Iron in PDB 6daw: X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate

The structure of X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate, PDB code: 6daw was solved by A.J.Mitchell, N.P.Dunham, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	121.631, 121.631, 82.054, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 24.8

The binding sites of Iron atom in the X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate (pdb code 6daw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate, PDB code: 6daw:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:34.0 occ:1.00 OE1 A:GLU148 2.0 29.5 1.0 OXT A:ACT404 2.2 38.6 1.0 NE2 A:HIS293 2.2 29.0 1.0 O A:ACT404 2.4 37.6 1.0 NE2 A:HIS146 2.4 30.6 1.0 C A:ACT404 2.6 38.5 1.0 CE1 A:HIS293 3.0 28.8 1.0 CD A:GLU148 3.1 29.1 1.0 CE1 A:HIS146 3.2 30.2 1.0 CD2 A:HIS293 3.3 28.9 1.0 CD2 A:HIS146 3.5 30.5 1.0 OE2 A:GLU148 3.5 31.8 1.0 CD A:ARG402 3.9 36.7 1.0 CH3 A:ACT404 4.1 38.4 1.0 ND1 A:HIS293 4.2 27.9 1.0 CG A:HIS293 4.3 28.0 1.0 ND1 A:HIS146 4.4 31.3 1.0 CG A:GLU148 4.4 28.0 1.0 CG A:HIS146 4.5 30.0 1.0 CD2 A:LEU159 4.6 27.8 1.0 CB A:ARG402 4.7 38.4 1.0 O A:HOH611 4.7 23.9 1.0 CB A:GLU148 4.7 27.1 1.0 CA A:GLU148 4.7 26.6 1.0 NZ A:LYS311 4.8 30.3 1.0 NE A:ARG402 4.8 35.7 1.0 CG A:ARG402 4.9 37.3 1.0

Iron binding site 2 out of 2 in the X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Napi L-Arginine Desaturase Bound to Fe(II), L-Arginine, and Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:34.5 occ:1.00 O B:ACT403 1.9 47.4 1.0 OE1 B:GLU148 2.0 32.8 1.0 NE2 B:HIS293 2.3 30.1 1.0 NE2 B:HIS146 2.4 28.6 1.0 OXT B:ACT403 2.5 46.1 1.0 C B:ACT403 2.5 47.2 1.0 CE1 B:HIS293 2.9 30.5 1.0 CE1 B:HIS146 3.1 28.4 1.0 CD B:GLU148 3.1 32.3 1.0 CD2 B:HIS293 3.5 29.9 1.0 CD2 B:HIS146 3.5 28.1 1.0 OE2 B:GLU148 3.5 32.9 1.0 CH3 B:ACT403 4.0 47.1 1.0 ND1 B:HIS293 4.0 30.0 1.0 CD B:ARG402 4.1 39.6 1.0 ND1 B:HIS146 4.3 29.1 1.0 CG B:HIS293 4.4 29.9 1.0 CG B:GLU148 4.4 31.3 1.0 CG B:HIS146 4.5 27.9 1.0 CD2 B:LEU159 4.5 25.1 1.0 NZ B:LYS311 4.5 28.2 1.0 CB B:GLU148 4.6 30.1 1.0 CA B:GLU148 4.7 29.2 1.0 O B:HOH539 4.8 24.3 1.0 CB B:ARG402 4.9 40.8 1.0 CD2 B:LEU143 5.0 32.3 1.0 NE B:ARG402 5.0 38.8 1.0

N.P.Dunham, W.C.Chang, A.J.Mitchell, R.J.Martinie, B.Zhang, J.A.Bergman, L.J.Rajakovich, B.Wang, A.Silakov, C.Krebs, A.K.Boal, J.M.Bollinger. Two Distinct Mechanisms For C-C Desaturation By Iron(II)- and 2-(Oxo)Glutarate-Dependent Oxygenases: Importance of Alpha-Heteroatom Assistance. J. Am. Chem. Soc. V. 140 7116 2018.
ISSN: ESSN 1520-5126
PubMed: 29708749
DOI: 10.1021/JACS.8B01933