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

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Dideoxysaxitoxin Bound, PDB code: 6wnd 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)	41.47 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.578, 96.976, 80.409, 90.00, 107.24, 90.00
R / Rfree (%)	16.8 / 20.8

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Dideoxysaxitoxin Bound also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Dideoxysaxitoxin Bound (pdb code 6wnd). 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 Gxta with Dideoxysaxitoxin Bound, PDB code: 6wnd:
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 Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:26.6 occ:1.00 FE1 A:FES501 0.0 26.6 1.0 S1 A:FES501 2.2 27.8 1.0 S2 A:FES501 2.2 28.1 1.0 ND1 A:HIS77 2.3 25.4 1.0 ND1 A:HIS57 2.3 29.7 1.0 FE2 A:FES501 2.8 25.9 1.0 CG A:HIS77 3.1 25.7 1.0 CG A:HIS57 3.2 32.3 1.0 CE1 A:HIS77 3.3 24.1 1.0 CB A:HIS57 3.3 32.6 1.0 CB A:HIS77 3.3 23.7 1.0 CE1 A:HIS57 3.3 35.2 1.0 N A:HIS77 3.8 26.9 1.0 CB A:TYR76 4.2 26.6 1.0 CA A:HIS77 4.2 24.9 1.0 N A:ARG58 4.2 33.9 1.0 CD2 A:HIS77 4.3 28.8 1.0 NE2 A:HIS77 4.3 26.6 1.0 CD2 A:HIS57 4.3 35.9 1.0 CB A:ARG58 4.4 35.5 1.0 NE2 A:HIS57 4.4 32.4 1.0 CG A:ARG58 4.5 33.0 1.0 CD2 A:TYR76 4.6 27.8 1.0 C A:TYR76 4.6 27.1 1.0 CA A:HIS57 4.6 33.2 1.0 CG A:TYR76 4.6 26.6 1.0 SG A:CYS55 4.6 27.4 1.0 NE1 A:TRP79 4.6 27.7 1.0 SG A:CYS74 4.7 30.2 1.0 C A:HIS57 4.7 37.2 1.0 CD1 A:TRP79 4.7 24.3 1.0 CE2 A:TRP79 4.8 31.3 1.0 CA A:TYR76 4.9 25.7 1.0 CA A:ARG58 5.0 35.7 1.0 CG A:TRP79 5.0 29.2 1.0

Iron binding site 2 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.9 occ:1.00 FE2 A:FES501 0.0 25.9 1.0 S2 A:FES501 2.2 28.1 1.0 S1 A:FES501 2.2 27.8 1.0 SG A:CYS74 2.4 30.2 1.0 SG A:CYS55 2.4 27.4 1.0 FE1 A:FES501 2.8 26.6 1.0 CB A:CYS74 3.1 25.6 1.0 CB A:CYS55 3.2 27.7 1.0 CB A:HIS57 4.1 32.6 1.0 CB A:TYR76 4.5 26.6 1.0 CA A:CYS74 4.6 24.7 1.0 CA A:CYS55 4.6 29.1 1.0 N A:HIS77 4.6 26.9 1.0 ND1 A:HIS57 4.7 29.7 1.0 N A:ARG58 4.7 33.9 1.0 ND1 A:HIS77 4.8 25.4 1.0 CG A:HIS57 4.9 32.3 1.0 CB A:VAL60 4.9 31.4 1.0 N A:TYR76 4.9 23.4 1.0 N A:HIS57 4.9 32.4 1.0 OH A:TYR81 5.0 31.7 1.0 C A:CYS55 5.0 32.0 1.0

Iron binding site 3 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe507 b:28.9 occ:1.00 O A:HOH601 1.6 39.3 1.0 OD1 A:ASP280 2.0 30.9 1.0 NE2 A:HIS169 2.0 33.1 1.0 NE2 A:HIS164 2.0 42.1 1.0 O A:HOH671 2.4 33.6 1.0 CG A:ASP280 2.6 36.6 1.0 OD2 A:ASP280 2.6 33.0 1.0 CE1 A:HIS164 2.9 36.0 1.0 CD2 A:HIS169 3.0 37.3 1.0 CE1 A:HIS169 3.0 36.1 1.0 CD2 A:HIS164 3.1 32.3 1.0 CD1 A:ILE168 3.9 42.0 1.0 OD1 A:ASN158 3.9 36.6 1.0 ND2 A:ASN158 4.0 38.2 1.0 ND1 A:HIS164 4.0 32.1 1.0 ND1 A:HIS169 4.1 32.4 1.0 CB A:ASP280 4.1 30.1 1.0 CG A:HIS169 4.1 38.9 1.0 CG A:HIS164 4.2 33.3 1.0 CG A:ASN158 4.4 36.8 1.0 CE1 A:PHE165 4.5 44.1 1.0 CG1 A:ILE168 4.6 35.9 1.0 O A:ASN158 4.6 29.8 1.0 CD1 A:PHE165 4.7 37.7 1.0 CG1 A:VAL276 4.7 38.0 1.0 C5 A:U5A506 4.7 45.3 1.0 CA A:ASP280 4.8 24.5 1.0 O A:VAL276 5.0 29.0 1.0

Iron binding site 4 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:31.5 occ:1.00 FE1 B:FES501 0.0 31.5 1.0 S1 B:FES501 2.2 31.9 1.0 S2 B:FES501 2.2 29.2 1.0 SG B:CYS74 2.4 35.0 1.0 SG B:CYS55 2.4 32.1 1.0 FE2 B:FES501 2.8 30.0 1.0 CB B:CYS74 3.2 29.4 1.0 CB B:CYS55 3.3 32.6 1.0 CB B:HIS57 4.0 35.0 1.0 CB B:TYR76 4.2 31.6 1.0 N B:HIS77 4.6 34.7 1.0 CA B:CYS74 4.6 29.6 1.0 ND1 B:HIS57 4.7 39.4 1.0 N B:ARG58 4.7 33.7 1.0 CA B:CYS55 4.7 35.0 1.0 CB B:VAL60 4.7 33.5 1.0 ND1 B:HIS77 4.8 36.5 1.0 N B:TYR76 4.8 37.3 1.0 CG B:HIS57 4.8 39.9 1.0 N B:HIS57 4.9 40.1 1.0 OH B:TYR81 4.9 38.8 1.0 CA B:HIS57 5.0 38.0 1.0

Iron binding site 5 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:30.0 occ:1.00 FE2 B:FES501 0.0 30.0 1.0 S2 B:FES501 2.2 29.2 1.0 S1 B:FES501 2.2 31.9 1.0 ND1 B:HIS77 2.3 36.5 1.0 ND1 B:HIS57 2.3 39.4 1.0 FE1 B:FES501 2.8 31.5 1.0 CG B:HIS57 3.1 39.9 1.0 CG B:HIS77 3.2 37.8 1.0 CE1 B:HIS77 3.3 34.3 1.0 CB B:HIS57 3.3 35.0 1.0 CE1 B:HIS57 3.3 36.8 1.0 CB B:HIS77 3.4 27.1 1.0 N B:HIS77 3.8 34.7 1.0 CB B:TYR76 4.0 31.6 1.0 CA B:HIS77 4.2 31.4 1.0 N B:ARG58 4.2 33.7 1.0 CD2 B:HIS57 4.3 40.0 1.0 CD2 B:HIS77 4.3 35.3 1.0 NE2 B:HIS77 4.3 35.0 1.0 NE2 B:HIS57 4.3 37.8 1.0 CG B:ARG58 4.4 39.1 1.0 CD2 B:TYR76 4.4 37.3 1.0 CB B:ARG58 4.4 40.1 1.0 CG B:TYR76 4.4 31.6 1.0 CA B:HIS57 4.5 38.0 1.0 NE1 B:TRP79 4.6 36.3 1.0 C B:TYR76 4.6 31.4 1.0 SG B:CYS55 4.6 32.1 1.0 C B:HIS57 4.7 41.3 1.0 SG B:CYS74 4.7 35.0 1.0 CE2 B:TRP79 4.8 36.9 1.0 CD1 B:TRP79 4.8 32.5 1.0 CA B:TYR76 4.8 32.0 1.0 CA B:ARG58 5.0 39.5 1.0

Iron binding site 6 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe505 b:22.8 occ:1.00 NE2 B:HIS169 2.0 27.1 1.0 O B:HOH610 2.0 41.7 1.0 NE2 B:HIS164 2.1 30.8 1.0 OD1 B:ASP280 2.1 25.7 1.0 O B:HOH672 2.1 28.7 1.0 OD2 B:ASP280 2.6 29.0 1.0 CG B:ASP280 2.7 27.8 1.0 CE1 B:HIS169 2.8 29.0 1.0 CE1 B:HIS164 2.9 34.7 1.0 CD2 B:HIS169 3.0 33.0 1.0 CD2 B:HIS164 3.1 29.3 1.0 ND2 B:ASN158 3.9 32.1 1.0 OD1 B:ASN158 4.0 32.4 1.0 ND1 B:HIS169 4.0 24.9 1.0 ND1 B:HIS164 4.0 35.5 1.0 CD1 B:ILE168 4.1 32.4 1.0 CG B:HIS169 4.1 28.8 1.0 CB B:ASP280 4.1 27.0 1.0 CG B:HIS164 4.2 27.4 1.0 CG B:ASN158 4.3 33.5 1.0 O B:ASN158 4.3 31.1 1.0 CE1 B:PHE165 4.5 37.3 1.0 CG1 B:ILE168 4.6 29.0 1.0 CG1 B:VAL276 4.6 26.1 1.0 CD1 B:PHE165 4.7 33.4 1.0 CA B:ASP280 4.8 25.7 1.0 C5 B:U5A504 4.9 47.4 1.0 O B:VAL276 4.9 27.1 1.0

Iron binding site 7 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:24.4 occ:1.00 FE1 C:FES501 0.0 24.4 1.0 S2 C:FES501 2.2 26.1 1.0 S1 C:FES501 2.2 27.2 1.0 SG C:CYS74 2.4 24.2 1.0 SG C:CYS55 2.4 21.6 1.0 FE2 C:FES501 2.8 29.1 1.0 CB C:CYS74 3.1 25.4 1.0 CB C:CYS55 3.2 25.1 1.0 CB C:HIS57 4.0 36.2 1.0 CB C:TYR76 4.3 25.5 1.0 CA C:CYS74 4.6 20.3 1.0 N C:HIS77 4.6 27.0 1.0 CA C:CYS55 4.6 24.1 1.0 N C:ARG58 4.7 37.9 1.0 ND1 C:HIS77 4.7 33.1 1.0 ND1 C:HIS57 4.8 33.4 1.0 CB C:VAL60 4.8 33.2 1.0 N C:TYR76 4.9 25.3 1.0 CG C:HIS57 4.9 39.8 1.0 N C:HIS57 4.9 40.6 1.0 CA C:HIS57 5.0 38.2 1.0 OH C:TYR81 5.0 28.1 1.0

Iron binding site 8 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:29.1 occ:1.00 FE2 C:FES501 0.0 29.1 1.0 S1 C:FES501 2.2 27.2 1.0 S2 C:FES501 2.2 26.1 1.0 ND1 C:HIS77 2.3 33.1 1.0 ND1 C:HIS57 2.3 33.4 1.0 FE1 C:FES501 2.8 24.4 1.0 CG C:HIS57 3.1 39.8 1.0 CB C:HIS57 3.2 36.2 1.0 CG C:HIS77 3.2 29.6 1.0 CE1 C:HIS77 3.2 26.9 1.0 CE1 C:HIS57 3.4 30.3 1.0 CB C:HIS77 3.5 23.0 1.0 N C:HIS77 3.8 27.0 1.0 CB C:TYR76 4.1 25.5 1.0 CG C:ARG58 4.2 46.2 1.0 N C:ARG58 4.3 37.9 1.0 CA C:HIS77 4.3 26.1 1.0 NE2 C:HIS77 4.3 28.5 1.0 CD2 C:HIS77 4.3 32.1 1.0 CD2 C:HIS57 4.3 36.2 1.0 CD2 C:TYR76 4.4 30.0 1.0 NE2 C:HIS57 4.4 40.3 1.0 SG C:CYS55 4.5 21.6 1.0 CB C:ARG58 4.5 39.4 1.0 CA C:HIS57 4.5 38.2 1.0 CG C:TYR76 4.6 28.1 1.0 NE1 C:TRP79 4.6 28.4 1.0 SG C:CYS74 4.7 24.2 1.0 C C:TYR76 4.7 25.6 1.0 CD1 C:TRP79 4.7 26.6 1.0 C C:HIS57 4.8 44.0 1.0 CE2 C:TRP79 4.8 32.2 1.0 CG C:TRP79 5.0 27.7 1.0 CA C:TYR76 5.0 28.1 1.0

Iron binding site 9 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta 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 Gxta with Dideoxysaxitoxin Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe506 b:27.6 occ:1.00 NE2 C:HIS164 2.0 30.9 1.0 NE2 C:HIS169 2.0 31.8 1.0 OD1 C:ASP280 2.1 28.6 1.0 O C:HOH694 2.3 35.8 1.0 O C:HOH700 2.4 41.6 1.0 OD2 C:ASP280 2.6 34.3 1.0 CG C:ASP280 2.7 29.6 1.0 CE1 C:HIS164 2.9 33.9 1.0 CD2 C:HIS169 3.0 31.5 1.0 CD2 C:HIS164 3.1 34.1 1.0 CE1 C:HIS169 3.1 25.7 1.0 ND1 C:HIS164 4.0 31.9 1.0 OD1 C:ASN158 4.1 29.4 1.0 ND2 C:ASN158 4.1 27.7 1.0 CG C:HIS164 4.1 29.8 1.0 CD1 C:ILE168 4.2 35.2 1.0 ND1 C:HIS169 4.2 27.4 1.0 CG C:HIS169 4.2 31.6 1.0 CB C:ASP280 4.2 25.1 1.0 CE1 C:PHE165 4.4 40.9 1.0 CG C:ASN158 4.5 28.0 1.0 CD1 C:PHE165 4.6 34.8 1.0 CG1 C:VAL276 4.6 30.2 1.0 O C:ASN158 4.7 31.5 1.0 CG1 C:ILE168 4.7 30.5 1.0 CA C:ASP280 4.8 24.9 1.0 O C:VAL276 4.9 29.4 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.