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Iron in PDB 6mp9: X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate

Enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate

All present enzymatic activity of X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate:
1.14.11.41;

Protein crystallography data

The structure of X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate, PDB code: 6mp9 was solved by 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) 59.39 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.676, 66.940, 62.856, 90.00, 109.12, 90.00
R / Rfree (%) 19.3 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate (pdb code 6mp9). 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), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate, PDB code: 6mp9:

Iron binding site 1 out of 1 in 6mp9

Go back to Iron Binding Sites List in 6mp9
Iron binding site 1 out of 1 in the X-Ray Crystal Structure of Vioc Bound to Fe(II), 2-Oxo-5- Guanidinopentanoic Acid, 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), 2-Oxo-5- Guanidinopentanoic Acid, and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:20.8
occ:1.00
 OE1 A:GLU170 2.0 16.9 1.0
O4 A:SIN402 2.2 18.1 1.0
NE2 A:HIS316 2.3 15.3 1.0
NE2 A:HIS168 2.4 16.6 1.0
O3 A:SIN402 2.5 19.0 1.0
C4 A:SIN402 2.7 18.9 1.0
O10 A:JX7401 2.7 34.7 1.0
CE1 A:HIS316 3.1 15.2 1.0
CD A:GLU170 3.1 17.0 1.0
CE1 A:HIS168 3.2 16.4 1.0
CD2 A:HIS316 3.4 15.2 1.0
OE2 A:GLU170 3.4 17.4 1.0
CD2 A:HIS168 3.5 16.4 1.0
C2 A:JX7401 3.9 34.1 1.0
C3 A:SIN402 4.2 18.5 1.0
ND1 A:HIS316 4.2 15.2 1.0
CG A:HIS316 4.4 15.1 1.0
ND1 A:HIS168 4.4 15.9 1.0
CG A:GLU170 4.4 16.4 1.0
NH1 A:ARG334 4.5 21.2 1.0
CG A:HIS168 4.6 16.0 1.0
CB A:GLU170 4.7 16.0 1.0
CD2 A:LEU165 4.8 16.3 1.0
C1 A:JX7401 4.8 34.2 1.0
C4 A:JX7401 4.8 32.6 1.0
C2 A:SIN402 4.8 18.2 1.0
O11 A:JX7401 4.9 34.5 1.0
CA A:GLU170 4.9 15.6 1.0
C3 A:JX7401 4.9 33.5 1.0

Reference:

N.P.Dunham, A.J.Mitchell, J.M.Del Rio Pantoja, C.Krebs, J.M.Bollinger Jr., A.K.Boal. Alpha-Amine Desaturation of D-Arginine By the Iron(II)- and 2-(Oxo)Glutarate-Dependent L-Arginine 3-Hydroxylase, Vioc. Biochemistry V. 57 6479 2018.
ISSN: ISSN 1520-4995
PubMed: 30403469
DOI: 10.1021/ACS.BIOCHEM.8B00901
Page generated: Wed Aug 6 09:55:12 2025

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