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Nickel in PDB 8ezh: A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Sulfite-Npn Adduct

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

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

Protein crystallography data

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Sulfite-Npn Adduct, PDB code: 8ezh 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) 37.79 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.011, 79.092, 121.171, 90, 90, 90
R / Rfree (%) 18.3 / 22.1

Other elements in 8ezh:

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

Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 3 atoms

Nickel Binding Sites:

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

Nickel binding site 1 out of 1 in 8ezh

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


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 Bond in Lactate Racemase R98A/R100A Variant Modeled with Sulfite-Npn Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni514

b:33.1
occ:0.25
 S2 B:ENJ506 2.4 48.5 1.0
S7 B:ENJ506 2.5 31.3 1.0
NE2 B:HIS200 2.5 56.9 1.0
C4 B:ENJ506 2.6 23.9 1.0
C5 B:ENJ506 3.2 24.9 1.0
C3 B:ENJ506 3.3 24.2 1.0
C1 B:ENJ506 3.3 32.3 1.0
C7 B:ENJ506 3.3 28.5 1.0
CD2 B:HIS200 3.3 54.8 1.0
CE1 B:HIS200 3.5 52.5 1.0
CG B:PRO188 3.6 21.8 1.0
O21 B:ENJ506 3.8 49.1 1.0
CZ B:PHE176 3.8 42.1 0.5
S B:ENJ506 3.8 49.0 1.0
CZ B:PHE176 4.1 42.2 0.5
C6 B:ENJ506 4.4 23.6 1.0
CB B:PRO188 4.4 21.5 1.0
C2 B:ENJ506 4.4 25.7 1.0
O1 B:ENJ506 4.4 32.8 1.0
OH B:TYR294 4.4 49.7 1.0
O2 B:ENJ506 4.4 32.0 1.0
CG B:HIS200 4.5 58.3 1.0
CE2 B:PHE176 4.5 37.5 0.5
CD B:PRO188 4.5 18.9 1.0
ND1 B:HIS200 4.5 58.6 1.0
CE1 B:PHE176 4.6 37.9 0.5
NZ B:LYS184 4.7 26.3 1.0
CE1 B:PHE176 4.8 40.5 0.5
NE1 B:TRP358 4.8 56.1 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 09:41:26 2024

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