Iron in PDB 1y3t: Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis

The structure of Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis, PDB code: 1y3t was solved by B.Gopal, L.L.Madan, S.F.Betz, A.A.Kossiakoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.29 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.417, 128.425, 51.189, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 27.7

The binding sites of Iron atom in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis (pdb code 1y3t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis, PDB code: 1y3t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis


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 Yxag, A Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:51.7 occ:1.00 O A:HOH469 2.0 66.3 1.0 OE1 A:GLU69 2.2 35.2 1.0 NE2 A:HIS64 2.3 37.6 1.0 NE2 A:HIS103 2.4 38.7 1.0 NE2 A:HIS62 2.6 38.3 1.0 CE1 A:HIS64 2.7 43.7 1.0 CE1 A:HIS62 2.9 46.7 1.0 CD A:GLU69 3.1 33.1 1.0 CE1 A:HIS103 3.2 46.1 1.0 OE2 A:GLU69 3.3 29.6 1.0 CD2 A:HIS103 3.5 32.3 1.0 CD2 A:HIS64 3.6 35.1 1.0 CD2 A:HIS62 3.9 41.2 1.0 ND1 A:HIS64 3.9 40.9 1.0 ND1 A:HIS62 4.1 43.5 1.0 ND1 A:HIS103 4.2 41.5 1.0 CG A:HIS64 4.4 37.4 1.0 CG A:HIS103 4.5 34.7 1.0 CG A:GLU69 4.5 36.3 1.0 CG A:HIS62 4.6 40.2 1.0 CB A:GLU69 4.8 35.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis


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 Yxag, A Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:43.0 occ:1.00 NE2 A:HIS236 2.3 36.2 1.0 NE2 A:HIS275 2.3 41.2 1.0 NE2 A:HIS234 2.4 49.1 1.0 O A:HOH445 2.5 47.1 1.0 OE1 A:GLU241 2.6 46.3 1.0 OE2 A:GLU241 2.8 50.6 1.0 CE1 A:HIS234 2.8 48.9 1.0 CD A:GLU241 2.9 44.3 1.0 CE1 A:HIS236 3.0 34.2 1.0 CE1 A:HIS275 3.2 47.3 1.0 CD2 A:HIS275 3.3 31.2 1.0 CD2 A:HIS236 3.4 29.2 1.0 CD2 A:HIS234 3.6 43.5 1.0 O A:HOH512 3.9 56.5 1.0 ND1 A:HIS234 4.0 45.1 1.0 ND1 A:HIS275 4.2 42.3 1.0 ND1 A:HIS236 4.2 38.8 1.0 CG A:HIS234 4.3 42.5 1.0 CG A:HIS275 4.3 38.7 1.0 CG A:GLU241 4.4 47.1 1.0 CG A:HIS236 4.4 37.5 1.0 CB A:GLU241 4.9 38.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis


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 Yxag, A Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:50.3 occ:1.00 OE1 B:GLU69 2.2 34.3 1.0 O B:HOH525 2.2 47.7 1.0 NE2 B:HIS103 2.3 37.3 1.0 NE2 B:HIS64 2.4 39.7 1.0 O B:HOH452 2.5 51.1 1.0 NE2 B:HIS62 2.8 37.8 1.0 CE1 B:HIS103 3.1 45.9 1.0 CD B:GLU69 3.1 33.1 1.0 CE1 B:HIS64 3.2 41.5 1.0 CD2 B:HIS103 3.4 30.7 1.0 CD2 B:HIS64 3.4 35.6 1.0 OE2 B:GLU69 3.4 31.0 1.0 O B:HOH494 3.7 47.5 1.0 CD2 B:HIS62 3.7 40.6 1.0 CE1 B:HIS62 3.8 47.7 1.0 ND1 B:HIS64 4.2 38.0 1.0 ND1 B:HIS103 4.2 41.5 1.0 CG B:HIS103 4.4 32.8 1.0 CG B:HIS64 4.4 36.3 1.0 CG B:GLU69 4.5 35.8 1.0 ND1 B:HIS62 4.7 44.7 1.0 CG B:HIS62 4.7 40.9 1.0 CB B:GLU69 4.9 35.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Yxag, A Dioxygenase From Bacillus Subtilis


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 Yxag, A Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:43.3 occ:1.00 NE2 B:HIS236 2.2 36.1 1.0 NE2 B:HIS275 2.3 41.8 1.0 O B:HOH458 2.4 39.7 1.0 NE2 B:HIS234 2.6 49.5 1.0 OE1 B:GLU241 2.6 49.4 1.0 OE2 B:GLU241 2.6 51.8 1.0 O B:HOH426 2.8 59.1 1.0 CD B:GLU241 2.8 46.1 1.0 CE1 B:HIS236 2.9 35.7 1.0 CE1 B:HIS275 3.0 49.4 1.0 CE1 B:HIS234 3.2 50.7 1.0 CD2 B:HIS236 3.3 28.7 1.0 CD2 B:HIS275 3.4 32.5 1.0 CD2 B:HIS234 3.6 42.5 1.0 O B:HOH572 3.9 64.1 1.0 ND1 B:HIS275 4.1 44.0 1.0 ND1 B:HIS236 4.1 39.3 1.0 ND1 B:HIS234 4.2 48.1 1.0 CG B:GLU241 4.3 46.1 1.0 CG B:HIS236 4.3 34.0 1.0 CG B:HIS275 4.3 35.3 1.0 CG B:HIS234 4.5 43.6 1.0 CB B:GLU241 4.9 37.2 1.0 CZ B:PHE243 4.9 45.0 1.0

B.Gopal, L.L.Madan, S.F.Betz, A.A.Kossiakoff. The Crystal Structure of A Quercetin 2,3-Dioxygenase From Bacillus Subtilis Suggests Modulation of Enzyme Activity By A Change in the Metal Ion at the Active Site(S) Biochemistry V. 44 193 2005.
ISSN: ISSN 0006-2960
PubMed: 15628860
DOI: 10.1021/BI0484421