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Nickel in PDB 8ezf: A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

Enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

All present enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant:
5.1.2.1;

Protein crystallography data

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant, PDB code: 8ezf was solved by S.Gatreddi, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.97 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.84, 79.913, 121.788, 90, 90, 90
R / Rfree (%) 18.6 / 24.3

Other elements in 8ezf:

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 2 atoms
Magnesium (Mg) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant (pdb code 8ezf). 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 A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant, PDB code: 8ezf:

Nickel binding site 1 out of 1 in 8ezf

Go back to Nickel Binding Sites List in 8ezf
Nickel binding site 1 out of 1 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni507

b:39.1
occ:1.00
 C4 B:ENJ506 2.2 19.5 1.0
S7 B:ENJ506 2.3 22.8 1.0
S2 B:ENJ506 2.4 30.0 1.0
NE2 B:HIS200 2.4 30.9 1.0
C3 B:ENJ506 2.9 20.8 1.0
C7 B:ENJ506 3.0 19.1 1.0
C5 B:ENJ506 3.0 15.6 1.0
C1 B:ENJ506 3.2 24.8 1.0
CD2 B:HIS200 3.3 46.0 1.0
CE1 B:HIS200 3.5 38.9 1.0
S B:ENJ506 3.5 27.4 1.0
CG B:PRO188 3.5 25.8 1.0
O1 B:ENJ506 3.7 35.0 1.0
O21 B:ENJ506 3.8 28.9 1.0
CZ B:PHE176 3.9 44.8 1.0
C2 B:ENJ506 4.1 18.3 1.0
C6 B:ENJ506 4.2 17.4 1.0
CB B:PRO188 4.3 26.7 1.0
CD B:PRO188 4.3 26.8 1.0
O2 B:ENJ506 4.3 24.5 1.0
NZ B:LYS184 4.4 15.9 1.0
CG B:HIS200 4.5 54.4 1.0
ND1 B:HIS200 4.5 49.3 1.0
OH B:TYR294 4.6 43.4 1.0
CE1 B:PHE176 4.7 29.8 1.0
N1 B:ENJ506 4.7 21.8 1.0
O B:ENJ506 4.8 33.2 1.0
CE2 B:PHE176 4.9 39.7 1.0
NE1 B:TRP358 4.9 45.5 1.0

Reference:

S.Gatreddi, D.Sui, R.P.Hausinger, J.Hu. Irreversible Inactivation of Lactate Racemase By Sodium Borohydride Reveals Reactivity of the Nickel-Pincer Nucleotide Cofactor Acs Catalysis 1441 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C05461
Page generated: Thu Oct 10 09:41:20 2024

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