Iron in PDB 7lvz: Crystal Structure of Ado

All present enzymatic activity of Crystal Structure of Ado:
1.13.11.19;

The structure of Crystal Structure of Ado, PDB code: 7lvz was solved by C.A.Bingman, R.L.Fernandez, R.W.Smith, B.G.Fox, T.C.Brunold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.17 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.296, 139.525, 142.007, 90, 90, 90
R / Rfree (%)	19.1 / 22.8

The structure of Crystal Structure of Ado also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Iron atom in the Crystal Structure of Ado (pdb code 7lvz). 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 Ado, PDB code: 7lvz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:30.4 occ:1.00 O A:HOH518 2.2 30.8 1.0 O A:HOH465 2.2 28.6 1.0 NE2 A:HIS102 2.3 24.8 1.0 NE2 A:HIS100 2.3 29.4 1.0 O A:HOH454 2.3 33.5 1.0 NE2 A:HIS179 2.4 27.8 1.0 CE1 A:HIS100 3.2 30.4 1.0 CD2 A:HIS102 3.2 30.1 1.0 CE1 A:HIS102 3.2 26.6 1.0 CD2 A:HIS100 3.3 25.5 1.0 CE1 A:HIS179 3.3 29.9 1.0 CD2 A:HIS179 3.3 28.7 1.0 HE1 A:HIS100 3.3 36.5 1.0 HD2 A:HIS102 3.4 36.2 1.0 HE1 A:HIS102 3.4 31.9 1.0 HD2 A:HIS100 3.4 30.6 1.0 HD2 A:HIS179 3.5 34.5 1.0 HE1 A:HIS179 3.5 35.9 1.0 O A:HOH431 4.0 34.7 1.0 HD11 A:ILE181 4.1 37.5 1.0 HD22 A:LEU194 4.2 43.5 1.0 OH A:TYR198 4.3 32.2 1.0 ND1 A:HIS100 4.3 29.3 1.0 ND1 A:HIS102 4.4 30.2 1.0 CG A:HIS100 4.4 27.8 1.0 CG A:HIS102 4.4 29.5 1.0 O A:HOH506 4.4 35.5 1.0 ND1 A:HIS179 4.4 31.7 1.0 HD21 A:LEU171 4.4 39.8 1.0 CG A:HIS179 4.5 29.3 1.0 OD2 A:ASP192 4.5 40.4 1.0 HH A:TYR198 4.6 38.8 1.0 HD13 A:LEU194 4.7 43.0 1.0 HG23 A:ILE97 4.8 37.0 1.0 HD12 A:ILE181 4.8 37.5 1.0 CD1 A:ILE181 4.9 31.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.1 occ:1.00 O B:HOH498 2.2 22.2 1.0 O B:HOH441 2.2 22.7 1.0 NE2 B:HIS102 2.3 21.4 1.0 NE2 B:HIS100 2.3 22.3 1.0 O B:HOH557 2.3 35.1 1.0 NE2 B:HIS179 2.5 25.6 1.0 CD2 B:HIS100 3.2 29.2 1.0 CE1 B:HIS102 3.2 24.2 1.0 CD2 B:HIS102 3.3 22.6 1.0 HD2 B:HIS100 3.3 35.1 1.0 CE1 B:HIS100 3.3 23.0 1.0 CE1 B:HIS179 3.3 25.2 1.0 HE1 B:HIS102 3.4 29.1 1.0 CD2 B:HIS179 3.4 27.8 1.0 HD2 B:HIS102 3.4 27.2 1.0 HE1 B:HIS179 3.5 30.3 1.0 HE1 B:HIS100 3.5 27.7 1.0 HD2 B:HIS179 3.6 33.4 1.0 O B:HOH434 3.9 32.7 1.0 HD12 B:ILE181 4.1 41.1 1.0 OH B:TYR198 4.3 29.2 1.0 HD23 B:LEU194 4.3 37.7 1.0 ND1 B:HIS102 4.4 26.4 1.0 CG B:HIS100 4.4 23.9 1.0 ND1 B:HIS100 4.4 25.6 1.0 ND1 B:HIS179 4.4 29.6 1.0 CG B:HIS102 4.4 26.5 1.0 OD2 B:ASP192 4.4 39.8 1.0 CG B:HIS179 4.5 24.6 1.0 O B:HOH506 4.5 33.2 1.0 HH B:TYR198 4.6 35.1 1.0 HD11 B:LEU194 4.6 44.0 1.0 HD22 B:LEU171 4.6 37.1 1.0 HD13 B:ILE181 4.7 41.1 1.0 HG21 B:ILE97 4.8 38.0 1.0 CD1 B:ILE181 4.9 34.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:31.3 occ:1.00 O B:HOH529 2.1 32.9 1.0 O C:HOH460 2.2 31.1 1.0 NE2 C:HIS102 2.2 27.0 1.0 NE2 C:HIS100 2.3 29.5 1.0 NE2 C:HIS179 2.3 25.0 1.0 O C:HOH485 2.4 35.4 1.0 CE1 C:HIS102 3.1 32.3 1.0 CD2 C:HIS102 3.2 30.4 1.0 CD2 C:HIS100 3.2 28.1 1.0 CE1 C:HIS179 3.3 30.8 1.0 CE1 C:HIS100 3.3 27.9 1.0 HE1 C:HIS102 3.3 38.9 1.0 HE2 B:HIS130 3.3 44.6 1.0 HD2 C:HIS100 3.3 33.8 1.0 CD2 C:HIS179 3.3 27.7 1.0 HD2 C:HIS102 3.3 36.5 1.0 HE1 C:HIS179 3.4 37.0 1.0 HE1 C:HIS100 3.5 33.6 1.0 HD2 C:HIS179 3.5 33.3 1.0 O C:HOH427 4.1 34.2 1.0 NE2 B:HIS130 4.1 37.5 1.0 HD22 C:LEU194 4.2 45.3 1.0 ND1 C:HIS102 4.3 28.7 1.0 OH C:TYR198 4.3 30.3 1.0 CG C:HIS102 4.3 33.2 1.0 HD11 C:ILE181 4.3 39.1 1.0 HD22 C:LEU171 4.4 38.8 1.0 ND1 C:HIS179 4.4 32.8 1.0 CG C:HIS100 4.4 26.2 1.0 ND1 C:HIS100 4.4 29.2 1.0 CG C:HIS179 4.4 27.1 1.0 HH C:TYR198 4.5 36.4 1.0 HD13 C:LEU194 4.5 50.7 1.0 O C:HOH462 4.5 33.4 1.0 OD2 C:ASP192 4.5 38.2 1.0 HE1 B:HIS130 4.6 45.1 1.0 CE1 B:HIS130 4.8 37.9 1.0 HG21 C:ILE97 4.9 43.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:42.6 occ:1.00 NE2 D:HIS100 2.3 35.0 1.0 NE2 D:HIS102 2.3 33.7 1.0 O D:HOH449 2.4 44.5 1.0 NE2 D:HIS179 2.4 29.9 1.0 O D:HOH414 2.5 35.2 1.0 O D:HOH491 2.6 46.7 1.0 CD2 D:HIS100 3.2 31.9 1.0 CE1 D:HIS102 3.2 31.7 1.0 CE1 D:HIS100 3.3 35.9 1.0 CE1 D:HIS179 3.3 34.9 1.0 CD2 D:HIS102 3.3 33.6 1.0 HD2 D:HIS100 3.3 38.4 1.0 HE1 D:HIS102 3.4 38.1 1.0 CD2 D:HIS179 3.4 33.5 1.0 HE2 A:HIS130 3.4 53.5 1.0 HE1 D:HIS179 3.5 42.0 1.0 HE1 D:HIS100 3.5 43.2 1.0 HD2 D:HIS179 3.5 40.3 1.0 HD2 D:HIS102 3.5 40.4 1.0 O D:HOH410 4.0 37.8 1.0 HD11 D:ILE181 4.2 58.3 1.0 HD23 D:LEU194 4.2 51.7 1.0 NE2 A:HIS130 4.2 44.8 1.0 OH D:TYR198 4.3 34.0 1.0 OD2 D:ASP192 4.4 52.2 1.0 ND1 D:HIS102 4.4 32.8 1.0 CG D:HIS100 4.4 36.6 1.0 ND1 D:HIS100 4.4 39.8 1.0 ND1 D:HIS179 4.4 35.3 1.0 HD11 D:LEU194 4.4 48.2 1.0 CG D:HIS102 4.5 32.8 1.0 HD23 D:LEU171 4.5 41.5 1.0 CG D:HIS179 4.5 35.3 1.0 O D:HOH422 4.6 39.8 1.0 HH D:TYR198 4.6 40.5 1.0 HD12 D:ILE181 4.7 58.3 1.0 HE1 A:HIS130 4.7 54.3 1.0 HG22 D:ILE97 4.8 53.5 1.0 CE1 A:HIS130 4.9 45.5 1.0 CD1 D:ILE181 4.9 48.5 1.0 HE2 D:TYR198 4.9 41.8 1.0

R.L.Fernandez, L.D.Elmendorf, R.W.Smith, C.A.Bingman, B.G.Fox, T.C.Brunold. The Crystal Structure of Cysteamine Dioxygenase Reveals the Origin of the Large Substrate Scope of This Vital Mammalian Enzyme. Biochemistry V. 60 3728 2021.
ISSN: ISSN 0006-2960
PubMed: 34762398
DOI: 10.1021/ACS.BIOCHEM.1C00463