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Zinc in PDB 1xm8: X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350

Enzymatic activity of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350

All present enzymatic activity of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350:
3.1.2.6;

Protein crystallography data

The structure of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350, PDB code: 1xm8 was solved by G.E.Wesenberg, D.W.Smith, G.N.Phillips Jr., E.Bitto, C.A.Bingman, S.T.M.Allard, Center For Eukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.71 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.494, 58.782, 69.049, 90.00, 109.22, 90.00
R / Rfree (%) 14 / 18.9

Other elements in 1xm8:

The structure of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 (pdb code 1xm8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350, PDB code: 1xm8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1xm8

Go back to Zinc Binding Sites List in 1xm8
Zinc binding site 1 out of 2 in the X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:11.1
occ:1.00
O A:HOH901 2.0 11.7 1.0
ND1 A:HIS56 2.1 10.2 1.0
NE2 A:HIS54 2.1 10.7 1.0
NE2 A:HIS112 2.1 8.2 1.0
OD2 A:ASP131 2.7 9.4 1.0
CD2 A:HIS54 3.0 9.7 1.0
CD2 A:HIS112 3.0 8.6 1.0
CE1 A:HIS56 3.0 11.9 1.0
CG A:HIS56 3.1 11.2 1.0
CE1 A:HIS54 3.2 9.2 1.0
CE1 A:HIS112 3.2 9.5 1.0
O B:HOH835 3.3 15.9 1.0
FE A:FE701 3.4 7.6 1.0
CB A:HIS56 3.5 9.9 1.0
CG A:ASP131 3.6 11.4 1.0
CB A:ASP131 3.9 10.7 1.0
NE2 A:HIS59 3.9 10.3 1.0
CD2 A:HIS59 4.0 7.3 1.0
NE2 A:HIS56 4.2 7.9 1.0
CG A:HIS54 4.2 7.6 1.0
CG A:HIS112 4.2 7.9 1.0
ND1 A:HIS54 4.2 7.7 1.0
CD2 A:HIS56 4.2 11.3 1.0
ND1 A:HIS112 4.3 10.5 1.0
O A:HOH954 4.3 17.4 1.0
OD1 A:ASP58 4.3 13.1 1.0
O B:HOH823 4.5 17.6 1.0
OD1 A:ASP131 4.6 8.4 1.0
OD2 A:ASP58 4.7 10.7 1.0
CE1 A:HIS59 4.9 7.5 1.0
CG A:ASP58 4.9 12.6 1.0
CA A:HIS56 5.0 9.1 1.0
CG A:HIS59 5.0 7.7 1.0

Zinc binding site 2 out of 2 in 1xm8

Go back to Zinc Binding Sites List in 1xm8
Zinc binding site 2 out of 2 in the X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:10.3
occ:1.00
O B:HOH802 1.9 11.6 1.0
ND1 B:HIS56 2.1 9.7 1.0
NE2 B:HIS54 2.1 10.2 1.0
NE2 B:HIS112 2.1 8.2 1.0
OD2 B:ASP131 2.7 8.8 1.0
CD2 B:HIS54 3.0 8.3 1.0
CD2 B:HIS112 3.0 8.1 1.0
CE1 B:HIS56 3.1 8.9 1.0
O B:HOH821 3.2 15.7 1.0
CG B:HIS56 3.2 8.2 1.0
CE1 B:HIS54 3.2 11.6 1.0
CE1 B:HIS112 3.2 10.8 1.0
FE B:FE704 3.3 7.4 1.0
CB B:HIS56 3.5 10.0 1.0
CG B:ASP131 3.6 8.5 1.0
CB B:ASP131 3.9 9.7 1.0
NE2 B:HIS59 3.9 7.0 1.0
CD2 B:HIS59 4.0 8.4 1.0
CG B:HIS54 4.2 9.9 1.0
NE2 B:HIS56 4.2 9.0 1.0
CG B:HIS112 4.2 7.4 1.0
ND1 B:HIS54 4.3 9.7 1.0
CD2 B:HIS56 4.3 6.6 1.0
ND1 B:HIS112 4.3 6.8 1.0
OD1 B:ASP58 4.3 9.8 1.0
O B:HOH843 4.3 16.9 1.0
O A:HOH937 4.5 15.4 1.0
OD1 B:ASP131 4.6 8.6 1.0
OD2 B:ASP58 4.7 9.7 1.0
CE1 B:HIS59 4.9 8.1 1.0
CG B:ASP58 4.9 9.2 1.0
CA B:HIS56 5.0 9.7 1.0

Reference:

G.P.Marasinghe, I.M.Sander, B.Bennett, G.Periyannan, K.W.Yang, C.A.Makaroff, M.W.Crowder. Structural Studies on A Mitochondrial Glyoxalase II. J.Biol.Chem. V. 280 40668 2005.
ISSN: ISSN 0021-9258
PubMed: 16227621
DOI: 10.1074/JBC.M509748200
Page generated: Wed Dec 16 03:12:33 2020

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