Iron in PDB 4y5r: Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.9.1;

The structure of Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4y5r was solved by C.Li, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%)	19.3 / 25.6

The structure of Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 4y5r). 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 A T67A Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4y5r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex


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 A T67A Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:43.2 occ:1.00 FE A:HEC402 0.0 43.2 1.0 ND A:HEC402 2.1 44.5 1.0 NA A:HEC402 2.1 46.0 1.0 NC A:HEC402 2.1 44.5 1.0 NB A:HEC402 2.1 45.9 1.0 NE2 A:HIS35 2.3 48.6 1.0 C4D A:HEC402 3.0 47.1 1.0 C1A A:HEC402 3.0 47.1 1.0 C4B A:HEC402 3.1 45.3 1.0 C4C A:HEC402 3.1 44.3 1.0 C1D A:HEC402 3.1 47.1 1.0 C1C A:HEC402 3.1 43.1 1.0 C1B A:HEC402 3.1 44.3 1.0 C4A A:HEC402 3.1 44.8 1.0 CE1 A:HIS35 3.2 48.8 1.0 CD2 A:HIS35 3.3 48.5 1.0 CHA A:HEC402 3.4 48.4 1.0 O A:HOH502 3.4 31.6 1.0 CHC A:HEC402 3.4 43.6 1.0 CHD A:HEC402 3.5 46.2 1.0 CHB A:HEC402 3.5 44.2 1.0 CG A:PRO107 4.3 55.2 1.0 C3D A:HEC402 4.3 49.2 1.0 ND1 A:HIS35 4.3 48.5 1.0 NE2 A:GLN103 4.3 53.2 1.0 C3B A:HEC402 4.4 46.3 1.0 C2A A:HEC402 4.4 46.6 1.0 C2D A:HEC402 4.4 48.9 1.0 C3C A:HEC402 4.4 42.1 1.0 CG A:HIS35 4.4 49.6 1.0 C2C A:HEC402 4.4 43.1 1.0 C3A A:HEC402 4.4 45.1 1.0 C2B A:HEC402 4.4 45.7 1.0 CB A:PRO107 4.9 57.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex


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 A T67A Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:44.4 occ:1.00 FE A:HEC403 0.0 44.4 1.0 OH A:TYR294 1.9 38.1 1.0 NA A:HEC403 2.1 43.2 1.0 ND A:HEC403 2.1 43.5 1.0 NB A:HEC403 2.1 43.8 1.0 NC A:HEC403 2.1 43.1 1.0 NE2 A:HIS205 2.2 45.9 1.0 CZ A:TYR294 2.9 41.6 1.0 C1A A:HEC403 3.0 43.9 1.0 C4A A:HEC403 3.1 44.1 1.0 C4C A:HEC403 3.1 42.7 1.0 C1D A:HEC403 3.1 43.7 1.0 C4D A:HEC403 3.1 44.2 1.0 C4B A:HEC403 3.1 45.3 1.0 C1B A:HEC403 3.1 44.0 1.0 C1C A:HEC403 3.1 42.4 1.0 CE1 A:HIS205 3.1 47.2 1.0 CD2 A:HIS205 3.1 46.0 1.0 CHA A:HEC403 3.4 45.8 1.0 CHD A:HEC403 3.4 43.9 1.0 CHB A:HEC403 3.4 44.9 1.0 CHC A:HEC403 3.5 44.3 1.0 CE1 A:TYR294 3.7 41.2 1.0 CE2 A:TYR294 3.7 41.0 1.0 ND1 A:HIS205 4.3 47.8 1.0 CG A:HIS205 4.3 45.2 1.0 C3A A:HEC403 4.3 44.6 1.0 C2A A:HEC403 4.4 44.5 1.0 C3C A:HEC403 4.4 43.1 1.0 C3B A:HEC403 4.4 43.9 1.0 C3D A:HEC403 4.4 43.8 1.0 C2D A:HEC403 4.4 42.8 1.0 C2C A:HEC403 4.4 41.5 1.0 C2B A:HEC403 4.4 43.5 1.0 CD1 A:TYR294 4.9 39.4 1.0 CD2 A:TYR294 5.0 40.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex


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 A T67A Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:45.4 occ:1.00 FE B:HEC402 0.0 45.4 1.0 NC B:HEC402 2.1 47.4 1.0 ND B:HEC402 2.1 47.8 1.0 NB B:HEC402 2.1 46.1 1.0 NA B:HEC402 2.1 43.1 1.0 NE2 B:HIS35 2.2 46.9 1.0 C4B B:HEC402 3.0 46.1 1.0 C1A B:HEC402 3.1 42.3 1.0 C4C B:HEC402 3.1 48.0 1.0 C1C B:HEC402 3.1 47.6 1.0 C4D B:HEC402 3.1 44.8 1.0 C1D B:HEC402 3.1 49.9 1.0 C4A B:HEC402 3.1 43.0 1.0 CD2 B:HIS35 3.1 48.3 1.0 C1B B:HEC402 3.1 44.4 1.0 CE1 B:HIS35 3.2 47.4 1.0 CHC B:HEC402 3.4 45.0 1.0 CHA B:HEC402 3.4 43.2 1.0 CHD B:HEC402 3.5 48.3 1.0 CHB B:HEC402 3.5 44.5 1.0 NE2 B:GLN103 4.2 49.7 1.0 CG B:HIS35 4.3 46.9 1.0 ND1 B:HIS35 4.3 47.5 1.0 C3B B:HEC402 4.3 46.7 1.0 C3C B:HEC402 4.4 50.6 1.0 C2A B:HEC402 4.4 42.4 1.0 C2C B:HEC402 4.4 51.0 1.0 CG B:PRO107 4.4 49.5 1.0 C3D B:HEC402 4.4 45.8 1.0 C3A B:HEC402 4.4 42.9 1.0 C2D B:HEC402 4.4 48.2 1.0 C2B B:HEC402 4.4 44.1 1.0 OE1 B:GLU113 4.9 75.8 1.0 CB B:PRO107 4.9 49.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A T67A Maug/Pre-Methylamine Dehydrogenase Complex


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 A T67A Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:32.5 occ:1.00 FE B:HEC403 0.0 32.5 1.0 OH B:TYR294 2.0 33.7 1.0 ND B:HEC403 2.1 31.4 1.0 NB B:HEC403 2.1 30.6 1.0 NA B:HEC403 2.1 31.8 1.0 NC B:HEC403 2.1 33.1 1.0 NE2 B:HIS205 2.2 37.2 1.0 CZ B:TYR294 3.0 34.0 1.0 C1D B:HEC403 3.0 31.2 1.0 C4C B:HEC403 3.1 31.7 1.0 C4A B:HEC403 3.1 32.1 1.0 C1A B:HEC403 3.1 31.5 1.0 C1B B:HEC403 3.1 31.5 1.0 C4D B:HEC403 3.1 31.3 1.0 C4B B:HEC403 3.1 31.6 1.0 CD2 B:HIS205 3.1 38.0 1.0 C1C B:HEC403 3.1 31.7 1.0 CE1 B:HIS205 3.3 37.3 1.0 CHD B:HEC403 3.4 31.3 1.0 CHB B:HEC403 3.4 32.0 1.0 CHA B:HEC403 3.4 31.6 1.0 CHC B:HEC403 3.5 30.5 1.0 CE2 B:TYR294 3.6 35.9 1.0 CE1 B:TYR294 3.9 33.2 1.0 CG B:HIS205 4.3 37.7 1.0 ND1 B:HIS205 4.3 38.1 1.0 C3C B:HEC403 4.4 32.2 1.0 C3B B:HEC403 4.4 32.4 1.0 C2D B:HEC403 4.4 31.6 1.0 C2A B:HEC403 4.4 31.8 1.0 C3A B:HEC403 4.4 32.8 1.0 C3D B:HEC403 4.4 32.6 1.0 C2B B:HEC403 4.4 31.8 1.0 C2C B:HEC403 4.4 32.6 1.0 CD2 B:TYR294 4.9 34.9 1.0

S.Shin, M.Feng, C.Li, H.R.Williamson, M.Choi, C.M.Wilmot, V.L.Davidson. A T67A Mutation in the Proximal Pocket of the High-Spin Heme of Maug Stabilizes Formation of A Mixed-Valent Fe(II)/Fe(III) State and Enhances Charge Resonance Stabilization of the Bis-Fe(IV) State. Biochim.Biophys.Acta V.1847 709 2015.
ISSN: ISSN 0006-3002
PubMed: 25896561
DOI: 10.1016/J.BBABIO.2015.04.008