Cobalt in PDB 2fdf: Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T

The structure of Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T, PDB code: 2fdf 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)	19.47 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	41.294, 41.294, 116.797, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.7

The binding sites of Cobalt atom in the Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T (pdb code 2fdf). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T, PDB code: 2fdf:

Cobalt binding site 1 out of 1 in the Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Alkb in Complex with Co(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T within 5.0Å range: probe atom residue distance (Å) B Occ A:Co300 b:13.5 occ:1.00 NE2 A:HIS131 2.1 9.9 1.0 NE2 A:HIS187 2.1 8.2 1.0 O2 A:AKG400 2.2 5.9 1.0 O5 A:AKG400 2.3 10.3 1.0 OD1 A:ASP133 2.3 11.9 1.0 O A:HOH697 2.7 28.5 1.0 C1 A:AKG400 2.9 10.4 1.0 CE1 A:HIS131 2.9 7.4 1.0 C2 A:AKG400 2.9 9.4 1.0 CD2 A:HIS187 3.0 3.5 1.0 CD2 A:HIS131 3.1 8.2 1.0 CG A:ASP133 3.1 14.5 1.0 CE1 A:HIS187 3.2 5.9 1.0 OD2 A:ASP133 3.3 14.9 1.0 ND1 A:HIS131 4.0 7.7 1.0 O1 A:AKG400 4.1 12.3 1.0 NH2 A:ARG210 4.1 22.2 1.0 CG A:HIS131 4.1 7.4 1.0 CG A:HIS187 4.2 6.8 1.0 ND1 A:HIS187 4.2 7.3 1.0 N1 B:MA7502 4.3 7.9 1.0 CN B:MA7502 4.4 6.1 1.0 C3 A:AKG400 4.4 9.3 1.0 C2 B:MA7502 4.5 2.7 1.0 CB A:ASP133 4.5 13.3 1.0 CZ2 A:TRP178 4.6 10.7 1.0 C6 B:MA7502 4.7 9.1 1.0 C4 A:AKG400 4.9 11.2 1.0 N A:ASP133 5.0 11.8 1.0 CA A:ASP133 5.0 12.0 1.0

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