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

Protein crystallography data

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

Iron Binding Sites:

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 6b9r

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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 6b9r

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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 6b9r

Go back to Iron Binding Sites List in 6b9r
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 6b9r

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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

Reference:

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
Page generated: Sun Dec 13 16:21:15 2020

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