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Iron in PDB 6y0q: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods

Enzymatic activity of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods

All present enzymatic activity of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods:
1.14.11.33;

Protein crystallography data

The structure of Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods, PDB code: 6y0q 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) 39.66 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.399, 39.078, 40.840, 78.99, 78.04, 66.88
R / Rfree (%) 16.2 / 19.1

Iron Binding Sites:

The binding sites of Iron atom in the Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods (pdb code 6y0q). 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, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods, PDB code: 6y0q:

Iron binding site 1 out of 1 in 6y0q

Go back to Iron Binding Sites List in 6y0q
Iron binding site 1 out of 1 in the Alpha-Ketoglutarate-Dependent Dioxygenase Alkb in Complex with Fe, Akg and Methylated Dna Under Anaerobic Environment 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, Akg and Methylated Dna Under Anaerobic Environment Using Ft-Ssx Methods within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:14.5
occ:1.00
 O2 A:AKG301 2.0 18.2 1.0
OD1 A:ASP133 2.1 21.6 1.0
NE2 A:HIS187 2.1 17.3 1.0
NE2 A:HIS131 2.2 17.5 1.0
O A:HOH496 2.3 15.1 1.0
O5 A:AKG301 2.4 16.3 1.0
C1 A:AKG301 2.8 20.0 1.0
C2 A:AKG301 3.0 16.7 1.0
CG A:ASP133 3.0 17.9 1.0
CE1 A:HIS187 3.1 12.6 1.0
CD2 A:HIS187 3.1 12.1 1.0
CD2 A:HIS131 3.1 13.8 1.0
CE1 A:HIS131 3.1 14.2 1.0
HE1 A:HIS187 3.2 15.2 1.0
OD2 A:ASP133 3.2 18.3 1.0
HD2 A:HIS131 3.3 16.6 1.0
HD2 A:HIS187 3.3 14.4 1.0
HE1 A:HIS131 3.3 17.1 1.0
HH22 A:ARG210 3.7 21.9 1.0
H012 A:O5W303 4.0 29.3 1.0
O1 A:AKG301 4.0 20.0 1.0
ND1 A:HIS187 4.2 12.7 1.0
ND1 A:HIS131 4.2 14.0 1.0
CG A:HIS187 4.2 12.2 1.0
H011 A:O5W303 4.3 29.3 1.0
CG A:HIS131 4.3 14.8 1.0
N02 A:O5W303 4.3 23.8 1.0
CB A:ASP133 4.4 15.7 1.0
C01 A:O5W303 4.4 24.4 1.0
HD21 A:LEU128 4.4 28.2 1.0
C42 A:O5W303 4.5 21.8 1.0
NH2 A:ARG210 4.5 18.2 1.0
C3 A:AKG301 4.5 17.9 1.0
HB2 A:ASP133 4.5 18.9 1.0
H421 A:O5W303 4.5 26.2 1.0
HH21 A:ARG210 4.7 21.9 1.0
C03 A:O5W303 4.8 24.0 1.0
H42 A:AKG301 4.8 22.1 1.0
H432 A:O5W303 4.8 26.1 1.0
H31 A:AKG301 4.9 21.4 1.0
HD23 A:LEU128 4.9 28.2 1.0
H41 A:AKG301 4.9 22.1 1.0
HD1 A:HIS187 4.9 15.3 1.0
H32 A:AKG301 5.0 21.4 1.0
N A:ASP133 5.0 15.9 1.0
N41 A:O5W303 5.0 22.7 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 15:48:51 2024

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