Manganese in PDB 6jvw: Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate

The structure of Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate, PDB code: 6jvw was solved by H.Hong, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.58 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.409, 74.181, 68.727, 90.00, 119.07, 90.00
R / Rfree (%)	15.3 / 20.3

The binding sites of Manganese atom in the Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate (pdb code 6jvw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate, PDB code: 6jvw:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:34.6 occ:1.00 OE2 A:GLU134 2.0 30.2 1.0 OD2 A:ASP163 2.0 29.0 1.0 O2 A:PYR401 2.1 46.9 1.0 OE1 A:GLU132 2.2 37.1 1.0 O A:HOH503 2.2 22.3 1.0 O3 A:PYR401 2.3 46.9 1.0 C1 A:PYR401 2.8 58.7 1.0 C2 A:PYR401 2.8 54.7 1.0 CD A:GLU134 3.1 26.8 1.0 CG A:ASP163 3.1 29.7 1.0 CD A:GLU132 3.4 35.9 1.0 OE1 A:GLU134 3.5 24.4 1.0 CB A:ASP163 3.5 28.7 1.0 NZ A:LYS176 3.7 48.0 1.0 O1 A:PYR401 3.9 53.2 1.0 OE2 A:GLU132 4.0 39.6 1.0 O A:TYR82 4.1 30.0 1.0 OD1 A:ASP163 4.2 29.9 1.0 C3 A:PYR401 4.3 53.3 1.0 CG A:GLU134 4.4 25.8 1.0 CZ A:PHE105 4.4 32.6 1.0 CB A:GLU132 4.5 31.1 1.0 CG A:GLU132 4.5 33.0 1.0 CA A:GLY245 4.7 23.7 1.0 CE2 A:PHE105 4.8 31.8 1.0 CG2 A:THR246 4.8 28.8 1.0 CB A:THR246 4.9 28.7 1.0 N A:THR246 4.9 28.0 1.0 O A:ASP163 4.9 31.9 1.0 C A:GLY245 4.9 23.7 1.0 CE A:LYS176 4.9 45.6 1.0 CA A:ASP163 5.0 29.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6 in Complex with Manganese (II) Ion and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:29.1 occ:1.00 OD2 B:ASP163 2.0 31.7 1.0 OE2 B:GLU134 2.0 27.5 1.0 O1 B:PYR401 2.2 41.8 1.0 OE1 B:GLU132 2.2 27.9 1.0 O3 B:PYR401 2.3 43.2 1.0 O B:HOH527 2.3 24.3 1.0 C1 B:PYR401 2.9 46.3 1.0 C2 B:PYR401 2.9 45.3 1.0 CG B:ASP163 3.1 30.9 1.0 CD B:GLU134 3.1 25.9 1.0 CD B:GLU132 3.4 31.0 1.0 OE1 B:GLU134 3.5 26.2 1.0 CB B:ASP163 3.5 29.1 1.0 NZ B:LYS176 4.0 42.5 1.0 O2 B:PYR401 4.0 43.2 1.0 OE2 B:GLU132 4.1 38.6 1.0 OD1 B:ASP163 4.2 30.4 1.0 O B:TYR82 4.2 29.1 1.0 C3 B:PYR401 4.3 42.2 1.0 CG B:GLU134 4.4 24.3 1.0 CB B:GLU132 4.4 27.0 1.0 CZ B:PHE105 4.5 37.1 1.0 CG B:GLU132 4.6 27.1 1.0 CA B:GLY245 4.7 22.9 1.0 CB B:THR246 4.7 25.7 1.0 CG2 B:THR246 4.8 25.4 1.0 CE1 B:PHE105 4.8 34.8 1.0 N B:THR246 4.8 26.0 1.0 C B:GLY245 4.9 23.4 1.0 O B:ASP163 4.9 31.8 1.0 CA B:ASP163 5.0 28.8 1.0 CB B:ALA81 5.0 23.3 1.0

H.Hong, H.Seo, K.J.Kim. Structural Insights Into A Maleylpyruvate Hydrolase From Sphingobium Sp. Syk-6, A Bacterium Degrading Lignin-Derived Aryls. Biochem.Biophys.Res.Commun. V. 514 765 2019.
ISSN: ESSN 1090-2104
PubMed: 31079929
DOI: 10.1016/J.BBRC.2019.05.030