIS58 4.9 26.5 1.0 H2 A:TLA403 4.9 21.8 0.5 HB3 A:HIS55 4.9 21.5 1.0 HD1 A:HIS165 5.0 21.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site


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 with L-Tartrate in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.8 occ:0.50 ZN A:ZN402 0.0 28.8 0.5 ZN A:ZN402 1.7 20.6 0.5 O A:HOH564 1.8 19.0 0.5 NE2 A:HIS110 2.3 17.9 1.0 OD2 A:ASP127 2.5 24.4 1.0 ND1 A:HIS55 2.5 22.0 1.0 NE2 A:HIS53 2.5 19.2 1.0 HD2 A:HIS110 2.7 20.3 1.0 CD2 A:HIS110 2.8 16.9 1.0 ZN A:ZN401 3.0 19.0 0.8 O3 A:TLA403 3.0 19.1 0.5 HB2 A:HIS55 3.1 21.5 1.0 CD2 A:HIS53 3.4 18.4 1.0 CG A:HIS55 3.4 19.8 1.0 O2 A:TLA403 3.4 18.1 0.5 CG A:ASP127 3.4 20.8 1.0 CE1 A:HIS55 3.5 20.9 1.0 HB A:TLA403 3.5 22.9 0.5 CE1 A:HIS110 3.5 19.9 1.0 CE1 A:HIS53 3.5 20.5 1.0 HD2 A:HIS53 3.5 22.1 1.0 HB2 A:ASP127 3.6 20.1 1.0 HE1 A:HIS55 3.6 25.0 1.0 CB A:HIS55 3.6 17.9 1.0 HE1 A:HIS53 3.7 24.6 1.0 NE2 A:HIS58 3.7 17.2 1.0 HB3 A:HIS55 3.7 21.5 1.0 HA A:TLA403 3.8 21.7 0.5 O11 A:TLA403 3.8 22.8 0.5 HE1 A:HIS110 3.9 23.9 1.0 HD2 A:HIS58 3.9 26.1 1.0 CB A:ASP127 3.9 16.7 1.0 CD2 A:HIS58 4.0 21.8 1.0 HB3 A:ASP127 4.0 20.1 1.0 C3 A:TLA403 4.1 21.2 0.5 CG A:HIS110 4.1 15.9 1.0 C2 A:TLA403 4.2 18.2 0.5 O41 A:TLA403 4.2 18.4 0.5 O A:HOH514 4.3 23.9 1.0 ND1 A:HIS110 4.3 18.3 1.0 C1 A:TLA403 4.4 24.6 0.5 OD1 A:ASP127 4.5 27.3 1.0 CD2 A:HIS55 4.5 21.3 1.0 NE2 A:HIS55 4.5 21.8 1.0 CE1 A:HIS58 4.6 21.2 1.0 CG A:HIS53 4.6 16.1 1.0 ND1 A:HIS53 4.6 17.8 1.0 C4 A:TLA403 4.6 21.8 0.5 OD1 A:ASP57 4.7 31.7 0.5 OD2 A:ASP57 4.8 30.9 0.5 H3 A:TLA403 4.8 25.4 0.5 HG23 A:THR111 4.9 21.8 1.0 HE1 A:HIS58 4.9 25.4 1.0 H A:HIS55 4.9 22.8 1.0 NE2 A:HIS165 4.9 17.6 1.0 CG A:HIS58 5.0 20.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Escherichia Coli Glyoxalase II with L-Tartrate in the Active Site


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 with L-Tartrate in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.6 occ:0.50 ZN A:ZN402 0.0 20.6 0.5 ZN A:ZN402 1.7 28.8 0.5 O A:HOH564 2.0 19.0 0.5 O2 A:TLA403 2.1 18.1 0.5 ND1 A:HIS55 2.1 22.0 1.0 O11 A:TLA403 2.2 22.8 0.5 HA A:TLA403 2.3 21.7 0.5 O3 A:TLA403 2.4 19.1 0.5 NE2 A:HIS110 2.5 17.9 1.0 C2 A:TLA403 2.7 18.2 0.5 C1 A:TLA403 2.8 24.6 0.5 CE1 A:HIS55 2.9 20.9 1.0 HE1 A:HIS55 3.0 25.0 1.0 C3 A:TLA403 3.1 21.2 0.5 HB A:TLA403 3.1 22.9 0.5 CG A:HIS55 3.3 19.8 1.0 CE1 A:HIS110 3.3 19.9 1.0 HE1 A:HIS110 3.3 23.9 1.0 HB3 A:HIS55 3.5 21.5 1.0 OD2 A:ASP127 3.6 24.4 1.0 ZN A:ZN401 3.6 19.0 0.8 CD2 A:HIS110 3.6 16.9 1.0 H2 A:TLA403 3.6 21.8 0.5 HB2 A:HIS55 3.7 21.5 1.0 CB A:HIS55 3.7 17.9 1.0 HD2 A:HIS110 3.8 20.3 1.0 H3 A:TLA403 3.8 25.4 0.5 C4 A:TLA403 3.9 21.8 0.5 O1 A:TLA403 4.0 21.3 0.5 O A:HOH574 4.0 36.2 1.0 O41 A:TLA403 4.0 18.4 0.5 O A:HOH514 4.0 23.9 1.0 NE2 A:HIS55 4.1 21.8 1.0 NE2 A:HIS53 4.1 19.2 1.0 HE2 A:PHE138 4.1 37.0 1.0 CD2 A:HIS55 4.3 21.3 1.0 OD1 A:ASP57 4.4 31.7 0.5 HD2 A:PHE138 4.4 31.2 1.0 ND1 A:HIS110 4.5 18.3 1.0 HD2 A:HIS53 4.6 22.1 1.0 HD2 A:HIS58 4.6 26.1 1.0 CE2 A:PHE138 4.6 30.8 1.0 CG A:HIS110 4.7 15.9 1.0 CG A:ASP127 4.7 20.8 1.0 CD2 A:HIS53 4.7 18.4 1.0 NE2 A:HIS58 4.8 17.2 1.0 O A:HOH634 4.8 15.3 0.5 CD2 A:PHE138 4.8 26.0 1.0 OD2 A:ASP57 4.8 30.9 0.5 HE2 A:HIS55 4.8 26.2 1.0 CD2 A:HIS58 5.0 21.8 1.0 O4 A:TLA403 5.0 20.4 0.5

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