Manganese in PDB 3i3q: Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate

The structure of Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate, PDB code: 3i3q was solved by B.Yu, J.F.Hunt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.97 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.746, 39.187, 72.407, 77.18, 74.80, 63.62
R / Rfree (%)	18.2 / 20.7

The binding sites of Manganese atom in the Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate (pdb code 3i3q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate, PDB code: 3i3q:
Jump to Manganese binding site number: 1; 2;

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


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) and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:9.9 occ:1.00 O2 A:AKG401 2.1 12.1 1.0 NE2 A:HIS187 2.2 10.6 1.0 OD1 A:ASP133 2.2 11.1 1.0 O A:HOH611 2.2 12.9 1.0 NE2 A:HIS131 2.2 10.5 1.0 O5 A:AKG401 2.3 12.2 1.0 C1 A:AKG401 2.9 12.5 1.0 C2 A:AKG401 3.0 11.6 1.0 CG A:ASP133 3.1 11.4 1.0 CE1 A:HIS187 3.1 9.7 1.0 CE1 A:HIS131 3.1 10.6 1.0 CD2 A:HIS187 3.2 10.1 1.0 CD2 A:HIS131 3.2 11.4 1.0 OD2 A:ASP133 3.4 13.8 1.0 O A:HOH826 4.0 30.3 1.0 NH2 A:ARG210 4.1 17.1 1.0 O1 A:AKG401 4.1 16.2 1.0 O A:HOH619 4.2 12.3 1.0 ND1 A:HIS187 4.2 9.3 1.0 ND1 A:HIS131 4.3 11.6 1.0 CG A:HIS187 4.3 9.2 1.0 CG A:HIS131 4.3 9.9 1.0 CB A:ASP133 4.5 12.3 1.0 C3 A:AKG401 4.5 11.8 1.0 CZ2 A:TRP178 4.6 14.1 1.0 N A:ASP133 4.9 11.7 1.0 CA A:ASP133 5.0 11.4 1.0 CD2 A:LEU128 5.0 15.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Alkb in Complex with Mn(II) and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:10.8 occ:1.00 O2 B:AKG402 2.1 13.1 1.0 OD1 B:ASP133 2.1 14.0 1.0 NE2 B:HIS187 2.2 10.6 1.0 NE2 B:HIS131 2.2 10.9 1.0 O B:HOH743 2.2 15.1 1.0 O5 B:AKG402 2.3 12.4 1.0 C1 B:AKG402 2.9 14.0 1.0 C2 B:AKG402 3.0 12.2 1.0 CG B:ASP133 3.1 13.6 1.0 CE1 B:HIS187 3.1 10.9 1.0 CE1 B:HIS131 3.1 10.4 1.0 CD2 B:HIS187 3.2 11.8 1.0 CD2 B:HIS131 3.2 11.1 1.0 OD2 B:ASP133 3.4 17.7 1.0 NH2 B:ARG210 4.1 21.2 1.0 O B:HOH938 4.1 33.5 1.0 O1 B:AKG402 4.1 15.5 1.0 O B:HOH618 4.2 13.7 1.0 ND1 B:HIS187 4.2 10.8 1.0 ND1 B:HIS131 4.2 12.5 1.0 CG B:HIS187 4.3 9.7 1.0 CG B:HIS131 4.3 10.1 1.0 CB B:ASP133 4.4 14.3 1.0 C3 B:AKG402 4.5 12.2 1.0 CZ2 B:TRP178 4.6 13.2 1.0 N B:ASP133 5.0 12.2 1.0 CA B:ASP133 5.0 12.9 1.0

B.Yu, J.F.Hunt. Enzymological and Structural Studies of the Mechanism of Promiscuous Substrate Recognition By the Oxidative Dna Repair Enzyme Alkb. Proc.Natl.Acad.Sci.Usa V. 106 14315 2009.
ISSN: ISSN 0027-8424
PubMed: 19706517
DOI: 10.1073/PNAS.0812938106