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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy