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Zinc in PDB 1qip: Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione

Enzymatic activity of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione

All present enzymatic activity of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione:
4.4.1.5;

Protein crystallography data

The structure of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione, PDB code: 1qip 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) 30.00 / 1.72
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 67.300, 67.300, 167.700, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione (pdb code 1qip). 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 I Complexed with S-P- Nitrobenzyloxycarbonylglutathione, PDB code: 1qip:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1qip

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Zinc binding site 1 out of 4 in the Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:12.3
occ:1.00
OE1 A:GLN33 1.9 13.4 1.0
OE1 B:GLU172 2.0 16.3 1.0
OE1 A:GLU99 2.0 20.3 1.0
O A:HOH1229 2.1 16.7 1.0
NE2 B:HIS126 2.1 11.1 1.0
O B:HOH1225 2.8 25.4 1.0
CD A:GLN33 3.0 12.8 1.0
CD A:GLU99 3.0 19.8 1.0
CD2 B:HIS126 3.0 9.6 1.0
CD B:GLU172 3.1 16.9 1.0
CE1 B:HIS126 3.2 9.7 1.0
OE2 A:GLU99 3.3 25.9 1.0
NE2 A:GLN33 3.4 11.7 1.0
OE2 B:GLU172 3.6 24.3 1.0
CG B:HIS126 4.2 10.2 1.0
ND1 B:HIS126 4.2 11.4 1.0
CG A:GLN33 4.3 10.8 1.0
CG B:GLU172 4.3 11.9 1.0
CG A:GLU99 4.4 12.6 1.0
CB B:GLU172 4.4 9.7 1.0
O A:HOH1037 4.5 14.6 1.0
CB A:MET35 4.5 10.3 1.0
CB A:GLU99 4.6 9.3 1.0
CG A:MET35 4.7 8.8 1.0
CZ B:PHE162 4.9 11.0 1.0
CE2 B:PHE162 4.9 10.7 1.0

Zinc binding site 2 out of 4 in 1qip

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Zinc binding site 2 out of 4 in the Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:13.0
occ:1.00
OE1 A:GLU172 2.0 19.0 1.0
OE1 B:GLU99 2.0 19.5 1.0
NE2 A:HIS126 2.0 12.0 1.0
OE1 B:GLN33 2.0 15.3 1.0
O A:HOH1227 2.2 25.0 1.0
O A:HOH1228 2.6 28.0 1.0
CE1 A:HIS126 3.0 11.9 1.0
CD B:GLN33 3.1 12.9 1.0
CD B:GLU99 3.1 20.5 1.0
CD2 A:HIS126 3.1 11.2 1.0
CD A:GLU172 3.1 15.9 1.0
OE2 B:GLU99 3.4 28.3 1.0
NE2 B:GLN33 3.5 10.8 1.0
OE2 A:GLU172 3.6 22.0 1.0
ND1 A:HIS126 4.1 11.2 1.0
CG A:HIS126 4.2 10.2 1.0
CG A:GLU172 4.4 12.7 1.0
CG B:GLN33 4.4 7.3 1.0
CG B:GLU99 4.4 15.2 1.0
O B:HOH1040 4.4 16.4 1.0
CB A:GLU172 4.4 11.1 1.0
CB B:MET35 4.5 9.8 1.0
CG B:MET35 4.7 11.4 1.0
CB B:GLU99 4.7 14.0 1.0
OZ1 B:GNB1001 4.8 36.4 1.0
CZ A:PHE162 4.9 14.5 1.0

Zinc binding site 3 out of 4 in 1qip

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Zinc binding site 3 out of 4 in the Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn904

b:13.2
occ:1.00
OE1 D:GLU172 2.0 14.1 1.0
OE1 C:GLN33 2.0 13.7 1.0
OE1 C:GLU99 2.1 16.1 1.0
NE2 D:HIS126 2.1 10.9 1.0
O C:HOH1233 2.1 15.1 1.0
O D:HOH1228 2.8 19.8 1.0
CD C:GLU99 3.0 17.6 1.0
CD C:GLN33 3.1 13.1 1.0
CD2 D:HIS126 3.1 8.7 1.0
CD D:GLU172 3.1 13.8 1.0
CE1 D:HIS126 3.1 9.0 1.0
OE2 C:GLU99 3.3 20.6 1.0
NE2 C:GLN33 3.5 13.0 1.0
OE2 D:GLU172 3.6 17.6 1.0
ND1 D:HIS126 4.2 11.1 1.0
CG D:HIS126 4.2 11.7 1.0
CG D:GLU172 4.3 11.1 1.0
CB D:GLU172 4.4 10.7 1.0
CG C:GLN33 4.4 11.5 1.0
CG C:GLU99 4.4 11.6 1.0
CB C:MET35 4.6 10.4 1.0
O C:HOH1038 4.7 13.4 1.0
CB C:GLU99 4.7 10.1 1.0
CG C:MET35 4.8 10.5 1.0
CZ D:PHE162 4.9 15.2 1.0
CE1 D:PHE162 4.9 14.8 1.0

Zinc binding site 4 out of 4 in 1qip

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Zinc binding site 4 out of 4 in the Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Glyoxalase I Complexed with S-P- Nitrobenzyloxycarbonylglutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn903

b:14.6
occ:1.00
OE1 C:GLU172 1.9 18.5 1.0
OE1 D:GLU99 2.0 22.7 1.0
OE1 D:GLN33 2.0 15.9 1.0
NE2 C:HIS126 2.1 13.5 1.0
O D:HOH1227 2.1 18.9 1.0
O C:HOH1232 2.8 26.8 1.0
CD D:GLU99 3.0 20.7 1.0
CD C:GLU172 3.1 17.0 1.0
CD2 C:HIS126 3.1 12.7 1.0
CD D:GLN33 3.1 18.2 1.0
CE1 C:HIS126 3.1 11.5 1.0
OE2 D:GLU99 3.3 26.8 1.0
NE2 D:GLN33 3.5 17.2 1.0
OE2 C:GLU172 3.5 25.5 1.0
ND1 C:HIS126 4.2 12.9 1.0
CG C:HIS126 4.2 11.7 1.0
CG C:GLU172 4.3 13.6 1.0
CG D:GLU99 4.3 12.6 1.0
O D:HOH1049 4.4 16.5 1.0
CB C:GLU172 4.4 11.3 1.0
CG D:GLN33 4.4 12.2 1.0
CB D:MET35 4.5 12.3 1.0
CG D:MET35 4.7 11.1 1.0
CB D:GLU99 4.7 13.4 1.0
CZ C:PHE162 5.0 16.2 1.0

Reference:

A.D.Cameron, M.Ridderstrom, B.Olin, M.J.Kavarana, D.J.Creighton, B.Mannervik. Reaction Mechanism of Glyoxalase I Explored By An X-Ray Crystallographic Analysis of the Human Enzyme in Complex with A Transition State Analogue. Biochemistry V. 38 13480 1999.
ISSN: ISSN 0006-2960
PubMed: 10521255
DOI: 10.1021/BI990696C
Page generated: Wed Dec 16 03:01:49 2020

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