Iron in PDB 3gl2: Crystal Structure of Dicamba Monooxygenase Bound to Dicamba

The structure of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba, PDB code: 3gl2 was solved by M.A.Wilson, R.Dumitru, W.Z.Jiang, D.P.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.00 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.323, 81.323, 159.282, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24.7

The structure of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba (pdb code 3gl2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba, PDB code: 3gl2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:49.1 occ:1.00 FE1 A:FES500 0.0 49.1 1.0 ND1 A:HIS71 2.1 47.7 1.0 ND1 A:HIS51 2.2 51.7 1.0 S1 A:FES500 2.2 53.3 1.0 S2 A:FES500 2.2 47.1 1.0 FE2 A:FES500 2.8 46.0 1.0 CE1 A:HIS71 3.1 51.0 1.0 CG A:HIS71 3.1 46.6 1.0 CG A:HIS51 3.1 53.1 1.0 CE1 A:HIS51 3.1 53.4 1.0 CB A:HIS71 3.4 52.2 1.0 CB A:HIS51 3.4 53.2 1.0 N A:HIS71 3.8 52.4 1.0 CB A:TYR70 4.0 49.3 1.0 CA A:HIS71 4.1 50.7 1.0 NE2 A:HIS71 4.1 47.4 1.0 CD2 A:HIS71 4.1 50.0 1.0 N A:ARG52 4.2 48.1 1.0 NE2 A:HIS51 4.3 51.8 1.0 CD2 A:HIS51 4.3 59.7 1.0 CG A:ARG52 4.3 56.9 1.0 SG A:CYS49 4.3 46.7 1.0 CG A:TYR70 4.4 46.2 1.0 CB A:ARG52 4.4 48.1 1.0 CD1 A:TYR70 4.4 47.4 1.0 SG A:CYS68 4.4 48.6 1.0 C A:TYR70 4.6 50.9 1.0 CA A:HIS51 4.7 49.5 1.0 C A:HIS71 4.8 56.9 1.0 C A:HIS51 4.8 49.9 1.0 CA A:TYR70 4.9 49.9 1.0 CA A:ARG52 4.9 48.2 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:46.0 occ:1.00 FE2 A:FES500 0.0 46.0 1.0 SG A:CYS49 2.1 46.7 1.0 SG A:CYS68 2.2 48.6 1.0 S1 A:FES500 2.2 53.3 1.0 S2 A:FES500 2.2 47.1 1.0 FE1 A:FES500 2.8 49.1 1.0 CB A:CYS49 3.0 44.1 1.0 CB A:CYS68 3.1 50.6 1.0 CB A:HIS51 4.1 53.2 1.0 CB A:TYR70 4.3 49.3 1.0 CA A:CYS49 4.4 45.5 1.0 ND1 A:HIS51 4.5 51.7 1.0 CB A:ALA54 4.5 45.6 1.0 N A:HIS71 4.5 52.4 1.0 ND1 A:HIS71 4.5 47.7 1.0 CA A:CYS68 4.5 50.9 1.0 N A:ARG52 4.7 48.1 1.0 CG A:HIS51 4.8 53.1 1.0 CD2 A:LEU56 4.9 44.0 1.0 C A:CYS49 4.9 45.5 1.0 CB A:LEU73 5.0 54.3 1.0 N A:HIS51 5.0 52.7 1.0 N A:TYR70 5.0 50.4 1.0 CD1 A:LEU73 5.0 51.6 1.0 N A:GLY72 5.0 56.1 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:48.3 occ:1.00 OD2 A:ASP294 1.9 52.5 1.0 NE2 A:HIS165 2.0 48.2 1.0 NE2 A:HIS160 2.0 43.9 1.0 O A:HOH483 2.3 58.2 1.0 CG A:ASP294 2.6 41.7 1.0 OD1 A:ASP294 2.7 58.9 1.0 CE1 A:HIS165 2.9 50.4 1.0 CD2 A:HIS160 3.0 46.2 1.0 CE1 A:HIS160 3.1 53.4 1.0 CD2 A:HIS165 3.1 43.8 1.0 OD1 A:ASN154 3.6 49.0 1.0 ND1 A:HIS165 4.1 51.2 1.0 CB A:ASP294 4.1 51.0 1.0 ND1 A:HIS160 4.1 45.4 1.0 CG A:HIS160 4.2 45.6 1.0 CG A:HIS165 4.2 46.5 1.0 ND2 A:ASN154 4.2 46.2 1.0 CG A:ASN154 4.3 46.7 1.0 CD2 A:LEU290 4.8 57.1 1.0 O A:ALA289 4.8 58.9 1.0 C8 A:D3M600 4.9 50.6 1.0 CG1 A:VAL164 4.9 40.0 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:41.7 occ:1.00 FE1 B:FES500 0.0 41.7 1.0 S2 B:FES500 2.2 47.1 1.0 S1 B:FES500 2.2 44.1 1.0 SG B:CYS68 2.3 44.3 1.0 SG B:CYS49 2.3 44.3 1.0 FE2 B:FES500 2.7 44.5 1.0 CB B:CYS49 3.1 43.2 1.0 CB B:CYS68 3.1 37.9 1.0 CB B:HIS51 4.1 45.1 1.0 ND1 B:HIS51 4.3 43.8 1.0 CB B:TYR70 4.3 44.1 1.0 N B:HIS71 4.4 45.3 1.0 CB B:ALA54 4.4 41.3 1.0 ND1 B:HIS71 4.5 40.6 1.0 CA B:CYS68 4.6 41.0 1.0 CA B:CYS49 4.6 40.9 1.0 CG B:HIS51 4.7 50.3 1.0 CD2 B:LEU56 4.8 37.0 1.0 N B:ARG52 4.8 44.9 1.0 CB B:LEU73 4.9 40.6 1.0 CD1 B:LEU73 4.9 38.1 1.0 CG B:LEU73 4.9 42.0 1.0 N B:ALA54 5.0 39.9 1.0 N B:TYR70 5.0 45.2 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:44.5 occ:1.00 FE2 B:FES500 0.0 44.5 1.0 ND1 B:HIS71 2.0 40.6 1.0 ND1 B:HIS51 2.1 43.8 1.0 S2 B:FES500 2.2 47.1 1.0 S1 B:FES500 2.2 44.1 1.0 FE1 B:FES500 2.7 41.7 1.0 CE1 B:HIS71 3.0 51.0 1.0 CE1 B:HIS51 3.0 58.4 1.0 CG B:HIS71 3.1 45.5 1.0 CG B:HIS51 3.2 50.3 1.0 CB B:HIS71 3.4 46.2 1.0 CB B:HIS51 3.5 45.1 1.0 N B:HIS71 3.7 45.3 1.0 CA B:HIS71 4.1 46.8 1.0 NE2 B:HIS71 4.1 44.5 1.0 CD2 B:HIS71 4.2 51.2 1.0 NE2 B:HIS51 4.2 52.8 1.0 CB B:TYR70 4.2 44.1 1.0 CD2 B:HIS51 4.3 51.1 1.0 N B:ARG52 4.3 44.9 1.0 CD1 B:TYR70 4.4 48.2 1.0 CG B:ARG52 4.5 52.3 1.0 SG B:CYS68 4.5 44.3 1.0 SG B:CYS49 4.5 44.3 1.0 CG B:TYR70 4.5 47.6 1.0 CB B:ARG52 4.6 46.5 1.0 C B:TYR70 4.6 44.3 1.0 CA B:HIS51 4.8 45.9 1.0 C B:HIS71 4.8 48.3 1.0 C B:HIS51 4.9 49.7 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:64.1 occ:1.00 O B:HOH366 1.6 60.5 1.0 OD2 B:ASP294 1.9 66.5 1.0 NE2 B:HIS165 2.2 65.3 1.0 NE2 B:HIS160 2.2 59.9 1.0 CG B:ASP294 2.5 65.4 1.0 OD1 B:ASP294 2.5 67.5 1.0 CD2 B:HIS160 3.2 61.1 1.0 CE1 B:HIS165 3.2 64.0 1.0 CD2 B:HIS165 3.2 58.2 1.0 CE1 B:HIS160 3.2 61.9 1.0 OD1 B:ASN154 3.3 57.4 1.0 CB B:ASP294 3.9 64.9 1.0 ND2 B:ASN154 4.1 61.4 1.0 CG B:ASN154 4.1 55.5 1.0 ND1 B:HIS165 4.3 71.5 1.0 ND1 B:HIS160 4.3 52.9 1.0 CG B:HIS160 4.3 60.9 1.0 CG B:HIS165 4.3 62.9 1.0 CD2 B:LEU290 4.8 61.3 1.0 O B:ALA289 4.9 67.6 1.0 CA B:ASP294 4.9 63.9 1.0 CG1 B:VAL164 5.0 63.5 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe500 b:44.8 occ:1.00 FE1 C:FES500 0.0 44.8 1.0 ND1 C:HIS71 2.1 38.7 1.0 ND1 C:HIS51 2.1 49.3 1.0 S2 C:FES500 2.2 50.6 1.0 S1 C:FES500 2.2 41.8 1.0 FE2 C:FES500 2.8 43.6 1.0 CE1 C:HIS71 3.0 41.6 1.0 CE1 C:HIS51 3.1 53.2 1.0 CG C:HIS51 3.1 47.9 1.0 CG C:HIS71 3.1 40.7 1.0 CB C:HIS51 3.4 47.4 1.0 CB C:HIS71 3.5 45.1 1.0 N C:HIS71 3.7 43.6 1.0 NE2 C:HIS71 4.1 43.0 1.0 CB C:TYR70 4.2 44.5 1.0 CA C:HIS71 4.2 44.0 1.0 NE2 C:HIS51 4.2 45.5 1.0 CD2 C:HIS71 4.2 47.0 1.0 CD2 C:HIS51 4.2 49.2 1.0 N C:ARG52 4.2 45.9 1.0 SG C:CYS68 4.5 44.6 1.0 CD1 C:TYR70 4.5 48.0 1.0 CG C:TYR70 4.5 45.3 1.0 CB C:ARG52 4.6 49.4 1.0 SG C:CYS49 4.6 43.7 1.0 C C:TYR70 4.6 44.7 1.0 CA C:HIS51 4.7 47.1 1.0 C C:HIS51 4.8 46.8 1.0 C C:HIS71 4.8 46.0 1.0 CD C:ARG52 4.9 55.3 1.0 CA C:TYR70 4.9 44.7 1.0 CA C:ARG52 5.0 47.5 1.0 CG C:ARG52 5.0 51.3 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to Dicamba


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Dicamba Monooxygenase Bound to Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe500 b:43.6 occ:1.00 FE2 C:FES500 0.0 43.6 1.0 S2 C:FES500 2.2 50.6 1.0 SG C:CYS68 2.2 44.6 1.0 S1 C:FES500 2.2 41.8 1.0 SG C:CYS49 2.4 43.7 1.0 FE1 C:FES500 2.8 44.8 1.0 CB C:CYS49 3.0 40.9 1.0 CB C:CYS68 3.1 43.3 1.0 CB C:HIS51 4.1 47.4 1.0 CB C:TYR70 4.4 44.5 1.0 ND1 C:HIS51 4.4 49.3 1.0 CA C:CYS49 4.5 43.5 1.0 N C:HIS71 4.5 43.6 1.0 CB C:ALA54 4.5 39.6 1.0 ND1 C:HIS71 4.6 38.7 1.0 CA C:CYS68 4.6 44.3 1.0 N C:ARG52 4.8 45.9 1.0 CG C:HIS51 4.8 47.9 1.0 CB C:LEU73 4.8 43.3 1.0 N C:HIS51 4.9 46.3 1.0 N C:TYR70 5.0 47.0 1.0 CG C:LEU73 5.0 43.8 1.0

R.Dumitru, W.Z.Jiang, D.P.Weeks, M.A.Wilson. Crystal Structure of Dicamba Monooxygenase: A Rieske Nonheme Oxygenase That Catalyzes Oxidative Demethylation. J.Mol.Biol. V. 392 498 2009.
ISSN: ISSN 0022-2836
PubMed: 19616011
DOI: 10.1016/J.JMB.2009.07.021