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Zinc in PDB 2q42: Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350

Enzymatic activity of Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350

All present enzymatic activity of Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350:
3.1.2.6;

Protein crystallography data

The structure of Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350, PDB code: 2q42 was solved by E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, G.N.Phillips Jr., Center Foreukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.97 / 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 (%) 14.7 / 19.3

Other elements in 2q42:

The structure of Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 also contains other interesting chemical elements:

Iron (Fe) 32 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 (pdb code 2q42). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350, PDB code: 2q42:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2q42

Go back to Zinc Binding Sites List in 2q42
Zinc binding site 1 out of 2 in the Ensemble Refinement of the Protein Crystal 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 Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:7.9
occ:0.06
 O A:HOH901 2.0 1.6 0.1
NE2 A:HIS54 2.1 6.5 0.1
ND1 A:HIS56 2.1 7.5 0.1
NE2 A:HIS112 2.1 7.0 0.1
OD2 A:ASP131 2.8 5.8 0.1
CD2 A:HIS54 2.9 6.2 0.1
CD2 A:HIS112 3.0 6.2 0.1
CE1 A:HIS56 3.0 8.5 0.1
CE1 A:HIS54 3.1 6.6 0.1
CG A:HIS56 3.1 8.1 0.1
CE1 A:HIS112 3.2 6.2 0.1
O A:HOH924 3.3 13.1 0.1
FE A:FE701 3.3 3.9 0.1
CB A:HIS56 3.5 7.8 0.1
CG A:ASP131 3.6 7.8 0.1
CB A:ASP131 3.8 6.9 0.1
NE2 A:HIS59 4.0 7.2 0.1
CD2 A:HIS59 4.0 5.6 0.1
CG A:HIS54 4.1 6.3 0.1
NE2 A:HIS56 4.2 6.5 0.1
ND1 A:HIS54 4.2 5.1 0.1
CG A:HIS112 4.2 6.3 0.1
CD2 A:HIS56 4.2 8.3 0.1
OD1 A:ASP58 4.3 9.3 0.1
ND1 A:HIS112 4.3 7.0 0.1
O A:HOH955 4.3 15.9 0.1
OD1 A:ASP131 4.6 5.5 0.1
OD2 A:ASP58 4.6 8.2 0.1
O B:HOH823 4.6 17.1 0.1
CG A:ASP58 4.9 9.8 0.1
CA A:HIS56 4.9 7.8 0.1
CE1 A:HIS59 5.0 5.0 0.1

Zinc binding site 2 out of 2 in 2q42

Go back to Zinc Binding Sites List in 2q42
Zinc binding site 2 out of 2 in the Ensemble Refinement of the Protein Crystal 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 Ensemble Refinement of the Protein Crystal Structure of Glyoxalase II From Arabidopsis Thaliana Gene AT2G31350 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:11.7
occ:0.06
 NE2 B:HIS112 2.3 6.9 0.1
CD2 B:HIS54 2.3 6.2 0.1
O B:HOH802 2.3 6.0 0.1
NE2 B:HIS54 2.5 6.4 0.1
OD2 B:ASP131 2.5 5.8 0.1
ND1 B:HIS56 2.6 6.3 0.1
CD2 B:HIS112 2.7 5.5 0.1
CG B:ASP131 3.1 6.3 0.1
FE B:FE704 3.2 3.9 0.1
CD2 B:HIS59 3.4 5.6 0.1
NE2 B:HIS59 3.4 5.0 0.1
CE1 B:HIS112 3.5 7.1 0.1
CG B:HIS56 3.5 6.0 0.1
CB B:ASP131 3.6 5.9 0.1
CE1 B:HIS56 3.6 6.5 0.1
CG B:HIS54 3.6 6.1 0.1
CB B:HIS56 3.7 6.5 0.1
CE1 B:HIS54 3.8 9.2 0.1
OD1 B:ASP131 3.9 6.5 0.1
CG B:HIS112 4.0 6.1 0.1
O B:HOH821 4.1 13.2 0.1
CG B:HIS59 4.3 4.3 0.1
ND1 B:HIS112 4.3 4.7 0.1
ND1 B:HIS54 4.3 6.5 0.1
CE1 B:HIS59 4.3 5.5 0.1
OD1 B:ASP58 4.6 8.5 0.1
CB B:HIS54 4.7 5.3 0.1
CD2 B:HIS56 4.7 5.3 0.1
O B:HOH842 4.7 13.4 0.1
NE2 B:HIS56 4.7 6.6 0.1
ND1 B:HIS59 4.8 5.1 0.1
OD2 B:ASP58 4.9 8.0 0.1
CA B:ASP131 4.9 6.1 0.1

Reference:

E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, G.N.Phillips. Ensemble Refinement of Protein Crystal Structures: Validation and Application. Structure V. 15 1040 2007.
ISSN: ISSN 0969-2126
PubMed: 17850744
DOI: 10.1016/J.STR.2007.06.019
Page generated: Wed Aug 20 05:19:44 2025

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