Iron in PDB 5vg2: Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae

The structure of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae, PDB code: 5vg2 was solved by C.Schlachter, V.Klapper, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.46
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.494, 43.067, 165.708, 90.00, 95.18, 90.00
R / Rfree (%)	19.1 / 23.1

The structure of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae also contains other interesting chemical elements:

Arsenic

(As)

9 atoms

The binding sites of Iron atom in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae (pdb code 5vg2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae, PDB code: 5vg2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range: probe atom residue distance (Å) B Occ U:Fe301 b:53.3 occ:1.00 OH U:TYR118 1.9 37.4 1.0 O U:HOH403 2.0 39.4 1.0 NE2 U:HIS171 2.2 39.0 1.0 NE2 U:HIS169 2.3 41.4 1.0 OH U:TYR163 2.5 55.1 1.0 CZ U:TYR118 3.0 39.0 1.0 CD2 U:HIS171 3.1 39.0 1.0 CE1 U:HIS171 3.1 39.1 1.0 CE1 U:HIS169 3.2 41.4 1.0 CD2 U:HIS169 3.4 43.1 1.0 CZ U:TYR163 3.6 52.4 1.0 CE2 U:TYR118 3.7 40.0 1.0 CE1 U:TYR163 3.9 52.0 1.0 CE1 U:TYR118 4.0 39.0 1.0 NH2 U:ARG166 4.1 57.6 1.0 ND1 U:HIS171 4.2 40.1 1.0 CG U:HIS171 4.3 39.5 1.0 O U:HOH418 4.3 32.6 1.0 ND1 U:HIS169 4.4 41.6 1.0 CG U:HIS169 4.5 42.4 1.0 CE2 U:TYR163 4.8 52.6 1.0 CD2 U:TYR67 4.8 56.3 1.0 CD2 U:TYR118 5.0 40.4 1.0

Iron binding site 2 out of 4 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:47.0 occ:1.00 OH A:TYR118 1.9 37.2 1.0 O A:HOH404 2.2 40.9 1.0 NE2 A:HIS169 2.2 37.7 1.0 NE2 A:HIS171 2.2 32.2 1.0 OH A:TYR163 2.4 43.4 1.0 CZ A:TYR118 3.1 38.7 1.0 CE1 A:HIS169 3.1 37.8 1.0 CD2 A:HIS171 3.2 32.7 1.0 CE1 A:HIS171 3.2 32.3 1.0 CD2 A:HIS169 3.3 37.0 1.0 CZ A:TYR163 3.5 41.7 1.0 CE2 A:TYR118 3.7 39.1 1.0 CE1 A:TYR163 3.8 41.7 1.0 CE1 A:TYR118 4.1 38.7 1.0 NH2 A:ARG166 4.1 48.5 1.0 ND1 A:HIS169 4.3 39.0 1.0 ND1 A:HIS171 4.3 32.9 1.0 O A:HOH418 4.3 32.3 1.0 CG A:HIS171 4.3 33.1 1.0 CG A:HIS169 4.4 36.7 1.0 CE2 A:TYR163 4.7 43.3 1.0

Iron binding site 3 out of 4 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:53.2 occ:1.00 OH B:TYR118 2.0 36.0 1.0 O B:HOH417 2.2 53.4 1.0 NE2 B:HIS171 2.3 33.3 1.0 OH B:TYR163 2.3 61.8 1.0 NE2 B:HIS169 2.3 39.3 1.0 CZ B:TYR118 3.1 37.4 1.0 CE1 B:HIS169 3.1 40.2 1.0 CE1 B:HIS171 3.2 32.6 1.0 CD2 B:HIS171 3.3 34.0 1.0 CD2 B:HIS169 3.4 39.6 1.0 CZ B:TYR163 3.4 58.7 1.0 CE2 B:TYR118 3.7 38.4 1.0 CE1 B:TYR163 3.7 56.1 1.0 NH2 B:ARG166 4.1 67.9 1.0 CE1 B:TYR118 4.1 37.2 1.0 O B:HOH415 4.2 33.2 1.0 ND1 B:HIS169 4.3 40.0 1.0 ND1 B:HIS171 4.4 33.4 1.0 CG B:HIS171 4.4 34.0 1.0 CG B:HIS169 4.5 40.2 1.0 CE2 B:TYR163 4.6 59.1 1.0 CD2 B:TYR67 4.8 42.0 1.0

Iron binding site 4 out of 4 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:58.0 occ:1.00 OH C:TYR118 1.9 44.1 1.0 NE2 C:HIS171 2.2 36.6 1.0 NE2 C:HIS169 2.2 44.4 1.0 O C:HOH419 2.3 43.8 1.0 OH C:TYR163 2.4 63.2 1.0 CZ C:TYR118 3.1 43.9 1.0 CE1 C:HIS169 3.1 47.8 1.0 CD2 C:HIS171 3.2 36.4 1.0 CE1 C:HIS171 3.2 37.1 1.0 CD2 C:HIS169 3.3 43.5 1.0 CZ C:TYR163 3.4 63.0 1.0 CE2 C:TYR118 3.7 44.1 1.0 CE1 C:TYR163 3.7 62.5 1.0 CE1 C:TYR118 4.1 42.9 1.0 NH2 C:ARG166 4.1 70.1 1.0 ND1 C:HIS169 4.3 46.6 1.0 O C:HOH409 4.3 39.7 1.0 CG C:HIS171 4.3 37.2 1.0 ND1 C:HIS171 4.3 38.0 1.0 CG C:HIS169 4.4 43.5 1.0 CE2 C:TYR163 4.7 64.8 1.0 CD2 C:TYR67 4.9 45.0 1.0

C.R.Schlachter, L.Daneshian, J.Amaya, V.Klapper, N.Wybouw, T.Borowski, T.Van Leeuwen, V.Grbic, M.Grbic, T.M.Makris, M.Chruszcz. Structural and Functional Characterization of An Intradiol Ring-Cleavage Dioxygenase From the Polyphagous Spider Mite Herbivore Tetranychus Urticae Koch. Insect Biochem.Mol.Biol. V. 107 19 2019.
ISSN: ISSN 0965-1748
PubMed: 30529144
DOI: 10.1016/J.IBMB.2018.12.001