Atomistry » Magnesium » PDB 8enc-8f19 » 8ezh
Atomistry »
  Magnesium »
    PDB 8enc-8f19 »
      8ezh »

Magnesium 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:

Calcium (Ca) 2 atoms
Nickel (Ni) 1 atom
Chlorine (Cl) 3 atoms

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 Sulfite-Npn Adduct (pdb code 8ezh). 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 Sulfite-Npn Adduct, PDB code: 8ezh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8ezh

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


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 Sulfite-Npn Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg509

b:12.9
occ:1.00
 OD2 B:ASP382 2.3 33.1 1.0
O B:HOH690 2.4 30.4 1.0
OD2 B:ASP380 2.6 33.4 1.0
OD1 B:ASP380 2.6 19.4 1.0
CG B:ASP380 2.9 27.4 1.0
CG B:ASP382 3.4 31.1 1.0
CB B:ASP382 3.7 24.2 1.0
CB B:ASP380 4.4 19.4 1.0
OD1 B:ASP382 4.5 24.9 1.0
N B:ASP382 4.7 23.3 1.0
CA B:ASP382 4.8 23.3 1.0

Magnesium binding site 2 out of 2 in 8ezh

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


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 Sulfite-Npn Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg510

b:32.4
occ:1.00
 O B:HOH615 2.2 22.8 1.0
O B:HOH684 2.2 25.6 1.0
O B:HOH649 2.3 26.3 1.0
O B:HOH797 3.8 43.7 1.0
O B:GLU406 4.1 16.3 1.0
OE1 B:GLU406 4.2 18.3 1.0
O B:ARG405 4.3 17.0 1.0
O B:HOH713 4.5 32.9 1.0
O B:HOH779 4.5 28.4 1.0
NZ B:LYS308 4.5 19.5 1.0
CA B:GLU406 4.6 21.8 1.0
C B:GLU406 4.6 20.5 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 01:25:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy