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Zinc in PDB 1qh3: Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site

Enzymatic activity of Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site

All present enzymatic activity of Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site:
3.1.2.6;

Protein crystallography data

The structure of Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site, PDB code: 1qh3 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) 15.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.080, 72.370, 162.060, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.9

Other elements in 1qh3:

The structure of Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site also contains other interesting chemical elements:

Arsenic (As) 4 atoms
Manganese (Mn) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site (pdb code 1qh3). 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 Cacodylate and Acetate Ions Present in the Active Site, PDB code: 1qh3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1qh3

Go back to Zinc Binding Sites List in 1qh3
Zinc binding site 1 out of 4 in the Human Glyoxalase II with Cacodylate and Acetate Ions Present 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 Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn261

b:20.4
occ:1.00
O A:HOH468 2.1 13.2 1.0
OD2 A:ASP134 2.2 11.2 1.0
O2 A:CAC463 2.2 39.7 1.0
NE2 A:HIS110 2.3 11.8 1.0
NE2 A:HIS54 2.3 10.4 1.0
ND1 A:HIS56 2.3 14.7 1.0
CG A:ASP134 3.1 9.9 1.0
CD2 A:HIS54 3.2 11.5 1.0
CE1 A:HIS110 3.2 12.4 1.0
CE1 A:HIS56 3.2 15.3 1.0
CD2 A:HIS110 3.3 10.3 1.0
AS A:CAC463 3.3 42.6 1.0
CG A:HIS56 3.3 15.6 1.0
CE1 A:HIS54 3.3 12.8 1.0
ZN A:ZN262 3.3 18.8 1.0
CB A:ASP134 3.5 9.3 1.0
O1 A:CAC463 3.7 40.3 1.0
CB A:HIS56 3.7 15.2 1.0
NE2 A:HIS59 4.2 12.4 1.0
OD1 A:ASP134 4.2 12.1 1.0
O A:HOH506 4.2 25.1 1.0
C2 A:CAC463 4.3 41.0 1.0
CD2 A:HIS59 4.3 14.2 1.0
ND1 A:HIS110 4.3 9.8 1.0
NE2 A:HIS56 4.4 15.0 1.0
CG A:HIS110 4.4 12.0 1.0
CG A:HIS54 4.4 12.2 1.0
CD2 A:HIS56 4.4 14.6 1.0
ND1 A:HIS54 4.4 11.8 1.0
OD1 A:ASP58 4.6 13.5 1.0

Zinc binding site 2 out of 4 in 1qh3

Go back to Zinc Binding Sites List in 1qh3
Zinc binding site 2 out of 4 in the Human Glyoxalase II with Cacodylate and Acetate Ions Present 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 Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn262

b:18.8
occ:1.00
OD2 A:ASP134 2.1 11.2 1.0
O A:HOH468 2.1 13.2 1.0
NE2 A:HIS173 2.1 12.5 1.0
NE2 A:HIS59 2.2 12.4 1.0
OD2 A:ASP58 2.3 13.5 1.0
O1 A:CAC463 2.4 40.3 1.0
CG A:ASP134 2.9 9.9 1.0
OD1 A:ASP134 3.0 12.1 1.0
CD2 A:HIS59 3.0 14.2 1.0
CD2 A:HIS173 3.1 14.2 1.0
CE1 A:HIS173 3.2 15.9 1.0
CG A:ASP58 3.2 15.8 1.0
CE1 A:HIS59 3.3 14.6 1.0
ZN A:ZN261 3.3 20.4 1.0
OD1 A:ASP58 3.4 13.5 1.0
AS A:CAC463 3.7 42.6 1.0
O A:HOH506 4.0 25.1 1.0
ND2 A:ASN12 4.1 12.2 1.0
O2 A:CAC463 4.2 39.7 1.0
CG A:HIS59 4.2 12.1 1.0
NE2 A:HIS54 4.2 10.4 1.0
CG A:HIS173 4.3 12.2 1.0
ND1 A:HIS173 4.3 14.9 1.0
ND1 A:HIS59 4.3 13.2 1.0
CE1 A:HIS54 4.3 12.8 1.0
CB A:ASP134 4.4 9.3 1.0
CB A:ASP58 4.6 13.5 1.0
C2 A:CAC463 4.6 41.0 1.0

Zinc binding site 3 out of 4 in 1qh3

Go back to Zinc Binding Sites List in 1qh3
Zinc binding site 3 out of 4 in the Human Glyoxalase II with Cacodylate and Acetate Ions Present 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 Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn261

b:18.1
occ:1.00
O2 B:CAC469 2.0 38.2 1.0
O B:HOH473 2.1 12.4 1.0
NE2 B:HIS54 2.2 10.8 1.0
ND1 B:HIS56 2.2 11.6 1.0
NE2 B:HIS110 2.3 8.5 1.0
OD2 B:ASP134 2.3 10.9 1.0
CE1 B:HIS56 3.1 13.4 1.0
CD2 B:HIS54 3.2 10.1 1.0
CD2 B:HIS110 3.2 11.7 1.0
CG B:ASP134 3.2 9.9 1.0
CE1 B:HIS54 3.3 11.4 1.0
CE1 B:HIS110 3.3 10.9 1.0
CG B:HIS56 3.3 11.9 1.0
AS B:CAC469 3.3 40.6 1.0
ZN B:ZN262 3.3 16.8 1.0
CB B:HIS56 3.6 13.0 1.0
CB B:ASP134 3.6 7.6 1.0
O1 B:CAC469 3.9 38.9 1.0
NE2 B:HIS59 4.1 11.9 1.0
O B:HOH511 4.2 18.6 1.0
CD2 B:HIS59 4.2 10.5 1.0
C2 B:CAC469 4.3 39.2 1.0
NE2 B:HIS56 4.3 13.0 1.0
OD1 B:ASP134 4.3 10.2 1.0
CG B:HIS110 4.4 11.0 1.0
ND1 B:HIS110 4.4 10.9 1.0
CG B:HIS54 4.4 10.8 1.0
ND1 B:HIS54 4.4 12.5 1.0
CD2 B:HIS56 4.4 12.4 1.0
OD1 B:ASP58 4.6 14.4 1.0
OD2 B:ASP58 4.9 13.9 1.0

Zinc binding site 4 out of 4 in 1qh3

Go back to Zinc Binding Sites List in 1qh3
Zinc binding site 4 out of 4 in the Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site


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 Cacodylate and Acetate Ions Present in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn262

b:16.8
occ:1.00
O B:HOH473 1.9 12.4 1.0
NE2 B:HIS59 2.1 11.9 1.0
NE2 B:HIS173 2.1 14.4 1.0
OD2 B:ASP134 2.1 10.9 1.0
OD2 B:ASP58 2.2 13.9 1.0
O1 B:CAC469 2.4 38.9 1.0
CD2 B:HIS59 2.9 10.5 1.0
CG B:ASP134 3.0 9.9 1.0
CE1 B:HIS173 3.1 14.1 1.0
OD1 B:ASP134 3.1 10.2 1.0
CD2 B:HIS173 3.2 12.8 1.0
CE1 B:HIS59 3.2 12.3 1.0
CG B:ASP58 3.2 16.3 1.0
ZN B:ZN261 3.3 18.1 1.0
OD1 B:ASP58 3.5 14.4 1.0
AS B:CAC469 3.5 40.6 1.0
O2 B:CAC469 3.8 38.2 1.0
O B:HOH511 3.9 18.6 1.0
ND2 B:ASN12 4.0 11.3 1.0
CG B:HIS59 4.1 11.4 1.0
ND1 B:HIS173 4.2 13.2 1.0
ND1 B:HIS59 4.2 10.6 1.0
NE2 B:HIS54 4.2 10.8 1.0
CE1 B:HIS54 4.2 11.4 1.0
CG B:HIS173 4.3 12.6 1.0
O B:HOH616 4.3 26.2 1.0
CB B:ASP134 4.4 7.6 1.0
C2 B:CAC469 4.5 39.2 1.0
CB B:ASP58 4.5 13.7 1.0
CG B:ASN12 5.0 13.8 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 Dec 16 03:01:48 2020

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