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Arsenic 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:

Manganese (Mn) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Human Glyoxalase II with Cacodylate and Acetate Ions Present in the Active Site, PDB code: 1qh3:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 1qh3

Go back to Arsenic Binding Sites List in 1qh3
Arsenic 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 Arsenic with other atoms in the As 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:As463

b:42.6
occ:1.00
 AS A:CAC463 0.0 42.6 1.0
O2 A:CAC463 1.8 39.7 1.0
O1 A:CAC463 1.8 40.3 1.0
C2 A:CAC463 2.0 41.0 1.0
C1 A:CAC463 2.0 41.0 1.0
O A:HOH468 2.8 13.2 1.0
ZN A:ZN261 3.3 20.4 1.0
O A:HOH506 3.3 25.1 1.0
OD2 A:ASP134 3.7 11.2 1.0
ZN A:ZN262 3.7 18.8 1.0
ND1 A:HIS56 4.1 14.7 1.0
O A:HOH473 4.2 17.6 1.0
CE1 A:HIS110 4.4 12.4 1.0
CE2 A:TYR145 4.4 21.3 1.0
NE2 A:HIS110 4.4 11.8 1.0
OD1 A:ASP58 4.6 13.5 1.0
OH A:TYR145 4.6 20.3 1.0
OD2 A:ASP58 4.7 13.5 1.0
CE1 A:HIS56 4.8 15.3 1.0
NE2 A:HIS173 4.8 12.5 1.0
CG A:ASP134 4.8 9.9 1.0
OH A:TYR175 4.9 18.3 1.0
CG A:ASP58 5.0 15.8 1.0

Arsenic binding site 2 out of 4 in 1qh3

Go back to Arsenic Binding Sites List in 1qh3
Arsenic 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 Arsenic with other atoms in the As 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:As265

b:30.9
occ:1.00
 SG A:CYS153 2.2 17.4 1.0
CB A:CYS153 3.0 18.0 1.0
OE2 A:GLU158 3.5 37.8 1.0
C A:CYS153 3.6 16.5 1.0
N A:LYS154 3.9 16.3 1.0
O A:CYS153 3.9 15.4 1.0
CA A:CYS153 3.9 16.4 1.0
CA A:LYS154 4.4 16.6 1.0
CG2 A:VAL242 4.4 18.7 1.0
CG A:LYS154 4.4 25.1 1.0
CD A:GLU158 4.4 34.5 1.0
CD1 A:LEU157 4.6 21.8 1.0
O A:ASP150 4.8 15.9 1.0

Arsenic binding site 3 out of 4 in 1qh3

Go back to Arsenic Binding Sites List in 1qh3
Arsenic 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 Arsenic with other atoms in the As 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:As469

b:40.6
occ:1.00
 AS B:CAC469 0.0 40.6 1.0
O2 B:CAC469 1.8 38.2 1.0
O1 B:CAC469 1.8 38.9 1.0
C2 B:CAC469 2.0 39.2 1.0
C1 B:CAC469 2.0 39.4 1.0
O B:HOH473 2.7 12.4 1.0
O B:HOH511 3.2 18.6 1.0
ZN B:ZN261 3.3 18.1 1.0
O B:HOH616 3.5 26.2 1.0
ZN B:ZN262 3.5 16.8 1.0
OD2 B:ASP134 3.6 10.9 1.0
ND1 B:HIS56 4.3 11.6 1.0
OD2 B:ASP58 4.4 13.9 1.0
O B:HOH478 4.4 17.2 1.0
OD1 B:ASP58 4.4 14.4 1.0
NE2 B:HIS110 4.4 8.5 1.0
CE1 B:HIS110 4.4 10.9 1.0
NE2 B:HIS173 4.5 14.4 1.0
CE2 B:TYR145 4.7 18.6 1.0
CG B:ASP58 4.8 16.3 1.0
OH B:TYR175 4.8 14.5 1.0
CG B:ASP134 4.8 9.9 1.0
CE1 B:HIS56 4.8 13.4 1.0
CE1 B:HIS173 4.9 14.1 1.0

Arsenic binding site 4 out of 4 in 1qh3

Go back to Arsenic Binding Sites List in 1qh3
Arsenic 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 Arsenic with other atoms in the As 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:As265

b:25.4
occ:1.00
 SG B:CYS153 2.2 14.8 1.0
CB B:CYS153 3.1 15.4 1.0
OE2 B:GLU158 3.3 28.4 1.0
C B:CYS153 3.4 15.2 1.0
N B:LYS154 3.6 15.6 1.0
O B:CYS153 3.6 16.0 1.0
CA B:CYS153 3.8 15.4 1.0
CD B:GLU158 4.0 30.6 1.0
CA B:LYS154 4.1 14.9 1.0
CG B:LYS154 4.5 22.2 1.0
CG B:GLU158 4.5 26.1 1.0
O B:HOH643 4.5 35.0 1.0
CD1 B:LEU157 4.6 20.9 1.0
OE1 B:GLU158 4.6 29.3 1.0
CG2 B:VAL242 4.6 15.3 1.0
CB B:LEU157 4.6 17.4 1.0
O B:ASP150 4.8 14.4 1.0
CB B:LYS154 4.9 16.6 1.0
CG B:LEU157 4.9 21.4 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: Tue Oct 27 16:47:16 2020

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