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Nickel in PDB 5i93: Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site

Enzymatic activity of Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site

All present enzymatic activity of Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site:
1.13.11.54;

Protein crystallography data

The structure of Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site, PDB code: 5i93 was solved by A.R.Deshpande, K.Wagenpfeil, T.C.Pochapsky, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.68 / 2.24
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.025, 79.025, 115.360, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site (pdb code 5i93). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site, PDB code: 5i93:

Nickel binding site 1 out of 1 in 5i93

Go back to Nickel Binding Sites List in 5i93
Nickel binding site 1 out of 1 in the Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Mouse Acireductone Dioxygenase with NI2+ and 2- Ketopentanoic Acid in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:20.9
occ:1.00
 OE1 A:GLU94 2.1 20.3 1.0
NE2 A:HIS90 2.1 20.9 1.0
NE2 A:HIS133 2.1 19.5 1.0
NE2 A:HIS88 2.2 18.1 1.0
O A:HOH307 2.2 20.0 1.0
O A:HOH313 2.5 23.8 1.0
CD A:GLU94 3.0 20.8 1.0
CD2 A:HIS133 3.1 16.1 1.0
CD2 A:HIS90 3.1 18.0 1.0
CD2 A:HIS88 3.1 18.4 1.0
CE1 A:HIS90 3.1 20.7 1.0
CE1 A:HIS133 3.1 16.3 1.0
CE1 A:HIS88 3.2 15.9 1.0
OE2 A:GLU94 3.3 21.1 1.0
O A:HOH347 4.0 18.1 1.0
O07 A:69O202 4.1 38.8 1.0
ND1 A:HIS90 4.2 19.1 1.0
ND1 A:HIS133 4.2 20.6 1.0
CG A:HIS133 4.2 20.1 1.0
CG A:HIS90 4.2 23.0 1.0
CG A:HIS88 4.2 21.7 1.0
ND1 A:HIS88 4.3 21.7 1.0
O A:HOH380 4.3 15.5 1.0
O08 A:69O202 4.3 39.5 1.0
O A:HOH466 4.4 29.4 1.0
CG A:GLU94 4.4 18.7 1.0
C06 A:69O202 4.6 45.1 1.0
CB A:GLU94 4.8 16.6 1.0

Reference:

A.R.Deshpande, K.Wagenpfeil, T.C.Pochapsky, G.A.Petsko, D.Ringe. Metal-Dependent Function of A Mammalian Acireductone Dioxygenase. Biochemistry V. 55 1398 2016.
ISSN: ISSN 0006-2960
PubMed: 26858196
DOI: 10.1021/ACS.BIOCHEM.5B01319
Page generated: Thu Oct 10 06:31:23 2024

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