Iron in PDB 5ucu: Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products

The structure of Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products, PDB code: 5ucu was solved by V.Vitvitsky, P.K.Yadav, S.An, J.Seravalli, U.-S.Cho, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.30 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.766, 53.766, 193.254, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.2

The binding sites of Iron atom in the Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products (pdb code 5ucu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products, PDB code: 5ucu:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.0 occ:1.00 FE A:HEM201 0.0 27.0 1.0 NB A:HEM201 2.0 22.2 1.0 NA A:HEM201 2.0 23.5 1.0 NC A:HEM201 2.1 24.1 1.0 ND A:HEM201 2.1 28.5 1.0 S A:H2S202 2.2 31.0 1.0 CE1 A:HIS87 2.4 26.3 1.0 C4A A:HEM201 3.0 25.9 1.0 C1B A:HEM201 3.0 24.7 1.0 C4B A:HEM201 3.1 21.4 1.0 C1C A:HEM201 3.1 27.9 1.0 C1D A:HEM201 3.1 27.1 1.0 C1A A:HEM201 3.1 27.0 1.0 C4C A:HEM201 3.1 25.4 1.0 C4D A:HEM201 3.1 26.4 1.0 NE2 A:HIS87 3.2 32.7 1.0 ND1 A:HIS87 3.4 28.7 1.0 CHB A:HEM201 3.4 25.2 1.0 CHC A:HEM201 3.4 26.0 1.0 CHD A:HEM201 3.5 27.1 1.0 CHA A:HEM201 3.5 28.9 1.0 C3A A:HEM201 4.3 30.4 1.0 C2B A:HEM201 4.3 25.0 1.0 C3B A:HEM201 4.3 22.7 1.0 C2C A:HEM201 4.3 24.8 1.0 C2A A:HEM201 4.3 27.6 1.0 C2D A:HEM201 4.3 29.1 1.0 C3C A:HEM201 4.3 29.2 1.0 C3D A:HEM201 4.3 31.7 1.0 NE2 A:HIS58 4.3 31.8 1.0 CD2 A:HIS87 4.4 26.6 1.0 CG A:HIS87 4.5 25.9 1.0 CE1 A:HIS58 5.0 33.9 1.0

Iron binding site 2 out of 2 in the Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:30.8 occ:0.84 FE B:HEM201 0.0 30.8 0.8 ND B:HEM201 2.0 33.9 1.0 NA B:HEM201 2.1 29.7 1.0 NB B:HEM201 2.1 33.3 1.0 NC B:HEM201 2.1 28.9 1.0 S B:H2S202 2.2 44.1 1.0 NE2 B:HIS92 2.3 35.5 1.0 C4D B:HEM201 3.0 39.9 1.0 C1A B:HEM201 3.0 40.0 1.0 C1D B:HEM201 3.1 41.4 1.0 C1C B:HEM201 3.1 32.4 1.0 C4B B:HEM201 3.1 35.9 1.0 C4C B:HEM201 3.1 34.3 1.0 C4A B:HEM201 3.1 34.6 1.0 C1B B:HEM201 3.1 36.3 1.0 CD2 B:HIS92 3.3 32.1 1.0 CE1 B:HIS92 3.3 38.4 1.0 CHA B:HEM201 3.4 37.6 1.0 CHC B:HEM201 3.4 34.0 1.0 CHD B:HEM201 3.4 37.8 1.0 CHB B:HEM201 3.5 32.5 1.0 C3D B:HEM201 4.3 42.9 1.0 C2D B:HEM201 4.3 42.3 1.0 C2C B:HEM201 4.3 27.9 1.0 C2A B:HEM201 4.3 33.0 1.0 C3C B:HEM201 4.3 27.5 1.0 C3A B:HEM201 4.3 31.2 1.0 C3B B:HEM201 4.3 35.9 1.0 C2B B:HEM201 4.3 34.7 1.0 NE2 B:HIS63 4.3 48.4 1.0 CG B:HIS92 4.4 36.5 1.0 ND1 B:HIS92 4.4 39.3 1.0 CG2 B:VAL67 4.6 36.1 1.0

V.Vitvitsky, P.K.Yadav, S.An, J.Seravalli, U.S.Cho, R.Banerjee. Structural and Mechanistic Insights Into Hemoglobin-Catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products. J. Biol. Chem. V. 292 5584 2017.
ISSN: ESSN 1083-351X
PubMed: 28213526
DOI: 10.1074/JBC.M117.774943