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

Protein crystallography data

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

Manganese Binding Sites:

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 3i3q

Go back to Manganese Binding Sites List in 3i3q
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 3i3q

Go back to Manganese Binding Sites List in 3i3q
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

Reference:

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
Page generated: Tue Dec 15 04:10:46 2020

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