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Zinc in PDB 1qh5: Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione

Enzymatic activity of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione

All present enzymatic activity of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione:
3.1.2.6;

Protein crystallography data

The structure of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione, PDB code: 1qh5 was solved by A.D.Cameron, M.Ridderstrom, B.Olin, B.Mannervik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.550, 73.800, 164.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.2

Other elements in 1qh5:

The structure of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione also contains other interesting chemical elements:

Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione (pdb code 1qh5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione, PDB code: 1qh5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1qh5

Go back to Zinc Binding Sites List in 1qh5
Zinc binding site 1 out of 4 in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn261

b:17.5
occ:1.00
 O A:HOH464 2.0 25.0 1.0
NE2 A:HIS110 2.1 15.2 1.0
NE2 A:HIS54 2.1 12.8 1.0
ND1 A:HIS56 2.2 16.8 1.0
O A:HOH465 2.5 35.9 1.0
OD2 A:ASP134 2.6 16.6 1.0
CE1 A:HIS56 3.1 17.0 1.0
CD2 A:HIS54 3.1 14.5 1.0
CD2 A:HIS110 3.1 15.0 1.0
CE1 A:HIS110 3.2 15.9 1.0
CE1 A:HIS54 3.2 14.9 1.0
CG A:HIS56 3.3 13.8 1.0
ZN A:ZN262 3.5 16.9 1.0
CG A:ASP134 3.5 14.8 1.0
CB A:HIS56 3.6 14.5 1.0
CB A:ASP134 3.8 13.6 1.0
NE2 A:HIS59 4.1 14.1 1.0
CD2 A:HIS59 4.2 14.3 1.0
SG2 A:GSH463 4.3 31.2 1.0
NE2 A:HIS56 4.3 17.8 1.0
CG A:HIS110 4.3 15.6 1.0
ND1 A:HIS54 4.3 13.7 1.0
CG A:HIS54 4.3 14.5 1.0
ND1 A:HIS110 4.3 15.1 1.0
CD2 A:HIS56 4.4 14.3 1.0
OD1 A:ASP58 4.5 16.1 1.0
OD1 A:ASP134 4.6 16.6 1.0
CB2 A:GSH463 4.6 28.5 1.0
O A:HOH601 4.7 37.8 1.0
OD2 A:ASP58 4.9 17.2 1.0

Zinc binding site 2 out of 4 in 1qh5

Go back to Zinc Binding Sites List in 1qh5
Zinc binding site 2 out of 4 in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn262

b:16.9
occ:1.00
 OD2 A:ASP134 2.1 16.6 1.0
NE2 A:HIS59 2.1 14.1 1.0
NE2 A:HIS173 2.1 17.4 1.0
O A:HOH464 2.1 25.0 1.0
OD2 A:ASP58 2.3 17.2 1.0
SG2 A:GSH463 2.8 31.2 1.0
CG A:ASP134 3.0 14.8 1.0
CD2 A:HIS59 3.0 14.3 1.0
CE1 A:HIS173 3.1 17.8 1.0
CD2 A:HIS173 3.1 17.6 1.0
CE1 A:HIS59 3.2 14.7 1.0
OD1 A:ASP134 3.2 16.6 1.0
CG A:ASP58 3.3 13.5 1.0
ZN A:ZN261 3.5 17.5 1.0
OD1 A:ASP58 3.6 16.1 1.0
CB2 A:GSH463 3.7 28.5 1.0
ND2 A:ASN12 4.1 17.4 1.0
O A:HOH465 4.1 35.9 1.0
ND1 A:HIS59 4.2 14.5 1.0
CG A:HIS59 4.2 15.1 1.0
ND1 A:HIS173 4.3 18.6 1.0
CG A:HIS173 4.3 17.0 1.0
NE2 A:HIS54 4.3 12.8 1.0
CE1 A:HIS54 4.4 14.9 1.0
CB A:ASP134 4.4 13.6 1.0
CB A:ASP58 4.6 16.0 1.0

Zinc binding site 3 out of 4 in 1qh5

Go back to Zinc Binding Sites List in 1qh5
Zinc binding site 3 out of 4 in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn261

b:14.7
occ:1.00
 O B:HOH466 2.0 16.9 1.0
NE2 B:HIS54 2.1 12.3 1.0
NE2 B:HIS110 2.1 12.1 1.0
ND1 B:HIS56 2.2 13.7 1.0
OD2 B:ASP134 2.6 13.1 1.0
CD2 B:HIS54 3.1 10.5 1.0
CD2 B:HIS110 3.1 11.4 1.0
CE1 B:HIS56 3.1 15.3 1.0
CE1 B:HIS110 3.2 12.0 1.0
CE1 B:HIS54 3.2 12.8 1.0
CG B:HIS56 3.3 14.9 1.0
OZ1 B:GBP464 3.3 33.6 1.0
ZN B:ZN262 3.3 14.6 1.0
CG B:ASP134 3.5 11.9 1.0
CB B:HIS56 3.6 15.8 1.0
CD2 B:GBP464 3.8 31.8 1.0
CB B:ASP134 3.8 12.4 1.0
NE2 B:HIS59 4.0 12.6 1.0
CD2 B:HIS59 4.1 12.6 1.0
ND1 B:HIS110 4.3 12.3 1.0
CG B:HIS110 4.3 12.6 1.0
CG B:HIS54 4.3 11.4 1.0
ND1 B:HIS54 4.3 11.9 1.0
NE2 B:GBP464 4.3 35.2 1.0
NE2 B:HIS56 4.3 15.8 1.0
CD2 B:HIS56 4.4 14.8 1.0
SG2 B:GBP464 4.4 28.0 1.0
OD1 B:ASP58 4.5 15.1 1.0
OD1 B:ASP134 4.6 12.8 1.0
CG2 B:GBP464 4.6 35.6 1.0
CB2 B:GBP464 4.7 24.3 1.0
OD2 B:ASP58 4.8 14.7 1.0
CL1 B:GBP464 5.0 36.7 1.0

Zinc binding site 4 out of 4 in 1qh5

Go back to Zinc Binding Sites List in 1qh5
Zinc binding site 4 out of 4 in the Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Glyoxalase II with S-(N-Hydroxy-N-Bromophenylcarbamoyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn262

b:14.6
occ:1.00
 O B:HOH466 2.0 16.9 1.0
NE2 B:HIS59 2.1 12.6 1.0
OD2 B:ASP134 2.1 13.1 1.0
NE2 B:HIS173 2.1 14.3 1.0
OD2 B:ASP58 2.3 14.7 1.0
CD2 B:HIS59 3.0 12.6 1.0
CG B:ASP134 3.0 11.9 1.0
CE1 B:HIS173 3.1 16.1 1.0
CD2 B:HIS173 3.1 11.7 1.0
CE1 B:HIS59 3.1 12.2 1.0
CG B:ASP58 3.2 15.1 1.0
OD1 B:ASP134 3.3 12.8 1.0
SG2 B:GBP464 3.3 28.0 1.0
ZN B:ZN261 3.3 14.7 1.0
OD1 B:ASP58 3.5 15.1 1.0
CB2 B:GBP464 3.9 24.3 1.0
CD2 B:GBP464 4.0 31.8 1.0
ND2 B:ASN12 4.1 15.1 1.0
NE2 B:HIS54 4.2 12.3 1.0
CG B:HIS59 4.2 11.8 1.0
ND1 B:HIS59 4.2 12.1 1.0
ND1 B:HIS173 4.3 13.5 1.0
CE1 B:HIS54 4.3 12.8 1.0
CG B:HIS173 4.3 12.1 1.0
OZ1 B:GBP464 4.4 33.6 1.0
CB B:ASP134 4.4 12.4 1.0
CB B:ASP58 4.6 16.1 1.0
NE2 B:GBP464 4.6 35.2 1.0
OF2 B:GBP464 4.7 37.3 1.0
NE2 B:HIS110 4.9 12.1 1.0

Reference:

A.D.Cameron, M.Ridderstrom, B.Olin, B.Mannervik. Crystal Structure of Human Glyoxalase II and Its Complex with A Glutathione Thiolester Substrate Analogue. Structure Fold.Des. V. 7 1067 1999.
ISSN: ISSN 0969-2126
PubMed: 10508780
DOI: 10.1016/S0969-2126(99)80174-9
Page generated: Wed Oct 16 18:09:22 2024

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