Iron in PDB 6r9n: Peroxy Diiron Species of Chemotaxis Sensor Odp

The structure of Peroxy Diiron Species of Chemotaxis Sensor Odp, PDB code: 6r9n was solved by A.R.Muok, B.R.Crane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.73 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.675, 85.451, 118.803, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.9

The structure of Peroxy Diiron Species of Chemotaxis Sensor Odp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Peroxy Diiron Species of Chemotaxis Sensor Odp (pdb code 6r9n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Peroxy Diiron Species of Chemotaxis Sensor Odp, PDB code: 6r9n:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Peroxy Diiron Species of Chemotaxis Sensor Odp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Peroxy Diiron Species of Chemotaxis Sensor Odp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:28.1 occ:1.00 O A:O304 2.1 22.6 1.0 OD2 A:ASP84 2.2 31.1 1.0 OD1 A:ASP167 2.2 22.1 1.0 NE2 A:HIS225 2.2 32.8 1.0 O1 A:PER303 2.3 26.2 1.0 OE1 A:GLN224 2.3 36.5 1.0 CE1 A:HIS225 3.1 29.5 1.0 CG A:ASP167 3.1 25.2 1.0 CG A:ASP84 3.2 32.8 1.0 CD2 A:HIS225 3.3 29.5 1.0 CD A:GLN224 3.3 37.9 1.0 O2 A:PER303 3.3 22.9 1.0 OD2 A:ASP167 3.4 25.7 1.0 FE A:FE302 3.5 22.6 1.0 OD1 A:ASP84 3.5 30.3 1.0 NE2 A:GLN224 3.7 36.6 1.0 ND1 A:HIS225 4.3 32.9 1.0 CG A:HIS225 4.4 34.2 1.0 CE1 A:HIS80 4.5 26.7 1.0 CB A:ASP167 4.5 22.5 1.0 CB A:ASP84 4.6 30.8 1.0 CG A:GLN224 4.6 34.4 1.0 NE2 A:HIS80 4.6 26.5 1.0 CE1 B:PHE109 4.6 37.4 1.0 CB A:GLN224 4.7 33.4 1.0 OD2 A:ASP82 4.8 28.5 1.0 CD1 B:PHE109 4.8 38.7 1.0 CG2 A:VAL85 4.9 33.7 1.0 CA A:ASP167 4.9 26.2 1.0

Iron binding site 2 out of 4 in the Peroxy Diiron Species of Chemotaxis Sensor Odp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Peroxy Diiron Species of Chemotaxis Sensor Odp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:22.6 occ:1.00 OD2 A:ASP82 2.0 28.5 1.0 O A:O304 2.1 22.6 1.0 OD2 A:ASP167 2.1 25.7 1.0 NE2 A:HIS148 2.2 22.7 1.0 O2 A:PER303 2.3 22.9 1.0 NE2 A:HIS80 2.4 26.5 1.0 CG A:ASP82 3.1 25.8 1.0 CE1 A:HIS148 3.1 21.6 1.0 O1 A:PER303 3.1 26.2 1.0 CG A:ASP167 3.2 25.2 1.0 CE1 A:HIS80 3.2 26.7 1.0 CD2 A:HIS148 3.2 21.3 1.0 CD2 A:HIS80 3.4 25.7 1.0 FE A:FE301 3.5 28.1 1.0 OD1 A:ASP167 3.5 22.1 1.0 CB A:ASP82 3.7 24.2 1.0 O A:HOH420 3.9 24.5 1.0 OD1 A:ASP82 4.0 22.4 1.0 ND1 A:HIS148 4.2 24.8 1.0 OD1 A:ASP84 4.3 30.3 1.0 CG A:HIS148 4.4 24.0 1.0 ND1 A:HIS80 4.4 26.1 1.0 CB A:ASP167 4.4 22.5 1.0 CG A:HIS80 4.5 26.9 1.0 OD2 A:ASP84 4.7 31.1 1.0 CZ3 B:TRP106 4.7 25.1 1.0 OE1 A:GLN224 4.9 36.5 1.0 CH2 B:TRP106 4.9 26.5 1.0 CG A:ASP84 5.0 32.8 1.0

Iron binding site 3 out of 4 in the Peroxy Diiron Species of Chemotaxis Sensor Odp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Peroxy Diiron Species of Chemotaxis Sensor Odp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:29.8 occ:1.00 O B:O304 2.1 28.6 1.0 NE2 B:HIS225 2.2 38.1 1.0 OD1 B:ASP167 2.2 27.1 1.0 OD2 B:ASP84 2.2 33.4 1.0 OE1 B:GLN224 2.2 30.6 1.0 O1 B:PER303 2.3 32.5 1.0 CE1 B:HIS225 3.0 36.1 1.0 CD B:GLN224 3.2 37.3 1.0 CG B:ASP167 3.2 27.4 1.0 CG B:ASP84 3.2 35.2 1.0 CD2 B:HIS225 3.3 31.1 1.0 OD2 B:ASP167 3.4 26.0 1.0 O2 B:PER303 3.5 30.8 1.0 FE B:FE302 3.5 26.2 1.0 OD1 B:ASP84 3.5 37.1 1.0 NE2 B:GLN224 3.6 38.6 1.0 ND1 B:HIS225 4.2 37.0 1.0 CG B:HIS225 4.3 32.6 1.0 CE1 B:HIS80 4.4 25.0 1.0 CG B:GLN224 4.5 32.7 1.0 NE2 B:HIS80 4.5 22.2 1.0 CB B:ASP167 4.6 24.1 1.0 CB B:ASP84 4.6 32.3 1.0 CB B:GLN224 4.7 32.1 1.0 CE2 A:PHE109 4.8 51.9 1.0 OD2 B:ASP82 4.9 23.4 1.0 CA B:ASP167 4.9 28.7 1.0

Iron binding site 4 out of 4 in the Peroxy Diiron Species of Chemotaxis Sensor Odp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Peroxy Diiron Species of Chemotaxis Sensor Odp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:26.2 occ:1.00 OD2 B:ASP167 2.1 26.0 1.0 O B:O304 2.1 28.6 1.0 OD2 B:ASP82 2.1 23.4 1.0 NE2 B:HIS148 2.2 18.8 1.0 NE2 B:HIS80 2.3 22.2 1.0 O2 B:PER303 2.4 30.8 1.0 O1 B:PER303 3.0 32.5 1.0 CE1 B:HIS148 3.1 21.8 1.0 CG B:ASP82 3.1 23.4 1.0 CG B:ASP167 3.2 27.4 1.0 CE1 B:HIS80 3.3 25.0 1.0 CD2 B:HIS148 3.3 22.6 1.0 CD2 B:HIS80 3.3 23.7 1.0 FE B:FE301 3.5 29.8 1.0 OD1 B:ASP167 3.6 27.1 1.0 CB B:ASP82 3.8 26.0 1.0 O B:HOH442 3.9 28.3 1.0 OD1 B:ASP82 4.1 24.4 1.0 ND1 B:HIS148 4.3 20.5 1.0 OD1 B:ASP84 4.3 37.1 1.0 CG B:HIS148 4.4 22.9 1.0 ND1 B:HIS80 4.4 27.0 1.0 CB B:ASP167 4.4 24.1 1.0 CG B:HIS80 4.5 24.5 1.0 CZ3 A:TRP106 4.7 22.7 1.0 OD2 B:ASP84 4.8 33.4 1.0 OE1 B:GLN224 4.8 30.6 1.0 CG B:ASP84 5.0 35.2 1.0 CH2 A:TRP106 5.0 19.7 1.0

A.R.Muok, Y.Deng, V.M.Gumerov, J.E.Chong, J.R.Derosa, K.Kurniyati, R.E.Coleman, K.M.Lancaster, C.Li, I.B.Zhulin, B.R.Crane. A Di-Iron Protein Recruited As An Fe[II] and Oxygen Sensor For Bacterial Chemotaxis Functions By Stabilizing An Iron-Peroxy Species. Proc.Natl.Acad.Sci.Usa V. 116 14955 2019.
ISSN: ESSN 1091-6490
PubMed: 31270241
DOI: 10.1073/PNAS.1904234116