Magnesium 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
Chlorine (Cl) 3 atoms
Nickel (Ni) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 8ezi

Go back to Magnesium Binding Sites List in 8ezi
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg510

b:12.9
occ:1.00
 OD2 B:ASP382 2.3 33.2 1.0
O B:HOH696 2.4 30.7 1.0
OD1 B:ASP380 2.6 19.6 1.0
OD2 B:ASP380 2.6 33.2 1.0
CG B:ASP380 2.9 27.4 1.0
CG B:ASP382 3.4 30.5 1.0
CB B:ASP382 3.7 24.4 1.0
CB B:ASP380 4.4 19.2 1.0
OD1 B:ASP382 4.5 24.7 1.0
N B:ASP382 4.7 23.2 1.0
CA B:ASP382 4.8 23.0 1.0

Magnesium binding site 2 out of 2 in 8ezi

Go back to Magnesium Binding Sites List in 8ezi
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg511

b:32.2
occ:1.00
 O B:HOH615 2.2 22.3 1.0
O B:HOH688 2.2 25.8 1.0
O B:HOH645 2.3 26.4 1.0
O B:HOH795 3.8 43.1 1.0
O B:GLU406 4.1 16.3 1.0
OE1 B:GLU406 4.2 18.2 1.0
O B:ARG405 4.3 17.1 1.0
O B:HOH709 4.5 32.8 1.0
O B:HOH779 4.5 28.4 1.0
NZ B:LYS308 4.5 19.1 1.0
CA B:GLU406 4.6 22.1 1.0
C B:GLU406 4.6 20.6 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: Fri Apr 7 09:36:48 2023

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