Iron in PDB 6vsh: Crystal Structure of Apo Dicamba Monooxygenase

The structure of Crystal Structure of Apo Dicamba Monooxygenase, PDB code: 6vsh was solved by T.J.Rydel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.26 / 3.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	80.170, 80.170, 159.346, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 25.2

The binding sites of Iron atom in the Crystal Structure of Apo Dicamba Monooxygenase (pdb code 6vsh). 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 Apo Dicamba Monooxygenase, PDB code: 6vsh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:36.6 occ:1.00 FE1 A:FES501 0.0 36.6 1.0 S2 A:FES501 2.2 35.5 1.0 S1 A:FES501 2.2 32.2 1.0 SG A:CYS68 2.4 42.6 1.0 SG A:CYS49 2.5 31.7 1.0 FE2 A:FES501 2.9 39.8 1.0 CB A:CYS68 3.0 33.8 1.0 CB A:CYS49 3.3 30.7 1.0 CB A:TYR70 4.1 39.5 1.0 N A:HIS71 4.1 38.6 1.0 CB A:HIS51 4.3 29.6 1.0 CA A:CYS68 4.5 28.2 1.0 CB A:ALA54 4.5 34.2 1.0 CA A:CYS49 4.8 24.4 1.0 N A:TYR70 4.8 34.5 1.0 ND1 A:HIS51 4.8 30.7 1.0 CA A:TYR70 4.9 38.0 1.0 CB A:LEU73 4.9 35.1 1.0 C A:CYS68 4.9 30.3 1.0 CD2 A:HIS71 4.9 39.5 1.0 N A:GLY72 4.9 37.0 1.0 CB A:HIS71 5.0 33.1 1.0 CA A:HIS71 5.0 32.4 1.0 C A:TYR70 5.0 41.4 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:39.8 occ:1.00 FE2 A:FES501 0.0 39.8 1.0 ND1 A:HIS51 2.2 30.7 1.0 S1 A:FES501 2.2 32.2 1.0 S2 A:FES501 2.2 35.5 1.0 CD2 A:HIS71 2.5 39.5 1.0 FE1 A:FES501 2.9 36.6 1.0 CG A:HIS51 2.9 32.6 1.0 CB A:HIS51 3.1 29.6 1.0 CG A:HIS71 3.2 39.7 1.0 CE1 A:HIS51 3.3 33.3 1.0 CB A:HIS71 3.3 33.1 1.0 NE2 A:HIS71 3.7 45.0 1.0 N A:HIS71 3.9 38.6 1.0 N A:ARG52 4.0 32.1 1.0 CD2 A:HIS51 4.1 41.7 1.0 CA A:HIS71 4.2 32.4 1.0 CB A:TYR70 4.2 39.5 1.0 NE2 A:HIS51 4.3 40.7 1.0 CD1 A:TYR70 4.3 42.7 1.0 CA A:HIS51 4.4 31.1 1.0 SG A:CYS49 4.4 31.7 1.0 ND1 A:HIS71 4.5 45.1 1.0 CB A:ARG52 4.5 28.2 1.0 CG A:TYR70 4.5 42.8 1.0 C A:HIS51 4.7 30.9 1.0 CE1 A:HIS71 4.7 47.3 1.0 CG A:ARG52 4.8 39.8 1.0 C A:TYR70 4.8 41.4 1.0 CA A:ARG52 4.8 33.1 1.0 SG A:CYS68 4.9 42.6 1.0 C A:HIS71 5.0 42.1 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:33.2 occ:1.00 FE1 B:FES501 0.0 33.2 1.0 S1 B:FES501 2.2 30.9 1.0 S2 B:FES501 2.2 28.5 1.0 SG B:CYS49 2.5 32.3 1.0 SG B:CYS68 2.5 37.2 1.0 CB B:CYS49 3.0 25.7 1.0 FE2 B:FES501 3.0 35.2 1.0 CB B:CYS68 3.2 33.0 1.0 CB B:HIS51 4.2 25.9 1.0 CB B:ALA54 4.2 26.2 1.0 CB B:TYR70 4.3 34.9 1.0 CA B:CYS49 4.5 25.4 1.0 N B:HIS71 4.5 38.0 1.0 CA B:CYS68 4.6 28.7 1.0 CB B:LEU73 4.8 34.4 1.0 CD1 B:LEU73 4.8 26.8 1.0 ND1 B:HIS51 4.8 31.0 1.0 N B:ARG52 4.9 31.8 1.0 CG B:LEU73 4.9 32.5 1.0 N B:ALA54 4.9 26.7 1.0 N B:TYR70 5.0 31.6 1.0 C B:CYS49 5.0 29.3 1.0 CD2 B:LEU56 5.0 26.9 1.0 N B:HIS51 5.0 26.3 1.0 CG B:HIS51 5.0 26.7 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:35.2 occ:1.00 FE2 B:FES501 0.0 35.2 1.0 S1 B:FES501 2.2 30.9 1.0 S2 B:FES501 2.2 28.5 1.0 ND1 B:HIS51 2.3 31.0 1.0 ND1 B:HIS71 2.4 32.0 1.0 FE1 B:FES501 3.0 33.2 1.0 CG B:HIS71 3.1 42.3 1.0 CB B:HIS71 3.1 38.5 1.0 CG B:HIS51 3.2 26.7 1.0 CE1 B:HIS51 3.3 35.8 1.0 CB B:HIS51 3.4 25.9 1.0 CE1 B:HIS71 3.5 39.5 1.0 N B:HIS71 3.8 38.0 1.0 CB B:TYR70 3.9 34.9 1.0 CA B:HIS71 4.0 35.2 1.0 CD1 B:TYR70 4.2 45.2 1.0 CD2 B:HIS71 4.3 52.7 1.0 N B:ARG52 4.3 31.8 1.0 CG B:TYR70 4.3 42.0 1.0 CD2 B:HIS51 4.4 33.8 1.0 NE2 B:HIS51 4.4 36.1 1.0 NE2 B:HIS71 4.4 51.4 1.0 CB B:ARG52 4.6 29.0 1.0 C B:TYR70 4.7 36.2 1.0 SG B:CYS68 4.7 37.2 1.0 CA B:HIS51 4.7 26.9 1.0 SG B:CYS49 4.7 32.3 1.0 C B:HIS71 4.8 37.3 1.0 CG B:ARG52 4.9 34.2 1.0 C B:HIS51 4.9 32.7 1.0 CA B:TYR70 4.9 35.8 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:59.2 occ:1.00 FE1 C:FES501 0.0 59.2 1.0 S2 C:FES501 2.2 48.3 1.0 S1 C:FES501 2.2 67.2 1.0 SG C:CYS68 2.6 40.5 1.0 SG C:CYS49 2.7 39.1 1.0 FE2 C:FES501 3.1 0.4 1.0 CB C:CYS49 3.5 39.6 1.0 CB C:TYR70 3.9 56.4 1.0 CB C:CYS68 3.9 57.9 1.0 CB C:HIS51 4.0 54.7 1.0 ND1 C:HIS71 4.1 68.3 1.0 ND1 C:HIS51 4.1 49.9 1.0 CB C:ALA54 4.2 36.2 1.0 N C:HIS71 4.3 61.5 1.0 N C:ARG52 4.4 47.5 1.0 CG C:HIS51 4.5 54.8 1.0 CD1 C:TYR70 4.6 58.4 1.0 N C:ALA54 4.6 35.2 1.0 CG C:TYR70 4.7 58.9 1.0 CA C:TYR70 4.9 56.2 1.0 CA C:CYS49 4.9 34.9 1.0 CE1 C:HIS71 4.9 66.7 1.0 CB C:HIS71 5.0 70.8 1.0 CG C:HIS71 5.0 75.5 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Apo Dicamba Monooxygenase


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 Apo Dicamba Monooxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:0.4 occ:1.00 FE2 C:FES501 0.0 0.4 1.0 S1 C:FES501 2.2 67.2 1.0 S2 C:FES501 2.2 48.3 1.0 ND1 C:HIS51 2.6 49.9 1.0 CB C:HIS71 2.7 70.8 1.0 ND1 C:HIS71 2.7 68.3 1.0 CG C:HIS71 3.0 75.5 1.0 FE1 C:FES501 3.1 59.2 1.0 CE1 C:HIS51 3.4 57.1 1.0 CG C:HIS51 3.5 54.8 1.0 CA C:HIS71 3.7 65.1 1.0 N C:HIS71 3.8 61.5 1.0 CB C:HIS51 3.8 54.7 1.0 CE1 C:HIS71 3.9 66.7 1.0 C C:HIS71 4.1 65.5 1.0 CG C:LEU73 4.2 58.6 1.0 CD2 C:HIS71 4.3 72.8 1.0 CD1 B:LEU318 4.4 49.5 1.0 NE2 C:HIS51 4.5 52.8 1.0 CD1 C:LEU73 4.5 55.8 1.0 CD2 C:HIS51 4.6 51.5 1.0 O C:HIS71 4.6 68.5 1.0 N C:GLY72 4.6 65.3 1.0 NE2 C:HIS71 4.7 64.4 1.0 SG C:CYS49 4.8 39.1 1.0 N C:LEU73 4.8 56.0 1.0 SG C:CYS68 4.9 40.5 1.0 CB C:LEU73 4.9 55.5 1.0 C C:TYR70 5.0 60.6 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.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