Sodium 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:

Nickel

(Ni)

6 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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 B:Na1143 b:22.2 occ:1.00 O B:HOH2136 2.3 20.9 0.5 O C:HOH2185 2.3 18.5 0.5 OG C:SER68 2.4 35.0 1.0 OG B:SER68 2.4 37.4 1.0 O B:HOH2137 2.5 18.1 1.0 O C:HOH2187 2.6 17.3 1.0 O C:HOH2121 3.4 14.4 0.5 CB C:SER68 3.5 34.6 1.0 CB B:SER68 3.6 35.0 1.0 O B:HOH2082 3.7 20.8 0.5 CA C:SER68 4.1 35.1 1.0 CA B:SER68 4.1 35.1 1.0 O B:ASP115 4.3 36.9 1.0 N C:TYR69 4.3 36.3 1.0 O C:ASP115 4.3 37.3 1.0 N B:TYR69 4.3 36.5 1.0 CA B:ASP115 4.4 37.5 1.0 O B:TYR69 4.5 38.3 1.0 O B:PRO114 4.5 38.4 1.0 O C:TYR69 4.5 38.5 1.0 C B:ASP115 4.5 37.5 1.0 OD1 B:ASP115 4.6 37.9 1.0 CA C:ASP115 4.6 36.6 1.0 O C:PRO114 4.6 37.3 1.0 OD1 C:ASP115 4.7 35.9 1.0 C C:ASP115 4.7 36.6 1.0 NH2 B:ARG18 4.7 40.0 1.0 NH2 C:ARG18 4.7 39.7 1.0 C C:SER68 4.7 35.9 1.0 C B:SER68 4.8 35.6 1.0 O C:THR67 5.0 36.9 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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 D:Na1144 b:27.8 occ:1.00 O D:HOH2138 2.1 23.0 0.5 O E:HOH2097 2.2 11.9 0.3 OG D:SER68 2.4 37.9 1.0 OG E:SER68 2.5 37.2 1.0 O E:HOH2099 2.5 20.8 1.0 O D:HOH2139 2.6 20.6 1.0 O E:HOH2098 3.0 23.1 0.7 O E:HOH2065 3.3 17.8 0.5 CB D:SER68 3.6 35.8 1.0 CB E:SER68 3.6 37.8 1.0 CA D:SER68 4.2 35.9 1.0 CA E:SER68 4.2 36.5 1.0 O E:ASP115 4.2 38.3 1.0 O D:ASP115 4.2 38.1 1.0 N E:TYR69 4.3 37.6 1.0 N D:TYR69 4.4 36.4 1.0 O D:TYR69 4.4 38.0 1.0 O E:TYR69 4.5 39.4 1.0 CA E:ASP115 4.5 37.6 1.0 O E:PRO114 4.5 36.5 1.0 CA D:ASP115 4.6 38.0 1.0 C E:ASP115 4.6 37.3 1.0 OD1 E:ASP115 4.6 37.0 1.0 C D:ASP115 4.6 37.8 1.0 O D:PRO114 4.6 38.3 1.0 OD1 D:ASP115 4.6 38.5 1.0 NH2 E:ARG18 4.7 41.5 1.0 NH2 D:ARG18 4.8 40.4 1.0 C E:SER68 4.8 37.3 1.0 C D:SER68 4.8 36.3 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