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Nickel in PDB 1f9z: Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli

Enzymatic activity of Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli

All present enzymatic activity of Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli:
4.4.1.5;

Protein crystallography data

The structure of Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli, PDB code: 1f9z was solved by M.M.He, S.L.Clugston, J.F.Honek, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.047, 56.478, 46.705, 90.00, 95.44, 90.00
R / Rfree (%) 20.5 / 27.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli (pdb code 1f9z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli, PDB code: 1f9z:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1f9z

Go back to Nickel Binding Sites List in 1f9z
Nickel binding site 1 out of 2 in the Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1200

b:17.9
occ:1.00
NE2 A:HIS5 2.0 10.1 1.0
OE1 B:GLU122 2.1 17.5 1.0
O B:HOH140 2.1 13.6 1.0
NE2 B:HIS74 2.2 11.4 1.0
OE1 A:GLU56 2.2 14.4 1.0
O B:HOH152 2.3 16.0 1.0
CE1 A:HIS5 2.8 9.0 1.0
CE1 B:HIS74 3.0 8.8 1.0
CD A:GLU56 3.2 25.9 1.0
CD B:GLU122 3.2 21.6 1.0
CD2 A:HIS5 3.2 12.9 1.0
CD2 B:HIS74 3.2 15.7 1.0
OE2 A:GLU56 3.6 17.0 1.0
OE2 B:GLU122 3.7 28.3 1.0
ND1 A:HIS5 4.1 14.1 1.0
O B:HOH185 4.1 31.7 1.0
O A:HOH1231 4.2 23.3 1.0
CG A:HIS5 4.2 9.7 1.0
ND1 B:HIS74 4.2 14.0 1.0
CG B:HIS74 4.3 12.3 1.0
CB B:ALA76 4.4 13.6 1.0
CG B:GLU122 4.5 11.8 1.0
CB A:MET7 4.5 10.1 1.0
CG A:GLU56 4.5 10.2 1.0
CB B:GLU122 4.6 11.8 1.0
CB A:GLU56 4.7 8.6 1.0
CG A:MET7 4.9 12.6 1.0
O A:HOH1304 4.9 32.0 1.0

Nickel binding site 2 out of 2 in 1f9z

Go back to Nickel Binding Sites List in 1f9z
Nickel binding site 2 out of 2 in the Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Ni(II)-Bound Glyoxalase I From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1201

b:17.3
occ:1.00
O B:HOH142 2.0 15.3 1.0
NE2 B:HIS5 2.0 11.9 1.0
OE1 A:GLU122 2.2 20.7 1.0
NE2 A:HIS74 2.2 10.9 1.0
OE1 B:GLU56 2.2 14.9 1.0
O A:HOH1213 2.2 17.4 1.0
CE1 A:HIS74 2.9 10.8 1.0
CE1 B:HIS5 2.9 8.9 1.0
CD2 B:HIS5 3.1 12.2 1.0
CD A:GLU122 3.2 19.8 1.0
CD B:GLU56 3.2 27.2 1.0
CD2 A:HIS74 3.4 15.0 1.0
OE2 A:GLU122 3.6 23.5 1.0
OE2 B:GLU56 3.6 23.7 1.0
O A:HOH1313 4.0 37.9 1.0
ND1 B:HIS5 4.1 11.5 1.0
ND1 A:HIS74 4.1 14.3 1.0
O B:HOH202 4.2 26.9 1.0
CG B:HIS5 4.2 11.5 1.0
CB A:ALA76 4.4 13.6 1.0
CG A:HIS74 4.4 13.5 1.0
CG A:GLU122 4.5 10.9 1.0
CG B:GLU56 4.5 12.6 1.0
CB B:MET7 4.6 11.4 1.0
CB A:GLU122 4.6 11.3 1.0
CB B:GLU56 4.7 13.6 1.0
CG B:MET7 4.9 13.2 1.0
O B:HOH176 4.9 26.5 1.0

Reference:

M.M.He, S.L.Clugston, J.F.Honek, B.W.Matthews. Determination of the Structure of Escherichia Coli Glyoxalase I Suggests A Structural Basis For Differential Metal Activation. Biochemistry V. 39 8719 2000.
ISSN: ISSN 0006-2960
PubMed: 10913283
DOI: 10.1021/BI000856G
Page generated: Fri Sep 25 07:52:24 2020
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