Iron in PDB 5ve3: Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans

All present enzymatic activity of Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans:
1.13.11.18; 2.8.1.1;

The structure of Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans, PDB code: 5ve3 was solved by N.Motl, M.A.Skiba, J.L.Smith, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.60 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.689, 108.333, 119.616, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.6

The binding sites of Iron atom in the Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans (pdb code 5ve3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans, PDB code: 5ve3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:29.6 occ:1.00 O B:HOH758 2.0 34.2 1.0 OD2 B:ASP133 2.0 29.0 1.0 NE2 B:HIS58 2.1 30.6 1.0 NE2 B:HIS114 2.2 29.7 1.0 O B:HOH616 2.2 31.1 1.0 O B:HOH659 2.3 29.2 1.0 CD2 B:HIS58 3.1 30.8 1.0 CG B:ASP133 3.1 32.3 1.0 CD2 B:HIS114 3.1 31.3 1.0 CE1 B:HIS58 3.1 30.6 1.0 CE1 B:HIS114 3.2 30.5 1.0 CB B:ASP133 3.5 26.5 1.0 OD1 B:ASP133 4.2 38.2 1.0 ND1 B:HIS58 4.2 27.4 1.0 O B:HOH842 4.2 34.5 1.0 CG B:HIS58 4.2 25.6 1.0 CG B:HIS114 4.3 28.4 1.0 ND1 B:HIS114 4.3 29.5 1.0 OD1 B:ASP62 4.3 39.9 1.0 O B:HOH823 4.4 42.0 1.0 CE1 B:HIS174 4.5 32.9 1.0 ND1 B:HIS60 4.5 29.7 1.0 N B:ALA61 4.5 28.7 1.0 CA B:HIS60 4.6 28.9 1.0 O B:HOH814 4.6 45.7 1.0 OE1 B:GLN146 4.6 33.3 1.0 O B:VAL59 4.7 30.5 1.0 ND1 B:HIS174 4.9 32.3 1.0 CA B:ASP133 5.0 27.5 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Wild-Type Persulfide Dioxygenase-Rhodanese Fusion Protein From Burkholderia Phytofirmans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:28.3 occ:1.00 O A:HOH744 2.0 29.6 1.0 NE2 A:HIS58 2.0 31.2 1.0 NE2 A:HIS114 2.2 32.6 1.0 OD2 A:ASP133 2.2 31.4 1.0 O A:HOH605 2.2 29.6 1.0 O A:HOH673 2.2 30.5 1.0 CD2 A:HIS58 3.0 31.3 1.0 CE1 A:HIS58 3.1 35.6 1.0 CD2 A:HIS114 3.1 26.8 1.0 CE1 A:HIS114 3.1 30.3 1.0 CG A:ASP133 3.2 31.4 1.0 CB A:ASP133 3.6 24.5 1.0 O A:HOH838 4.1 36.8 1.0 CG A:HIS58 4.1 32.9 1.0 ND1 A:HIS58 4.2 34.1 1.0 ND1 A:HIS114 4.2 27.2 1.0 CG A:HIS114 4.2 26.7 1.0 OD1 A:ASP133 4.3 33.4 1.0 OD1 A:ASP62 4.4 41.4 1.0 N A:ALA61 4.4 28.8 1.0 ND1 A:HIS60 4.4 33.8 1.0 CE1 A:HIS174 4.5 30.1 1.0 CA A:HIS60 4.5 32.6 1.0 OE1 A:GLN146 4.5 32.4 1.0 O A:HOH817 4.6 43.7 1.0 O A:VAL59 4.6 29.9 1.0 O A:HOH816 4.7 52.7 1.0 ND1 A:HIS174 5.0 29.4 1.0

N.Motl, M.A.Skiba, O.Kabil, J.L.Smith, R.Banerjee. Structural and Biochemical Analyses Indicate That A Bacterial Persulfide Dioxygenase-Rhodanese Fusion Protein Functions in Sulfur Assimilation. J. Biol. Chem. V. 292 14026 2017.
ISSN: ESSN 1083-351X
PubMed: 28684420
DOI: 10.1074/JBC.M117.790170