Nickel in PDB 2c21: Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme

The structure of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme, PDB code: 2c21 was solved by A.Ariza, T.J.Vickers, N.Greig, K.A.Armour, I.M.Eggleston, A.H.Fairlamb, C.S.Bond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	129.10 / 2.0
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	130.193, 148.957, 50.698, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 20.1

The structure of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Nickel atom in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme (pdb code 2c21). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme, PDB code: 2c21:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1142 b:35.4 occ:0.50 O A:HOH2139 1.8 38.8 1.0 NE2 A:HIS8 2.1 37.3 1.0 OE1 B:GLU120 2.3 41.6 1.0 NE2 B:HIS77 2.3 35.8 1.0 OE1 A:GLU59 2.4 39.1 1.0 CE1 A:HIS8 3.1 40.0 1.0 CD2 A:HIS8 3.1 39.8 1.0 CE1 B:HIS77 3.2 35.5 1.0 CD B:GLU120 3.3 41.8 1.0 CD2 B:HIS77 3.4 35.7 1.0 CD A:GLU59 3.4 41.4 1.0 O A:HOH2080 3.4 44.7 1.0 OE2 B:GLU120 3.8 46.5 1.0 OE2 A:GLU59 3.8 43.5 1.0 CB B:ALA79 4.2 35.8 1.0 ND1 A:HIS8 4.2 37.1 1.0 CG A:HIS8 4.2 38.0 1.0 O4 A:MRD2144 4.3 29.2 0.5 ND1 B:HIS77 4.3 35.3 1.0 CG B:HIS77 4.5 35.3 1.0 CB A:MET10 4.5 36.9 1.0 CG B:GLU120 4.6 39.8 1.0 O4 A:MPD1144 4.7 30.4 0.5 CG A:GLU59 4.7 38.5 1.0 O B:HOH2157 4.8 44.9 1.0 CB B:GLU120 4.8 37.8 1.0 CG A:MET10 4.9 37.8 1.0 CB A:GLU59 4.9 38.2 1.0 C5 A:MRD2144 4.9 29.5 0.5

Nickel binding site 2 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1143 b:36.4 occ:0.50 O A:HOH2130 1.9 40.8 1.0 NE2 A:HIS77 2.2 35.1 1.0 OE1 A:GLU120 2.2 42.4 1.0 NE2 B:HIS8 2.3 40.0 1.0 OE1 B:GLU59 2.3 47.3 1.0 CE1 A:HIS77 3.0 36.7 1.0 CE1 B:HIS8 3.2 39.0 1.0 CD A:GLU120 3.2 40.8 1.0 CD2 B:HIS8 3.3 38.6 1.0 CD2 A:HIS77 3.4 35.8 1.0 CD B:GLU59 3.4 44.5 1.0 OE2 A:GLU120 3.6 44.4 1.0 OE2 B:GLU59 3.8 50.6 1.0 ND1 A:HIS77 4.2 37.4 1.0 CB A:ALA79 4.3 37.0 1.0 ND1 B:HIS8 4.3 39.5 1.0 CG A:HIS77 4.4 36.3 1.0 CG B:HIS8 4.4 38.4 1.0 CB B:MET10 4.5 37.8 1.0 CG A:GLU120 4.5 39.5 1.0 CB A:GLU120 4.6 38.0 1.0 CG B:GLU59 4.7 40.0 1.0 CG B:MET10 4.8 36.4 1.0 CB B:GLU59 4.9 37.9 1.0

Nickel binding site 3 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1142 b:32.5 occ:0.50 O D:HOH2145 2.1 42.4 1.0 NE2 D:HIS77 2.3 36.0 1.0 OE1 D:GLU120 2.3 41.0 1.0 NE2 C:HIS8 2.3 34.3 1.0 OE1 C:GLU59 2.3 45.0 1.0 O C:HOH2116 3.0 54.3 1.0 CE1 D:HIS77 3.1 34.8 1.0 CE1 C:HIS8 3.1 35.2 1.0 CD D:GLU120 3.2 41.7 1.0 CD C:GLU59 3.3 44.0 1.0 CD2 D:HIS77 3.4 36.1 1.0 CD2 C:HIS8 3.4 35.8 1.0 OE2 D:GLU120 3.6 42.6 1.0 OE2 C:GLU59 3.7 49.4 1.0 ND1 D:HIS77 4.3 35.5 1.0 ND1 C:HIS8 4.3 35.4 1.0 CB D:ALA79 4.4 35.9 1.0 CG D:HIS77 4.4 35.0 1.0 CG C:HIS8 4.4 34.8 1.0 CB C:MET10 4.5 37.0 1.0 CG D:GLU120 4.5 39.4 1.0 CG C:GLU59 4.7 40.2 1.0 CB D:GLU120 4.7 37.9 1.0 CG C:MET10 4.8 38.2 1.0 O D:HOH2074 4.9 59.0 1.0 CB C:GLU59 4.9 38.9 1.0

Nickel binding site 4 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1143 b:29.8 occ:0.50 O D:HOH2164 1.9 38.3 1.0 NE2 D:HIS8 2.2 37.5 1.0 NE2 C:HIS77 2.3 35.3 1.0 OE1 D:GLU59 2.4 40.6 1.0 OE1 C:GLU120 2.4 39.3 1.0 CD2 D:HIS8 3.1 38.9 1.0 CE1 C:HIS77 3.1 35.5 1.0 CE1 D:HIS8 3.2 38.4 1.0 CD2 C:HIS77 3.4 36.9 1.0 CD D:GLU59 3.4 43.4 1.0 CD C:GLU120 3.4 43.5 1.0 O D:HOH2087 3.6 36.9 1.0 OE2 D:GLU59 3.8 43.2 1.0 OE2 C:GLU120 3.9 45.5 1.0 CB C:ALA79 4.2 35.2 1.0 ND1 D:HIS8 4.3 37.7 1.0 CG D:HIS8 4.3 37.7 1.0 ND1 C:HIS77 4.3 35.4 1.0 CB D:MET10 4.4 36.7 1.0 O4 D:MRD1142 4.4 27.4 0.5 CG C:HIS77 4.5 35.1 1.0 CG C:GLU120 4.7 38.9 1.0 CG D:GLU59 4.7 37.3 1.0 CB C:GLU120 4.7 37.2 1.0 O4 D:MPD1141 4.8 30.7 0.5 O C:HOH2190 4.8 47.5 1.0 CG D:MET10 4.9 36.3 1.0 CB D:GLU59 4.9 37.6 1.0

Nickel binding site 5 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni1142 b:42.7 occ:0.50 O E:HOH2061 2.0 60.6 1.0 OE1 F:GLU120 2.2 40.0 1.0 NE2 E:HIS8 2.3 34.1 1.0 NE2 F:HIS77 2.3 34.5 1.0 OE1 E:GLU59 2.4 44.4 1.0 CE1 F:HIS77 3.1 35.4 1.0 CE1 E:HIS8 3.2 34.8 1.0 CD F:GLU120 3.3 40.3 1.0 CD2 E:HIS8 3.3 35.1 1.0 CD E:GLU59 3.3 42.8 1.0 CD2 F:HIS77 3.5 35.1 1.0 OE2 E:GLU59 3.7 46.7 1.0 OE2 F:GLU120 3.7 43.3 1.0 CB F:ALA79 4.3 37.5 1.0 ND1 F:HIS77 4.3 35.0 1.0 ND1 E:HIS8 4.3 34.0 1.0 CG E:HIS8 4.5 34.5 1.0 CG F:GLU120 4.5 39.6 1.0 CB E:MET10 4.5 36.9 1.0 CG F:HIS77 4.5 34.6 1.0 CB F:GLU120 4.6 38.9 1.0 CG E:GLU59 4.7 39.9 1.0 CG E:MET10 4.8 36.5 1.0 CB E:GLU59 4.9 38.5 1.0

Nickel binding site 6 out of 6 in the Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Specificity of the Trypanothione-Dependednt Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni1143 b:46.8 occ:0.50 OE1 E:GLU120 2.0 35.4 1.0 O F:HOH2024 2.1 54.8 1.0 OE1 F:GLU59 2.2 45.4 1.0 NE2 E:HIS77 2.2 34.9 1.0 NE2 F:HIS8 2.4 33.3 1.0 CD E:GLU120 3.1 38.0 1.0 CE1 E:HIS77 3.1 34.6 1.0 O E:HOH2105 3.1 51.4 1.0 CD F:GLU59 3.1 46.3 1.0 CE1 F:HIS8 3.3 34.7 1.0 CD2 E:HIS77 3.3 35.5 1.0 CD2 F:HIS8 3.4 35.2 1.0 OE2 F:GLU59 3.4 49.7 1.0 OE2 E:GLU120 3.5 38.8 1.0 CB E:ALA79 4.1 36.9 1.0 ND1 E:HIS77 4.2 34.3 1.0 CG E:GLU120 4.3 37.4 1.0 CG E:HIS77 4.4 35.5 1.0 ND1 F:HIS8 4.4 34.2 1.0 CG F:HIS8 4.5 35.6 1.0 CB F:MET10 4.5 37.0 1.0 CG F:GLU59 4.5 43.1 1.0 O F:HOH2009 4.6 57.5 1.0 CB E:GLU120 4.6 37.0 1.0 CG F:MET10 4.8 37.1 1.0 CB F:GLU59 5.0 41.1 1.0 CD1 E:LEU122 5.0 35.6 1.0

A.Ariza, T.J.Vickers, N.Greig, K.A.Armour, M.J.Dixon, I.M.Eggleston, A.H.Fairlamb, C.S.Bond. Specificity of the Trypanothione-Dependent Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme. Mol.Microbiol. V. 59 1239 2006.
ISSN: ISSN 0950-382X
PubMed: 16430697
DOI: 10.1111/J.1365-2958.2006.05022.X