Iron in PDB 2fdi: Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours)

The structure of Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours), PDB code: 2fdi was solved by B.Yu, J.Benach, W.C.Edstrom, B.R.Gibney, J.F.Hunt, Northeast Structuralgenomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.21 / 1.80
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	40.646, 40.656, 117.924, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.6

The binding sites of Iron atom in the Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours) (pdb code 2fdi). 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 Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours), PDB code: 2fdi:

Iron binding site 1 out of 1 in the Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Alkb in Complex with Fe(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (Air 3 Hours) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:16.5 occ:1.00 O A:HOH606 1.9 28.2 0.8 O2 A:AKG400 2.1 18.1 0.4 OD1 A:ASP133 2.1 19.5 1.0 NE2 A:HIS131 2.2 17.7 1.0 O5 A:AKG400 2.2 19.0 0.4 O4 A:SIN401 2.2 15.1 0.5 NE2 A:HIS187 2.2 15.9 1.0 C1 A:AKG400 2.8 17.9 0.4 C2 A:AKG400 2.8 18.5 0.4 O A:HOH601 3.0 40.1 1.0 C4 A:SIN401 3.0 19.9 0.5 CG A:ASP133 3.1 21.0 1.0 CE1 A:HIS131 3.1 16.0 1.0 CD2 A:HIS187 3.1 16.6 1.0 CD2 A:HIS131 3.2 16.7 1.0 O3 A:SIN401 3.2 19.3 0.5 CE1 A:HIS187 3.3 16.7 1.0 OD2 A:ASP133 3.3 21.7 1.0 O1 A:AKG400 3.9 18.0 0.4 ND1 A:HIS131 4.2 14.4 1.0 CG A:HIS131 4.3 17.5 1.0 CG A:HIS187 4.3 16.2 1.0 ND1 A:HIS187 4.3 16.6 1.0 C3 A:AKG400 4.3 17.8 0.4 CB A:ASP133 4.4 18.8 1.0 C3 A:SIN401 4.4 18.8 0.5 N1 B:MA7502 4.5 14.8 0.9 NH2 A:ARG210 4.5 12.4 1.0 CN B:MA7502 4.6 16.5 1.0 O A:HOH602 4.6 50.6 1.0 C2 B:MA7502 4.7 13.6 0.9 C6 B:MA7502 4.8 14.6 0.9 O A:HOH603 4.8 56.0 1.0 C4 A:AKG400 4.9 16.1 0.4

B.Yu, W.C.Edstrom, J.Benach, Y.Hamuro, P.C.Weber, B.R.Gibney, J.F.Hunt. Crystal Structures of Catalytic Complexes of the Oxidative Dna/Rna Repair Enzyme Alkb. Nature V. 439 879 2006.
ISSN: ISSN 0028-0836
PubMed: 16482161
DOI: 10.1038/NATURE04561