Iron in PDB 6wnb: Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound, PDB code: 6wnb was solved by J.Bridwell-Rabb, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.16 / 2.10
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.276, 159.577, 115.979, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.8

The binding sites of Iron atom in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound (pdb code 6wnb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound, PDB code: 6wnb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:29.4 occ:1.00 FE1 A:FES501 0.0 29.4 1.0 ND1 A:HIS57 2.2 30.8 1.0 ND1 A:HIS77 2.2 29.7 1.0 S1 A:FES501 2.2 31.5 1.0 S2 A:FES501 2.2 30.7 1.0 FE2 A:FES501 2.7 28.8 1.0 CE1 A:HIS77 3.1 28.8 1.0 CE1 A:HIS57 3.1 31.0 1.0 CG A:HIS77 3.2 31.1 1.0 CG A:HIS57 3.2 30.2 1.0 CB A:HIS57 3.4 26.6 1.0 CB A:HIS77 3.5 27.3 1.0 N A:HIS77 3.7 28.0 1.0 CB A:TYR76 4.1 31.4 1.0 CA A:HIS77 4.2 26.4 1.0 NE2 A:HIS77 4.2 29.9 1.0 NE2 A:HIS57 4.3 28.1 1.0 CD2 A:HIS77 4.3 31.1 1.0 CD2 A:HIS57 4.3 28.6 1.0 CD2 A:TYR76 4.3 28.1 1.0 N A:ARG58 4.3 28.9 1.0 SG A:CYS74 4.3 27.3 0.5 CB A:ARG58 4.5 31.4 1.0 CG A:TYR76 4.5 31.9 1.0 SG A:CYS55 4.5 29.2 1.0 CG A:ARG58 4.6 28.5 1.0 NE1 A:TRP79 4.6 29.0 1.0 C A:TYR76 4.6 32.0 1.0 CA A:HIS57 4.7 31.5 1.0 CD1 A:TRP79 4.7 28.1 1.0 CE2 A:TRP79 4.8 29.1 1.0 SG A:CYS74 4.8 30.0 0.5 C A:HIS57 4.8 34.2 1.0 CA A:TYR76 4.9 32.5 1.0 CG A:TRP79 5.0 27.4 1.0 CD2 A:TRP79 5.0 27.9 1.0

Iron binding site 2 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.8 occ:1.00 FE2 A:FES501 0.0 28.8 1.0 SG A:CYS74 2.1 27.3 0.5 S1 A:FES501 2.2 31.5 1.0 S2 A:FES501 2.2 30.7 1.0 SG A:CYS55 2.4 29.2 1.0 SG A:CYS74 2.5 30.0 0.5 FE1 A:FES501 2.7 29.4 1.0 CB A:CYS55 3.2 29.4 1.0 CB A:CYS74 3.2 28.9 0.5 CB A:CYS74 3.3 28.9 0.5 CB A:HIS57 4.2 26.6 1.0 CB A:TYR76 4.4 31.4 1.0 ND1 A:HIS57 4.4 30.8 1.0 N A:HIS77 4.6 28.0 1.0 CA A:CYS55 4.6 27.1 1.0 ND1 A:HIS77 4.7 29.7 1.0 CA A:CYS74 4.7 30.6 0.5 CA A:CYS74 4.7 30.5 0.5 CB A:VAL60 4.7 28.6 1.0 N A:ARG58 4.8 28.9 1.0 CG A:HIS57 4.8 30.2 1.0 N A:TYR76 4.9 32.9 1.0

Iron binding site 3 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:36.7 occ:1.00 NE2 A:HIS164 2.0 33.6 1.0 O A:HOH702 2.1 54.4 1.0 NE2 A:HIS169 2.1 41.1 1.0 O A:HOH649 2.2 46.1 1.0 OD1 A:ASP280 2.2 33.3 1.0 OD2 A:ASP280 2.3 42.2 1.0 CG A:ASP280 2.6 37.1 1.0 CD2 A:HIS169 2.9 39.1 1.0 CE1 A:HIS164 3.0 39.3 1.0 CD2 A:HIS164 3.0 41.0 1.0 CE1 A:HIS169 3.2 43.1 1.0 CB A:ASP280 4.1 38.5 1.0 ND1 A:HIS164 4.1 42.1 1.0 CG A:HIS169 4.1 48.0 1.0 CG A:HIS164 4.2 37.6 1.0 OD1 A:ASN158 4.2 39.1 1.0 ND2 A:ASN158 4.2 35.2 1.0 ND1 A:HIS169 4.2 39.7 1.0 CD1 A:ILE168 4.3 46.9 1.0 O A:ASN158 4.4 37.2 1.0 CE1 A:PHE165 4.5 48.6 1.0 CG A:ASN158 4.6 36.8 1.0 CD1 A:PHE165 4.8 45.6 1.0 O A:HOH614 4.8 62.5 1.0 O A:HOH671 4.8 53.6 1.0 CG1 A:ILE168 4.9 45.8 1.0 CA A:ASP280 4.9 37.3 1.0 C6 A:U5A504 4.9 64.3 1.0 O A:THR276 4.9 41.1 1.0

Iron binding site 4 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:30.4 occ:1.00 FE1 B:FES501 0.0 30.4 1.0 ND1 B:HIS77 2.0 31.0 1.0 S1 B:FES501 2.2 32.2 1.0 S2 B:FES501 2.2 32.1 1.0 ND1 B:HIS57 2.3 32.6 1.0 FE2 B:FES501 2.8 29.9 1.0 CE1 B:HIS77 2.9 31.6 1.0 CG B:HIS77 3.1 28.9 1.0 CG B:HIS57 3.1 35.7 1.0 CE1 B:HIS57 3.3 29.4 1.0 CB B:HIS57 3.3 30.4 1.0 CB B:HIS77 3.5 30.3 1.0 N B:HIS77 3.9 33.4 1.0 NE2 B:HIS77 4.1 28.9 1.0 CD2 B:HIS77 4.2 27.0 1.0 CB B:TYR76 4.2 26.4 1.0 CA B:HIS77 4.3 32.1 1.0 N B:ARG58 4.3 30.9 1.0 CD2 B:HIS57 4.3 33.5 1.0 SG B:CYS55 4.3 30.9 0.5 CD2 B:TYR76 4.3 26.3 1.0 NE2 B:HIS57 4.4 33.6 1.0 SG B:CYS55 4.4 30.9 0.5 CB B:ARG58 4.5 33.5 1.0 CG B:TYR76 4.5 32.8 1.0 SG B:CYS74 4.6 32.2 0.5 CG B:ARG58 4.6 34.7 1.0 SG B:CYS74 4.6 32.2 0.5 NE1 B:TRP79 4.6 30.5 1.0 CA B:HIS57 4.6 30.1 1.0 C B:TYR76 4.7 32.3 1.0 CD1 B:TRP79 4.7 27.9 1.0 CE2 B:TRP79 4.7 28.5 1.0 C B:HIS57 4.8 35.4 1.0 CG B:TRP79 5.0 28.7 1.0 CD2 B:TRP79 5.0 27.5 1.0

Iron binding site 5 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.9 occ:1.00 FE2 B:FES501 0.0 29.9 1.0 S2 B:FES501 2.2 32.1 1.0 S1 B:FES501 2.2 32.2 1.0 SG B:CYS55 2.3 30.9 0.5 SG B:CYS74 2.3 32.2 0.5 SG B:CYS74 2.3 32.2 0.5 SG B:CYS55 2.3 30.9 0.5 FE1 B:FES501 2.8 30.4 1.0 CB B:CYS55 3.2 34.3 0.5 CB B:CYS55 3.2 34.3 0.5 CB B:CYS74 3.2 25.0 0.5 CB B:CYS74 3.2 25.0 0.5 CB B:HIS57 4.2 30.4 1.0 CB B:TYR76 4.4 26.4 1.0 ND1 B:HIS77 4.5 31.0 1.0 CA B:CYS55 4.6 32.3 0.5 CA B:CYS55 4.6 32.3 0.5 N B:HIS77 4.6 33.4 1.0 ND1 B:HIS57 4.6 32.6 1.0 CA B:CYS74 4.7 27.9 0.5 CA B:CYS74 4.7 27.9 0.5 CB B:VAL60 4.7 29.5 1.0 N B:ARG58 4.8 30.9 1.0 CG B:HIS57 4.9 35.7 1.0 N B:TYR76 4.9 31.0 1.0

Iron binding site 6 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe506 b:28.8 occ:1.00 NE2 B:HIS164 2.1 32.2 1.0 O B:HOH661 2.1 37.0 1.0 O B:HOH688 2.1 41.0 1.0 NE2 B:HIS169 2.1 28.3 1.0 OD1 B:ASP280 2.2 32.2 1.0 OD2 B:ASP280 2.2 32.3 1.0 CG B:ASP280 2.5 35.4 1.0 CE1 B:HIS164 3.0 36.5 1.0 CD2 B:HIS164 3.0 33.5 1.0 CE1 B:HIS169 3.1 35.7 1.0 CD2 B:HIS169 3.2 31.5 1.0 CB B:ASP280 4.0 27.1 1.0 ND2 B:ASN158 4.1 23.3 1.0 ND1 B:HIS164 4.1 32.9 1.0 CG B:HIS164 4.2 31.2 1.0 OD1 B:ASN158 4.2 28.6 1.0 ND1 B:HIS169 4.2 33.0 1.0 CG B:HIS169 4.3 31.9 1.0 CD1 B:ILE168 4.4 35.8 1.0 CE1 B:PHE165 4.4 32.7 1.0 O B:ASN158 4.5 28.5 1.0 CG B:ASN158 4.5 34.8 1.0 O B:HOH614 4.6 57.5 1.0 N4 B:U5A505 4.6 71.1 0.8 CD1 B:PHE165 4.7 27.3 1.0 C6 B:U5A505 4.7 44.6 0.8 CA B:ASP280 4.8 28.6 1.0 C5 B:U5A505 4.9 51.7 0.8 O B:HOH696 4.9 50.0 1.0 O B:THR276 4.9 33.5 1.0 N5 B:U5A505 5.0 56.6 0.8

Iron binding site 7 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:34.8 occ:1.00 FE1 C:FES501 0.0 34.8 1.0 S1 C:FES501 2.2 37.6 1.0 S2 C:FES501 2.2 37.2 1.0 SG C:CYS55 2.3 34.9 1.0 SG C:CYS74 2.3 37.5 1.0 FE2 C:FES501 2.8 35.5 1.0 CB C:CYS74 3.2 36.1 1.0 CB C:CYS55 3.2 29.1 1.0 CB C:HIS57 4.1 37.9 1.0 ND1 C:HIS57 4.4 38.4 1.0 CB C:TYR76 4.5 34.1 1.0 CA C:CYS74 4.6 37.3 1.0 CA C:CYS55 4.6 31.9 1.0 ND1 C:HIS77 4.7 39.7 1.0 N C:HIS77 4.7 38.8 1.0 CB C:VAL60 4.7 30.8 1.0 N C:ARG58 4.8 34.0 1.0 CG C:HIS57 4.8 37.0 1.0 N C:TYR76 5.0 32.8 1.0

Iron binding site 8 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:35.5 occ:1.00 FE2 C:FES501 0.0 35.5 1.0 ND1 C:HIS77 2.1 39.7 1.0 ND1 C:HIS57 2.2 38.4 1.0 S2 C:FES501 2.2 37.2 1.0 S1 C:FES501 2.2 37.6 1.0 FE1 C:FES501 2.8 34.8 1.0 CE1 C:HIS77 3.1 38.2 1.0 CE1 C:HIS57 3.1 36.0 1.0 CG C:HIS77 3.1 41.1 1.0 CG C:HIS57 3.1 37.0 1.0 CB C:HIS57 3.5 37.9 1.0 CB C:HIS77 3.5 35.9 1.0 N C:HIS77 3.8 38.8 1.0 CB C:TYR76 4.2 34.1 1.0 NE2 C:HIS77 4.2 42.0 1.0 NE2 C:HIS57 4.2 36.0 1.0 CA C:HIS77 4.2 39.2 1.0 CD2 C:HIS77 4.2 38.0 1.0 N C:ARG58 4.2 34.0 1.0 CD2 C:HIS57 4.3 35.1 1.0 SG C:CYS55 4.4 34.9 1.0 CD2 C:TYR76 4.4 36.2 1.0 CB C:ARG58 4.4 28.4 1.0 CG C:ARG58 4.5 34.7 1.0 CG C:TYR76 4.5 34.8 1.0 SG C:CYS74 4.6 37.5 1.0 NE1 C:TRP79 4.6 32.9 1.0 C C:TYR76 4.7 39.2 1.0 CA C:HIS57 4.7 37.9 1.0 CD1 C:TRP79 4.7 31.9 1.0 C C:HIS57 4.8 39.0 1.0 CE2 C:TRP79 4.8 33.3 1.0 CA C:ARG58 5.0 31.7 1.0 CA C:TYR76 5.0 36.8 1.0 CG C:TRP79 5.0 39.7 1.0

Iron binding site 9 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Rieske Non-Heme Iron Oxygenase Sxtt with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe505 b:30.5 occ:1.00 O C:HOH691 2.1 36.8 1.0 O C:HOH670 2.1 32.0 1.0 OD1 C:ASP280 2.1 30.7 1.0 NE2 C:HIS169 2.1 32.4 1.0 NE2 C:HIS164 2.1 32.2 1.0 OD2 C:ASP280 2.4 30.0 1.0 CG C:ASP280 2.6 36.0 1.0 CD2 C:HIS169 3.1 32.2 1.0 CE1 C:HIS164 3.1 31.4 1.0 CE1 C:HIS169 3.1 33.9 1.0 CD2 C:HIS164 3.1 31.8 1.0 CB C:ASP280 4.1 29.2 1.0 ND2 C:ASN158 4.1 26.6 1.0 ND1 C:HIS164 4.2 35.9 1.0 ND1 C:HIS169 4.2 32.1 1.0 CG C:HIS169 4.2 32.6 1.0 CG C:HIS164 4.2 31.3 1.0 OD1 C:ASN158 4.2 33.7 1.0 CE1 C:PHE165 4.4 39.3 1.0 CD1 C:ILE168 4.6 36.6 1.0 O C:HOH609 4.6 53.9 1.0 CG C:ASN158 4.6 32.2 1.0 O C:ASN158 4.6 31.4 1.0 O C:HOH624 4.6 47.6 1.0 CD1 C:PHE165 4.7 36.0 1.0 CA C:ASP280 4.9 30.3 1.0 CG1 C:ILE168 4.9 30.2 1.0 O C:THR276 5.0 31.7 1.0

J.Liu, A.Lukowski, A.R.H.Narayan, J.Bridwell-Rabb. Structural Basis For Divergent C-H Hydroxylation Selectivity in Two Rieske Oxygenases To Be Published.