Manganese in PDB 2fdh: Crystal Structure of Alkb in Complex with Mn(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T

The structure of Crystal Structure of Alkb in Complex with Mn(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T, PDB code: 2fdh 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)	19.24 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	40.680, 40.680, 118.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.8

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Alkb in Complex with Mn(II), 2-Oxoglutarate, and Methylated Trinucleotide T-Mea-T within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:15.8 occ:1.00 NE2 A:HIS131 2.1 17.3 1.0 O2 A:AKG400 2.1 15.3 1.0 OD1 A:ASP133 2.1 17.9 1.0 NE2 A:HIS187 2.2 17.2 1.0 O5 A:AKG400 2.4 19.2 1.0 O A:HOH687 2.8 24.8 1.0 C1 A:AKG400 2.9 16.6 1.0 CD2 A:HIS131 2.9 17.0 1.0 C2 A:AKG400 3.0 18.2 1.0 CG A:ASP133 3.0 20.6 1.0 CE1 A:HIS131 3.1 17.5 1.0 CD2 A:HIS187 3.2 18.8 1.0 CE1 A:HIS187 3.2 19.1 1.0 OD2 A:ASP133 3.3 19.5 1.0 O1 A:AKG400 4.1 17.6 1.0 CG A:HIS131 4.1 19.3 1.0 ND1 A:HIS131 4.1 15.9 1.0 N1 B:MA7502 4.2 17.8 1.0 ND1 A:HIS187 4.2 18.0 1.0 CG A:HIS187 4.3 19.1 1.0 CN B:MA7502 4.3 18.0 1.0 CB A:ASP133 4.4 18.3 1.0 C2 B:MA7502 4.4 15.5 1.0 NH2 A:ARG210 4.5 12.4 1.0 C3 A:AKG400 4.5 15.4 1.0 C6 B:MA7502 4.6 18.2 1.0 O A:HOH673 4.6 34.5 1.0 O A:HOH659 4.9 43.2 1.0 N6 B:MA7502 5.0 16.7 1.0 N3 B:MA7502 5.0 15.9 1.0 N A:ASP133 5.0 18.6 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