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Iron in PDB 6ypv: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods

Enzymatic activity of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods

All present enzymatic activity of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods:
1.14.11.33;

Protein crystallography data

The structure of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods, PDB code: 6ypv was solved by P.Rabe, J.H.Beale, P.A.Lang, A.S.Dirr, T.M.Leissing, A.Butryn, P.Aller, J.J.A.G.Kamps, D.Axford, M.A.Mcdonough, A.M.Orville, R.Owen, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.35 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.037, 39.107, 40.860, 78.14, 76.04, 66.51
R / Rfree (%) 21.9 / 25.1

Iron Binding Sites:

The binding sites of Iron atom in the Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods (pdb code 6ypv). 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 Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods, PDB code: 6ypv:

Iron binding site 1 out of 1 in 6ypv

Go back to Iron Binding Sites List in 6ypv
Iron binding site 1 out of 1 in the Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe and Akg After Oxygen Exposure Using Ft-Ssx Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:28.9
occ:1.00
 OD2 A:ASP133 2.0 33.1 1.0
NE2 A:HIS187 2.1 25.9 1.0
O2 A:AKG302 2.2 38.6 1.0
O5 A:AKG302 2.3 33.8 1.0
NE2 A:HIS131 2.4 18.8 1.0
CG A:ASP133 2.9 32.0 1.0
C2 A:AKG302 2.9 35.6 1.0
C1 A:AKG302 2.9 37.9 1.0
CD2 A:HIS187 3.1 24.5 1.0
CE1 A:HIS187 3.1 25.9 1.0
OD1 A:ASP133 3.2 33.1 1.0
HD2 A:HIS187 3.2 29.4 1.0
CD2 A:HIS131 3.3 20.1 1.0
HE1 A:HIS187 3.3 31.1 1.0
CE1 A:HIS131 3.3 18.6 1.0
HD2 A:HIS131 3.4 24.2 1.0
HE1 A:HIS131 3.5 22.4 1.0
HH22 A:ARG210 3.9 36.2 1.0
O1 A:AKG302 4.2 38.6 1.0
ND1 A:HIS187 4.2 25.5 1.0
CG A:HIS187 4.2 24.1 1.0
CB A:ASP133 4.3 30.9 1.0
HB2 A:ASP133 4.3 37.1 1.0
HD21 A:LEU128 4.3 31.2 1.0
ND1 A:HIS131 4.4 19.9 1.0
C3 A:AKG302 4.4 35.1 1.0
CG A:HIS131 4.4 21.2 1.0
NH2 A:ARG210 4.5 30.1 1.0
HG21 A:THR208 4.6 19.4 1.0
H42 A:AKG302 4.6 40.6 1.0
HH21 A:ARG210 4.7 36.2 1.0
HD23 A:LEU128 4.8 31.2 1.0
H41 A:AKG302 4.8 40.6 1.0
H31 A:AKG302 4.8 42.1 1.0
HB3 A:ASP133 4.8 37.1 1.0
C4 A:AKG302 4.9 33.8 1.0
H32 A:AKG302 5.0 42.1 1.0
HD1 A:HIS187 5.0 30.6 1.0

Reference:

P.Rabe, J.H.Beale, A.Butryn, P.Aller, A.Dirr, P.A.Lang, D.N.Axford, S.B.Carr, T.M.Leissing, M.A.Mcdonough, B.Davy, A.Ebrahim, J.Orlans, S.L.S.Storm, A.M.Orville, C.J.Schofield, R.L.Owen. Anaerobic Fixed-Target Serial Crystallography. Iucrj V. 7 901 2020.
ISSN: ESSN 2052-2525
PubMed: 32939282
DOI: 10.1107/S2052252520010374
Page generated: Wed Aug 7 16:41:48 2024

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