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Magnesium 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:

Nickel (Ni) 1 atom
Chlorine (Cl) 1 atom
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where 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:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8ezf

Go back to Magnesium Binding Sites List in 8ezf
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg503

b:35.5
occ:1.00
 OD2 B:ASP382 2.0 42.1 1.0
O B:HOH603 2.2 36.3 1.0
O B:HOH612 2.3 25.9 1.0
CG B:ASP382 3.1 37.7 1.0
OD1 B:ASP382 3.6 26.6 1.0
OD1 B:ASP380 4.1 38.8 1.0
CB B:ASP382 4.3 25.1 1.0
OD2 B:ASP380 4.7 44.8 1.0
CG B:ASP380 4.9 36.0 1.0

Magnesium binding site 2 out of 2 in 8ezf

Go back to Magnesium Binding Sites List in 8ezf
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg504

b:40.4
occ:1.00
 O B:HOH696 2.0 37.8 1.0
O B:HOH614 2.2 30.4 1.0
O B:HOH639 2.5 35.1 1.0
O B:GLU406 4.1 24.6 1.0
O B:HOH680 4.4 41.4 1.0
OE1 B:GLU406 4.4 23.2 1.0
O B:ARG405 4.6 18.9 1.0
NZ B:LYS308 4.7 23.4 1.0
C B:GLU406 4.7 21.2 1.0
CA B:GLU406 4.8 18.9 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: Fri Oct 4 01:24:45 2024

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