Iron in PDB 3gb4: Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba

The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba, PDB code: 3gb4 was solved by T.J.Rydel, E.J.Sturman, F.Moshiri, G.R.Brown, Y.Qi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.05
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.550, 81.550, 161.290, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba also contains other interesting chemical elements:

Cobalt	(Co)	7 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba (pdb code 3gb4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba, PDB code: 3gb4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:32.3 occ:1.00 FE1 A:FES501 0.0 32.3 1.0 S1 A:FES501 2.2 34.7 1.0 S2 A:FES501 2.3 32.3 1.0 SG A:CYS49 2.3 33.3 1.0 SG A:CYS68 2.3 30.3 1.0 FE2 A:FES501 2.7 34.2 1.0 CB A:CYS49 3.1 32.0 1.0 CB A:CYS68 3.2 32.1 1.0 CB A:HIS51 4.1 31.3 1.0 CB A:TYR70 4.3 33.1 1.0 N A:HIS71 4.4 34.9 1.0 CB A:ALA54 4.5 34.2 1.0 ND1 A:HIS51 4.6 32.4 1.0 CA A:CYS49 4.6 32.6 1.0 CA A:CYS68 4.7 30.3 1.0 N A:ARG52 4.8 33.8 1.0 CG A:HIS51 4.8 33.9 1.0 ND1 A:HIS71 4.8 35.0 1.0 CD1 A:LEU73 4.8 32.7 1.0 N A:HIS51 4.9 31.1 1.0 CB A:LEU73 4.9 31.8 1.0 N A:TYR70 5.0 33.3 1.0 CG A:LEU73 5.0 32.9 1.0 N A:ALA54 5.0 31.6 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:34.2 occ:1.00 FE2 A:FES501 0.0 34.2 1.0 S1 A:FES501 2.2 34.7 1.0 S2 A:FES501 2.3 32.3 1.0 ND1 A:HIS51 2.3 32.4 1.0 ND1 A:HIS71 2.4 35.0 1.0 FE1 A:FES501 2.7 32.3 1.0 CG A:HIS51 3.2 33.9 1.0 CG A:HIS71 3.3 32.6 1.0 CE1 A:HIS51 3.3 33.4 1.0 CB A:HIS51 3.4 31.3 1.0 CB A:HIS71 3.4 32.5 1.0 CE1 A:HIS71 3.5 32.3 1.0 N A:HIS71 3.8 34.9 1.0 CB A:TYR70 4.1 33.1 1.0 CA A:HIS71 4.1 34.1 1.0 N A:ARG52 4.2 33.8 1.0 CD2 A:HIS51 4.4 33.5 1.0 NE2 A:HIS51 4.4 34.2 1.0 CD1 A:TYR70 4.4 33.8 1.0 CG A:TYR70 4.4 32.3 1.0 CD2 A:HIS71 4.5 30.7 1.0 SG A:CYS49 4.5 33.3 1.0 SG A:CYS68 4.5 30.3 1.0 CB A:ARG52 4.5 36.6 1.0 NE2 A:HIS71 4.5 33.1 1.0 C A:TYR70 4.6 34.6 1.0 CA A:HIS51 4.7 32.9 1.0 C A:HIS51 4.8 34.5 1.0 CG A:ARG52 4.9 39.4 1.0 CA A:TYR70 5.0 32.5 1.0 C A:HIS71 5.0 34.4 1.0 CA A:ARG52 5.0 34.5 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:30.5 occ:1.00 FE1 B:FES501 0.0 30.5 1.0 S1 B:FES501 2.2 28.8 1.0 S2 B:FES501 2.3 30.1 1.0 SG B:CYS68 2.3 29.3 1.0 SG B:CYS49 2.4 31.9 1.0 FE2 B:FES501 2.7 31.1 1.0 CB B:CYS49 3.1 28.8 1.0 CB B:CYS68 3.2 26.5 1.0 CB B:HIS51 4.1 30.5 1.0 CB B:TYR70 4.3 29.2 1.0 N B:HIS71 4.4 28.6 1.0 CB B:ALA54 4.5 28.6 1.0 ND1 B:HIS51 4.6 28.4 1.0 CA B:CYS49 4.6 30.1 1.0 CA B:CYS68 4.7 27.2 1.0 N B:ARG52 4.8 31.1 1.0 ND1 B:HIS71 4.8 30.0 1.0 CG B:HIS51 4.8 30.7 1.0 CD1 B:LEU73 4.9 31.8 1.0 N B:HIS51 4.9 30.1 1.0 CB B:LEU73 4.9 29.4 1.0 CG B:LEU73 4.9 31.7 1.0 N B:TYR70 5.0 29.0 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:31.1 occ:1.00 FE2 B:FES501 0.0 31.1 1.0 S2 B:FES501 2.3 30.1 1.0 S1 B:FES501 2.3 28.8 1.0 ND1 B:HIS51 2.3 28.4 1.0 ND1 B:HIS71 2.4 30.0 1.0 FE1 B:FES501 2.7 30.5 1.0 CG B:HIS71 3.2 33.2 1.0 CG B:HIS51 3.2 30.7 1.0 CB B:HIS71 3.3 30.4 1.0 CE1 B:HIS51 3.3 31.3 1.0 CB B:HIS51 3.4 30.5 1.0 CE1 B:HIS71 3.4 30.2 1.0 N B:HIS71 3.7 28.6 1.0 CB B:TYR70 4.1 29.2 1.0 CA B:HIS71 4.1 30.6 1.0 N B:ARG52 4.3 31.1 1.0 CD2 B:HIS51 4.4 31.1 1.0 CD2 B:HIS71 4.4 31.5 1.0 CG B:TYR70 4.4 29.6 1.0 NE2 B:HIS51 4.4 34.8 1.0 CD1 B:TYR70 4.5 30.6 1.0 SG B:CYS68 4.5 29.3 1.0 NE2 B:HIS71 4.5 31.5 1.0 SG B:CYS49 4.5 31.9 1.0 CB B:ARG52 4.6 29.7 1.0 C B:TYR70 4.6 30.3 1.0 CA B:HIS51 4.7 30.5 1.0 C B:HIS71 4.9 29.0 1.0 C B:HIS51 4.9 31.2 1.0 CA B:TYR70 4.9 28.9 1.0 CG B:ARG52 5.0 31.7 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:29.7 occ:1.00 FE1 C:FES501 0.0 29.7 1.0 S1 C:FES501 2.2 29.6 1.0 S2 C:FES501 2.3 28.4 1.0 SG C:CYS68 2.3 28.4 1.0 SG C:CYS49 2.4 26.5 1.0 FE2 C:FES501 2.7 29.9 1.0 CB C:CYS49 3.1 26.1 1.0 CB C:CYS68 3.2 27.0 1.0 CB C:HIS51 4.0 27.9 1.0 CB C:TYR70 4.3 28.6 1.0 N C:HIS71 4.4 30.2 1.0 ND1 C:HIS51 4.5 27.0 1.0 CB C:ALA54 4.6 27.0 1.0 CA C:CYS49 4.6 28.2 1.0 CA C:CYS68 4.7 28.7 1.0 N C:ARG52 4.7 30.3 1.0 CD1 C:LEU73 4.8 26.6 1.0 CG C:HIS51 4.8 30.6 1.0 ND1 C:HIS71 4.8 29.1 1.0 CG C:LEU73 4.9 31.0 1.0 N C:HIS51 4.9 29.3 1.0 CB C:LEU73 4.9 28.1 1.0 CA C:HIS51 5.0 30.0 1.0 N C:TYR70 5.0 28.9 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dicamba within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:29.9 occ:1.00 FE2 C:FES501 0.0 29.9 1.0 S2 C:FES501 2.2 28.4 1.0 S1 C:FES501 2.3 29.6 1.0 ND1 C:HIS51 2.3 27.0 1.0 ND1 C:HIS71 2.4 29.1 1.0 FE1 C:FES501 2.7 29.7 1.0 CG C:HIS51 3.2 30.6 1.0 CG C:HIS71 3.3 30.4 1.0 CE1 C:HIS51 3.3 28.9 1.0 CB C:HIS51 3.3 27.9 1.0 CB C:HIS71 3.4 28.9 1.0 CE1 C:HIS71 3.5 29.5 1.0 N C:HIS71 3.8 30.2 1.0 CB C:TYR70 4.0 28.6 1.0 N C:ARG52 4.2 30.3 1.0 CA C:HIS71 4.2 30.1 1.0 CD2 C:HIS51 4.3 27.9 1.0 NE2 C:HIS51 4.4 29.7 1.0 CG C:TYR70 4.4 29.2 1.0 CD1 C:TYR70 4.4 28.4 1.0 CB C:ARG52 4.4 31.0 1.0 CD2 C:HIS71 4.5 31.2 1.0 SG C:CYS68 4.5 28.4 1.0 SG C:CYS49 4.5 26.5 1.0 NE2 C:HIS71 4.5 28.3 1.0 C C:TYR70 4.6 29.9 1.0 CA C:HIS51 4.6 30.0 1.0 C C:HIS51 4.8 30.2 1.0 CA C:ARG52 4.9 29.9 1.0 CG C:ARG52 4.9 29.2 1.0 CA C:TYR70 4.9 29.2 1.0 C C:HIS71 5.0 30.8 1.0

R.L.D'ordine, T.J.Rydel, M.J.Storek, E.J.Sturman, F.Moshiri, R.K.Bartlett, G.R.Brown, R.J.Eilers, C.Dart, Y.Qi, S.Flasinski, S.J.Franklin. Dicamba Monooxygenase: Structural Insights Into A Dynamic Rieske Oxygenase That Catalyzes An Exocyclic Monooxygenation. J.Mol.Biol. V. 392 481 2009.
ISSN: ISSN 0022-2836
PubMed: 19616009
DOI: 10.1016/J.JMB.2009.07.022