Iron in PDB 5xbp: Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2

The structure of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2, PDB code: 5xbp was solved by S.Ramaswamy, A.Kumari, D.Singh, R.Gurunath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.804, 178.804, 242.323, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 28.4

The binding sites of Iron atom in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 (pdb code 5xbp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2, PDB code: 5xbp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:51.2 occ:1.00 NE2 A:HIS206 1.8 41.6 1.0 OD2 A:ASP360 2.1 54.4 1.0 NE2 A:HIS211 2.1 33.7 1.0 OD1 A:ASP360 2.2 51.3 1.0 CG A:ASP360 2.5 48.5 1.0 CE1 A:HIS206 2.5 42.9 1.0 CD2 A:HIS211 2.9 38.9 1.0 CD2 A:HIS206 3.0 41.0 1.0 CE1 A:HIS211 3.3 38.7 1.0 O A:HOH614 3.5 29.0 1.0 ND1 A:HIS206 3.7 44.1 1.0 CG A:HIS206 4.0 44.6 1.0 CB A:ASP360 4.0 45.6 1.0 ND2 A:ASN199 4.1 36.8 1.0 CG A:HIS211 4.1 36.0 1.0 ND1 A:HIS211 4.3 34.5 1.0 CE3 A:TRP356 4.7 31.4 1.0 O A:TRP356 4.9 31.2 1.0 OD1 A:ASN199 5.0 45.1 1.0

Iron binding site 2 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:70.9 occ:1.00 FE1 A:FES502 0.0 70.9 1.0 S1 A:FES502 2.1 60.4 1.0 S2 A:FES502 2.2 67.3 1.0 ND1 A:HIS81 2.2 39.9 1.0 ND1 A:HIS102 2.3 48.2 1.0 FE2 A:FES502 2.9 60.3 1.0 CE1 A:HIS102 3.0 49.2 1.0 CG A:HIS81 3.1 36.4 1.0 CB A:HIS81 3.2 36.8 1.0 CE1 A:HIS81 3.3 43.4 1.0 CG A:HIS102 3.4 52.2 1.0 N A:ARG82 3.9 32.9 1.0 CB A:HIS102 3.9 50.3 1.0 NE2 A:HIS102 4.1 49.4 1.0 N A:HIS102 4.2 40.0 1.0 CB A:TYR101 4.2 39.9 1.0 CD2 A:HIS81 4.2 41.8 1.0 CG A:ARG82 4.3 39.2 1.0 NE2 A:HIS81 4.3 48.0 1.0 CD2 A:HIS102 4.4 50.0 1.0 CB A:ARG82 4.4 35.6 1.0 CA A:HIS81 4.5 34.5 1.0 CG A:TYR101 4.5 42.8 1.0 CD2 A:TYR101 4.5 43.1 1.0 C A:HIS81 4.6 39.4 1.0 CA A:HIS102 4.7 45.4 1.0 SG A:CYS79 4.7 34.6 1.0 CA A:ARG82 4.8 29.9 1.0 SG A:CYS99 4.9 32.8 1.0 C A:TYR101 4.9 42.2 1.0 CD1 A:TRP104 4.9 39.1 1.0 NE1 A:TRP104 4.9 35.2 1.0

Iron binding site 3 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:60.3 occ:1.00 FE2 A:FES502 0.0 60.3 1.0 S1 A:FES502 2.2 60.4 1.0 S2 A:FES502 2.2 67.3 1.0 SG A:CYS99 2.4 32.8 1.0 SG A:CYS79 2.5 34.6 1.0 FE1 A:FES502 2.9 70.9 1.0 CB A:CYS79 3.2 32.2 1.0 CB A:CYS99 3.6 38.1 1.0 CB A:HIS81 4.2 36.8 1.0 CB A:TYR101 4.3 39.9 1.0 CB A:LYS84 4.5 28.5 1.0 O A:CYS99 4.5 38.8 1.0 N A:ARG82 4.6 32.9 1.0 CA A:CYS79 4.7 33.7 1.0 ND1 A:HIS102 4.7 48.2 1.0 ND1 A:HIS81 4.8 39.9 1.0 N A:LYS84 4.8 32.5 1.0 N A:HIS81 4.8 28.2 1.0 CA A:CYS99 4.9 40.8 1.0 CB A:TRP104 4.9 31.8 1.0 C A:CYS99 4.9 36.4 1.0 N A:HIS102 5.0 40.0 1.0 CG A:HIS81 5.0 36.4 1.0

Iron binding site 4 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:71.1 occ:1.00 NE2 D:HIS206 1.9 43.1 1.0 NE2 D:HIS211 2.0 40.8 1.0 OD2 D:ASP360 2.3 44.4 1.0 O D:HOH608 2.5 55.6 1.0 CE1 D:HIS206 2.7 46.6 1.0 CD2 D:HIS211 2.9 42.5 1.0 CD2 D:HIS206 3.1 47.5 1.0 CE1 D:HIS211 3.1 45.9 1.0 CG D:ASP360 3.2 54.0 1.0 CB D:ASP360 3.9 50.5 1.0 ND1 D:HIS206 3.9 41.5 1.0 ND2 D:ASN199 4.0 42.5 1.0 CG D:HIS211 4.1 40.4 1.0 OD1 D:ASP360 4.1 60.2 1.0 CG D:HIS206 4.1 45.3 1.0 ND1 D:HIS211 4.2 40.2 1.0 CE3 D:TRP356 4.6 37.6 1.0 O D:TRP356 4.9 40.3 1.0 CZ3 D:TRP356 5.0 37.2 1.0

Iron binding site 5 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:69.7 occ:1.00 FE1 D:FES502 0.0 69.7 1.0 S1 D:FES502 2.2 65.7 1.0 S2 D:FES502 2.2 73.3 1.0 ND1 D:HIS102 2.3 42.6 1.0 ND1 D:HIS81 2.4 37.6 1.0 CE1 D:HIS102 2.8 49.4 1.0 FE2 D:FES502 2.9 66.5 1.0 CG D:HIS81 3.2 40.5 1.0 CB D:HIS81 3.3 36.4 1.0 CE1 D:HIS81 3.5 40.0 1.0 CG D:HIS102 3.5 45.5 1.0 N D:ARG82 4.0 35.2 1.0 NE2 D:HIS102 4.1 45.0 1.0 CB D:HIS102 4.1 44.6 1.0 CB D:TYR101 4.2 40.3 1.0 N D:HIS102 4.3 46.5 1.0 CG D:ARG82 4.4 32.4 1.0 CD2 D:HIS102 4.4 46.2 1.0 CD2 D:HIS81 4.4 38.9 1.0 CB D:ARG82 4.5 39.6 1.0 NE2 D:HIS81 4.5 42.0 1.0 CG D:TYR101 4.5 45.6 1.0 CA D:HIS81 4.5 35.3 1.0 CD2 D:TYR101 4.6 39.1 1.0 SG D:CYS79 4.7 34.5 1.0 C D:HIS81 4.7 40.8 1.0 SG D:CYS99 4.8 34.1 1.0 CA D:ARG82 4.8 34.5 1.0 CA D:HIS102 4.8 44.6 1.0 CD1 D:TRP104 4.8 36.2 1.0 CG D:TRP104 4.9 35.3 1.0 NE1 D:TRP104 4.9 40.7 1.0

Iron binding site 6 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:66.5 occ:1.00 FE2 D:FES502 0.0 66.5 1.0 S1 D:FES502 2.2 65.7 1.0 S2 D:FES502 2.2 73.3 1.0 SG D:CYS99 2.4 34.1 1.0 SG D:CYS79 2.5 34.5 1.0 FE1 D:FES502 2.9 69.7 1.0 CB D:CYS79 3.2 34.5 1.0 CB D:CYS99 3.4 36.7 1.0 CB D:HIS81 4.3 36.4 1.0 O D:CYS99 4.4 35.1 1.0 CB D:TRP104 4.5 31.8 1.0 CB D:TYR101 4.6 40.3 1.0 CB D:LYS84 4.7 19.4 1.0 CA D:CYS79 4.7 30.1 1.0 ND1 D:HIS102 4.7 42.6 1.0 CA D:CYS99 4.7 35.3 1.0 CG D:TRP104 4.8 35.3 1.0 C D:CYS99 4.8 34.4 1.0 N D:ARG82 4.9 35.2 1.0 N D:LYS84 4.9 25.1 1.0 N D:HIS81 4.9 30.5 1.0 ND1 D:HIS81 5.0 37.6 1.0

Iron binding site 7 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe501 b:54.1 occ:1.00 NE2 G:HIS206 1.8 38.0 1.0 NE2 G:HIS211 1.9 38.0 1.0 OD2 G:ASP360 2.3 49.3 1.0 OD1 G:ASP360 2.5 46.6 1.0 CE1 G:HIS206 2.7 41.4 1.0 CD2 G:HIS211 2.7 43.5 1.0 CG G:ASP360 2.7 48.3 1.0 CD2 G:HIS206 3.0 41.7 1.0 CE1 G:HIS211 3.1 44.6 1.0 ND1 G:HIS206 3.9 40.3 1.0 CG G:HIS211 4.0 44.0 1.0 CG G:HIS206 4.0 40.4 1.0 ND1 G:HIS211 4.1 44.8 1.0 O G:HOH611 4.1 38.5 1.0 ND2 G:ASN199 4.1 31.8 1.0 CB G:ASP360 4.3 46.9 1.0 CE3 G:TRP356 4.4 32.4 1.0 O G:TRP356 4.8 38.0 1.0 CZ3 G:TRP356 4.9 28.2 1.0

Iron binding site 8 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe502 b:75.0 occ:1.00 FE1 G:FES502 0.0 75.0 1.0 ND1 G:HIS81 2.1 37.8 1.0 S2 G:FES502 2.2 66.7 1.0 S1 G:FES502 2.2 56.6 1.0 ND1 G:HIS102 2.2 37.8 1.0 CE1 G:HIS102 2.8 48.6 1.0 CG G:HIS81 2.9 37.7 1.0 FE2 G:FES502 2.9 61.9 1.0 CB G:HIS81 2.9 32.8 1.0 CE1 G:HIS81 3.2 40.4 1.0 CG G:HIS102 3.3 48.2 1.0 CB G:HIS102 3.9 54.4 1.0 NE2 G:HIS102 3.9 45.2 1.0 N G:ARG82 4.0 38.0 1.0 CD2 G:HIS81 4.1 37.7 1.0 CD2 G:HIS102 4.2 50.3 1.0 NE2 G:HIS81 4.2 40.7 1.0 N G:HIS102 4.3 45.5 1.0 CA G:HIS81 4.3 32.9 1.0 CG G:ARG82 4.4 41.0 1.0 CB G:TYR101 4.4 48.5 1.0 SG G:CYS79 4.5 31.1 1.0 CB G:ARG82 4.6 41.7 1.0 C G:HIS81 4.7 38.3 1.0 CG G:TYR101 4.7 47.7 1.0 CA G:HIS102 4.7 52.4 1.0 CD2 G:TYR101 4.8 42.3 1.0 NE1 G:TRP104 4.8 38.2 1.0 CD1 G:TRP104 4.8 32.9 1.0 CE2 G:TRP104 4.8 30.5 1.0 CG G:TRP104 4.9 33.0 1.0 CA G:ARG82 4.9 39.5 1.0 CD2 G:TRP104 4.9 33.0 1.0 SG G:CYS99 4.9 35.8 1.0

Iron binding site 9 out of 9 in the Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Oxygenase Component of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe502 b:61.9 occ:1.00 FE2 G:FES502 0.0 61.9 1.0 S1 G:FES502 2.2 56.6 1.0 S2 G:FES502 2.2 66.7 1.0 SG G:CYS99 2.4 35.8 1.0 SG G:CYS79 2.4 31.1 1.0 FE1 G:FES502 2.9 75.0 1.0 CB G:CYS79 3.3 30.6 1.0 CB G:CYS99 3.5 35.8 1.0 CB G:HIS81 4.1 32.8 1.0 O G:CYS99 4.3 37.0 1.0 ND1 G:HIS102 4.4 37.8 1.0 CB G:TYR101 4.5 48.5 1.0 CB G:TRP104 4.6 31.0 1.0 CB G:LYS84 4.7 32.7 1.0 CA G:CYS79 4.7 32.2 1.0 CA G:CYS99 4.8 39.6 1.0 ND1 G:HIS81 4.8 37.8 1.0 C G:CYS99 4.8 39.0 1.0 CG G:TRP104 4.8 33.0 1.0 N G:ARG82 4.9 38.0 1.0 N G:HIS81 4.9 32.1 1.0 CG G:HIS81 4.9 37.7 1.0 N G:HIS102 4.9 45.5 1.0

A.Kumari, D.Singh, S.Ramaswamy, G.Ramanathan. Structural and Functional Studies of Ferredoxin and Oxygenase Components of 3-Nitrotoluene Dioxygenase From Diaphorobacter Sp. Strain DS2. Plos One V. 12 76398 2017.
ISSN: ESSN 1932-6203
PubMed: 28448625
DOI: 10.1371/JOURNAL.PONE.0176398