Iron in PDB 6b9r: Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound

The structure of Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9r was solved by D.A.Born, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.17 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.238, 100.707, 99.088, 90.00, 92.27, 90.00
R / Rfree (%)	15.2 / 18.9

The binding sites of Iron atom in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound (pdb code 6b9r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound, PDB code: 6b9r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.4 occ:1.00 OE1 A:GLN153 2.1 25.7 1.0 NE2 A:HIS190 2.2 26.7 1.0 O4 A:2HE502 2.2 36.8 1.0 NE2 A:HIS149 2.3 22.5 1.0 O3 A:2HE502 2.5 33.1 1.0 O A:HOH717 2.6 29.6 1.0 CE1 A:HIS190 2.8 27.2 1.0 CD2 A:HIS149 3.1 23.9 1.0 CD A:GLN153 3.2 28.6 1.0 CB A:2HE502 3.4 40.6 1.0 CE1 A:HIS149 3.4 23.9 1.0 CD2 A:HIS190 3.4 29.6 1.0 NE2 A:GLN153 3.6 23.3 1.0 P A:2HE502 3.8 44.4 1.0 NZ D:LYS29 3.9 38.6 1.0 ND2 A:ASN146 3.9 20.0 1.0 CA A:2HE502 4.0 39.7 1.0 ND1 A:HIS190 4.1 25.6 1.0 CG A:HIS149 4.3 28.1 1.0 CG A:HIS190 4.4 20.1 1.0 ND1 A:HIS149 4.4 24.2 1.0 CG A:GLN153 4.5 24.7 1.0 CG2 A:THR207 4.7 21.5 1.0 O1 A:2HE502 4.7 27.8 1.0 CB A:GLN153 4.8 28.5 1.0 CE D:LYS29 4.9 35.0 1.0 O2 A:2HE502 4.9 35.3 1.0

Iron binding site 2 out of 4 in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:35.3 occ:1.00 O4 B:2HE502 2.1 31.1 1.0 OE1 B:GLN153 2.2 22.2 1.0 NE2 B:HIS190 2.3 27.3 1.0 NE2 B:HIS149 2.3 21.2 1.0 O B:HOH846 2.5 30.3 1.0 O1 B:2HE502 2.5 27.7 1.0 CE1 B:HIS190 3.0 30.8 1.0 CD B:GLN153 3.1 22.9 1.0 CD2 B:HIS149 3.2 19.9 1.0 CB B:2HE502 3.2 32.8 1.0 NE2 B:GLN153 3.4 17.4 1.0 CE1 B:HIS149 3.4 20.3 1.0 CD2 B:HIS190 3.4 33.0 1.0 P B:2HE502 3.8 33.5 1.0 NZ C:LYS29 3.8 24.1 1.0 CA B:2HE502 3.9 22.7 1.0 ND2 B:ASN146 4.0 17.6 1.0 ND1 B:HIS190 4.2 29.3 1.0 CG B:HIS149 4.4 20.7 1.0 CG B:HIS190 4.5 26.7 1.0 CG B:GLN153 4.5 20.2 1.0 ND1 B:HIS149 4.5 19.2 1.0 CG2 B:THR207 4.7 16.2 1.0 O3 B:2HE502 4.7 27.5 1.0 CE C:LYS29 4.8 18.1 1.0 CB B:GLN153 4.9 22.3 1.0 O B:HOH947 4.9 32.3 1.0 O2 B:2HE502 4.9 27.4 1.0

Iron binding site 3 out of 4 in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:39.4 occ:1.00 O4 C:2HE502 2.1 37.0 1.0 NE2 C:HIS190 2.1 16.3 1.0 NE2 C:HIS149 2.2 19.4 1.0 O C:HOH942 2.3 23.3 1.0 O2 C:2HE502 2.4 30.4 1.0 O C:HOH602 2.7 30.4 1.0 CD2 C:HIS149 2.9 19.3 1.0 CE1 C:HIS190 3.0 14.6 1.0 CD2 C:HIS190 3.2 16.9 1.0 CE1 C:HIS149 3.4 19.1 1.0 CB C:2HE502 3.5 31.6 1.0 P C:2HE502 3.7 34.1 1.0 NZ B:LYS29 3.8 37.7 1.0 ND2 C:ASN146 3.8 16.0 1.0 CA C:2HE502 4.0 24.9 1.0 O C:HOH612 4.0 35.7 1.0 ND1 C:HIS190 4.2 16.1 1.0 CG C:HIS149 4.2 18.9 1.0 CG C:HIS190 4.3 12.6 1.0 ND1 C:HIS149 4.4 19.6 1.0 CG C:GLN153 4.5 26.4 1.0 O3 C:2HE502 4.7 19.8 1.0 CG2 C:THR207 4.7 14.3 1.0 O1 C:2HE502 4.8 27.5 1.0 CE B:LYS29 4.8 26.1 1.0 NE2 C:GLN153 4.8 11.9 1.0 CD C:GLN153 4.9 24.1 1.0 CE1 C:PHE192 4.9 13.5 1.0 O C:HOH887 5.0 24.5 1.0

Iron binding site 4 out of 4 in the Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Streptomyces Albus Hepd with Substrate 2-Hydroxyethylphosphonate (2- Hep) and Fe(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:35.3 occ:1.00 NE2 D:HIS190 2.1 20.1 1.0 O4 D:2HE502 2.2 42.2 1.0 NE2 D:HIS149 2.2 23.2 1.0 O D:HOH933 2.2 26.0 1.0 O1 D:2HE502 2.3 35.8 1.0 O D:HOH621 2.6 31.5 1.0 CE1 D:HIS190 2.9 20.9 1.0 CD2 D:HIS149 3.1 22.9 1.0 CE1 D:HIS149 3.3 18.7 1.0 CD2 D:HIS190 3.3 22.7 1.0 CB D:2HE502 3.6 34.3 1.0 P D:2HE502 3.7 39.0 1.0 ND2 D:ASN146 3.9 19.5 1.0 O D:HOH617 3.9 37.2 1.0 CA D:2HE502 4.1 33.2 1.0 ND1 D:HIS190 4.1 20.8 1.0 CG D:HIS149 4.3 18.2 1.0 CG D:HIS190 4.3 20.3 1.0 ND1 D:HIS149 4.3 18.9 1.0 NZ A:LYS29 4.7 33.4 1.0 O2 D:2HE502 4.7 29.5 1.0 OE1 D:GLN153 4.7 23.1 1.0 CE A:LYS29 4.7 30.4 1.0 CG2 D:THR207 4.8 19.9 1.0 O3 D:2HE502 4.8 25.9 1.0 CE1 D:PHE192 4.9 16.9 1.0 CB D:GLN153 4.9 34.9 1.0

D.A.Born, E.C.Ulrich, K.S.Ju, S.C.Peck, W.A.Van Der Donk, C.L.Drennan. Structural Basis For Methylphosphonate Biosynthesis. Science V. 358 1336 2017.
ISSN: ESSN 1095-9203
PubMed: 29217579
DOI: 10.1126/SCIENCE.AAO3435