Iron in PDB 3eqq: Apo Toluene 2,3-Dioxygenase

All present enzymatic activity of Apo Toluene 2,3-Dioxygenase:
1.14.12.11;

The structure of Apo Toluene 2,3-Dioxygenase, PDB code: 3eqq was solved by R.Friemann, K.Lee, E.N.Brown, D.T.Gibson, H.Eklund, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.17 / 3.20
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	235.873, 235.873, 235.873, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 27.9

The binding sites of Iron atom in the Apo Toluene 2,3-Dioxygenase (pdb code 3eqq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Apo Toluene 2,3-Dioxygenase, PDB code: 3eqq:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Apo Toluene 2,3-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Apo Toluene 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe451 b:70.6 occ:1.00 FE1 A:FES451 0.0 70.6 1.0 ND1 A:HIS119 2.1 69.4 1.0 ND1 A:HIS98 2.1 61.2 1.0 S2 A:FES451 2.2 67.1 1.0 S1 A:FES451 2.2 66.6 1.0 FE2 A:FES451 2.8 68.8 1.0 CG A:HIS119 3.0 69.7 1.0 CG A:HIS98 3.0 62.1 1.0 CE1 A:HIS98 3.1 61.7 1.0 CE1 A:HIS119 3.1 70.4 1.0 CB A:HIS119 3.2 70.4 1.0 CB A:HIS98 3.3 62.5 1.0 N A:HIS119 3.9 71.3 1.0 SG A:CYS96 4.0 61.1 1.0 CD2 A:HIS98 4.1 61.9 1.0 NE2 A:HIS98 4.1 61.8 1.0 N A:ARG99 4.1 63.9 1.0 CD2 A:HIS119 4.1 69.6 1.0 CA A:HIS119 4.2 70.3 1.0 NE2 A:HIS119 4.2 69.3 1.0 CB A:TYR118 4.3 73.7 1.0 SG A:CYS116 4.5 69.9 1.0 CB A:ARG99 4.5 64.7 1.0 CA A:HIS98 4.5 62.8 1.0 C A:HIS98 4.6 63.5 1.0 CD1 A:TYR118 4.6 73.4 1.0 C A:TYR118 4.7 72.1 1.0 CG A:TYR118 4.8 74.2 1.0 CG A:ARG99 4.9 64.9 1.0 CA A:ARG99 4.9 64.5 1.0 C A:HIS119 5.0 69.6 1.0

Iron binding site 2 out of 3 in the Apo Toluene 2,3-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Apo Toluene 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe451 b:68.8 occ:1.00 FE2 A:FES451 0.0 68.8 1.0 SG A:CYS116 1.9 69.9 1.0 S1 A:FES451 2.2 66.6 1.0 S2 A:FES451 2.2 67.1 1.0 SG A:CYS96 2.4 61.1 1.0 FE1 A:FES451 2.8 70.6 1.0 CB A:CYS116 3.2 70.2 1.0 CB A:CYS96 3.2 61.5 1.0 CB A:MET101 4.0 60.9 1.0 N A:HIS119 4.1 71.3 1.0 CB A:TYR118 4.1 73.7 1.0 ND1 A:HIS119 4.4 69.4 1.0 O A:CYS116 4.4 70.7 1.0 CA A:CYS116 4.5 70.3 1.0 CB A:HIS98 4.5 62.5 1.0 C A:CYS116 4.6 70.8 1.0 ND1 A:HIS98 4.6 61.2 1.0 N A:TYR118 4.6 73.0 1.0 CG A:MET101 4.7 60.9 1.0 CA A:CYS96 4.7 61.3 1.0 CB A:HIS119 4.7 70.4 1.0 CA A:TYR118 4.7 72.9 1.0 N A:MET101 4.8 61.5 1.0 C A:TYR118 4.9 72.1 1.0 CA A:HIS119 4.9 70.3 1.0 CB A:TRP121 4.9 62.7 1.0 CG A:HIS119 5.0 69.7 1.0 CA A:MET101 5.0 61.3 1.0

Iron binding site 3 out of 3 in the Apo Toluene 2,3-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Apo Toluene 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe188 b:94.9 occ:0.33 NE2 B:HIS24 2.4 88.0 1.0 CD2 B:HIS24 3.1 86.6 1.0 CE1 B:HIS24 3.5 87.9 1.0 CG B:HIS24 4.4 83.3 1.0 ND1 B:HIS24 4.5 86.8 1.0 OE2 B:GLU27 4.5 75.2 1.0

R.Friemann, K.Lee, E.N.Brown, D.T.Gibson, H.Eklund, S.Ramaswamy. Structures of the Multicomponent Rieske Non-Heme Iron Toluene 2,3-Dioxygenase Enzyme System Acta Crystallogr.,Sect.D V. 65 24 2009.
ISSN: ISSN 0907-4449
PubMed: 19153463
DOI: 10.1107/S0907444908036524