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

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

All present enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon Bond in Lactate Racemase R98A/R100A Variant Modeled with Separated Sulfite and Npn:
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 Separated Sulfite and Npn, PDB code: 8ezi 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 8ezi:

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

Calcium (Ca) 2 atoms
Magnesium (Mg) 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 Separated Sulfite and Npn (pdb code 8ezi). 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 Separated Sulfite and Npn, PDB code: 8ezi:

Nickel binding site 1 out of 1 in 8ezi

Go back to Nickel Binding Sites List in 8ezi
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 Separated Sulfite and Npn


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 Separated Sulfite and Npn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni515

b:34.4
occ:0.25
 C4 B:4EY507 2.3 30.0 1.0
S2 B:4EY507 2.5 48.7 1.0
S7 B:4EY507 2.5 31.2 1.0
NE2 B:HIS200 2.5 57.8 1.0
C3 B:4EY507 3.2 26.4 1.0
C5 B:4EY507 3.2 26.1 1.0
C7 B:4EY507 3.3 30.4 1.0
C1 B:4EY507 3.3 32.5 1.0
CD2 B:HIS200 3.3 55.6 1.0
CE1 B:HIS200 3.5 52.6 1.0
CG B:PRO188 3.6 22.1 1.0
O2 B:SO3506 3.7 48.0 1.0
CZ B:PHE176 3.8 42.2 0.5
CZ B:PHE176 4.0 42.4 0.5
S B:SO3506 4.3 47.0 1.0
CB B:PRO188 4.4 21.6 1.0
OH B:TYR294 4.4 49.5 1.0
CG B:HIS200 4.5 58.5 1.0
C6 B:4EY507 4.5 23.8 1.0
C2 B:4EY507 4.5 26.1 1.0
O2 B:4EY507 4.5 33.3 1.0
CE2 B:PHE176 4.5 37.5 0.5
ND1 B:HIS200 4.5 58.7 1.0
CD B:PRO188 4.5 18.8 1.0
CE1 B:PHE176 4.6 37.9 0.5
O1 B:SO3506 4.7 34.5 1.0
NZ B:LYS184 4.7 25.9 1.0
NE1 B:TRP358 4.8 56.3 1.0
CE1 B:PHE176 4.8 40.3 0.5
N1 B:4EY507 5.0 24.6 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 09:41:27 2024

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