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

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 8ezh

Go back to Calcium Binding Sites List in 8ezh
Calcium 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 Sulfite-Npn Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca507

b:19.8
occ:1.00
 O B:HOH674 2.4 18.9 1.0
OE2 B:GLU400 2.4 24.3 1.0
O B:HOH769 2.5 23.8 1.0
OE1 B:GLU400 2.7 18.0 1.0
CD B:GLU400 2.9 19.8 1.0
CA B:CA508 4.0 17.3 1.0
OD2 B:ASP396 4.2 18.0 1.0
CG B:GLU400 4.4 17.3 1.0

Calcium binding site 2 out of 2 in 8ezh

Go back to Calcium Binding Sites List in 8ezh
Calcium 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 Sulfite-Npn Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 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:Ca508

b:17.3
occ:1.00
 OE1 B:GLU400 2.3 18.0 1.0
O B:HOH613 2.4 17.9 1.0
OD2 B:ASP396 2.5 18.0 1.0
CG B:ASP396 3.4 16.0 1.0
CD B:GLU400 3.5 19.8 1.0
OD1 B:ASP396 3.6 20.0 1.0
CA B:CA507 4.0 19.8 1.0
O B:HOH674 4.0 18.9 1.0
CG B:GLU400 4.2 17.3 1.0
OE2 B:GLU400 4.4 24.3 1.0
CB B:ASP396 4.8 17.4 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: Tue Apr 4 19:38:22 2023

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