Iron in PDB 6daz: X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate

Enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate

All present enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate:
1.14.11.41;

Protein crystallography data

The structure of X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate, PDB code: 6daz was solved by N.P.Dunham, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.39 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.788, 66.388, 63.042, 90.00, 109.60, 90.00
R / Rfree (%) 20.1 / 23.9

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate (pdb code 6daz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate, PDB code: 6daz:

Iron binding site 1 out of 1 in 6daz

Go back to Iron Binding Sites List in 6daz
Iron binding site 1 out of 1 in the X-Ray Crystal Structure of Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate


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 Vioc Bound to Fe(II), 3S-Hydroxy-L- Homoarginine, and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:16.3
occ:1.00
 OE1 A:GLU170 2.0 16.4 1.0
O4 A:SIN402 2.2 17.6 1.0
NE2 A:HIS316 2.3 16.6 1.0
O3 A:SIN402 2.3 17.6 1.0
NE2 A:HIS168 2.3 16.4 1.0
O12 A:G3M403 2.5 20.1 1.0
C4 A:SIN402 2.6 17.6 1.0
CD A:GLU170 3.0 16.4 1.0
CE1 A:HIS316 3.1 16.5 1.0
CD2 A:HIS316 3.2 16.6 1.0
CE1 A:HIS168 3.2 16.3 1.0
OE2 A:GLU170 3.4 16.6 1.0
CD2 A:HIS168 3.4 16.4 1.0
C4 A:G3M403 3.6 20.4 1.0
C3 A:SIN402 4.1 17.4 1.0
C5 A:G3M403 4.2 21.1 1.0
ND1 A:HIS316 4.2 16.5 1.0
NH1 A:ARG334 4.3 20.1 1.0
CG A:HIS316 4.3 16.4 1.0
ND1 A:HIS168 4.4 16.1 1.0
CG A:GLU170 4.4 16.1 1.0
CG A:HIS168 4.5 16.3 1.0
CB A:GLU170 4.7 15.9 1.0
C2 A:SIN402 4.8 17.4 1.0
CD2 A:LEU165 4.8 18.2 1.0
C3 A:G3M403 4.9 19.9 1.0
CA A:GLU170 5.0 15.8 1.0

Reference:

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
Page generated: Sun Dec 13 16:24:12 2020

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