Magnesium in PDB 9axj: Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form

All present enzymatic activity of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form:
2.5.1.48;

The structure of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form, PDB code: 9axj was solved by L.J.Perkins, A.P.Zmich, C.A.Bingman, A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 1.50
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	116.946, 116.946, 116.946, 90, 90, 90
R / Rfree (%)	13.7 / 15.6

The structure of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Magnesium atom in the Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form (pdb code 9axj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form, PDB code: 9axj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:39.5 occ:1.00 O A:HOH519 2.0 32.3 1.0 O A:HOH813 2.1 36.3 1.0 O A:HOH544 2.1 36.1 1.0 MG A:MG407 2.8 46.4 1.0 O A:ALA17 4.1 20.4 1.0 O A:GLU16 4.3 22.1 1.0 O A:HOH526 4.4 26.4 1.0 CB A:GLU16 4.5 28.3 1.0 N A:ALA19 4.5 20.4 1.0 O A:HOH652 4.6 42.9 1.0 O A:HOH721 4.6 33.5 1.0 OE1 A:GLU16 4.8 52.3 1.0 C A:ALA17 4.9 19.1 1.0 C A:GLU16 4.9 23.7 1.0 CA A:ASP18 4.9 19.8 1.0 CB A:ALA19 4.9 24.6 1.0 CG A:GLU16 5.0 38.5 1.0

Magnesium binding site 2 out of 3 in the Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:43.4 occ:1.00 O A:HOH740 2.0 46.0 1.0 O A:HOH579 2.1 38.1 1.0 O A:HOH827 2.3 42.0 1.0 OE1 A:GLU353 4.1 29.9 1.0 OE2 A:GLU353 4.3 37.4 1.0 O A:HOH858 4.3 42.4 1.0 CD A:GLU353 4.7 30.2 1.0 O A:HOH812 4.7 39.0 1.0 O A:HOH850 4.7 51.1 1.0

Magnesium binding site 3 out of 3 in the Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cystathionine Gamma Lyase From Thermobifida Fusca in An Amino Crotonate Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:46.4 occ:1.00 O A:HOH526 1.9 26.4 1.0 O A:HOH544 2.4 36.1 1.0 MG A:MG405 2.8 39.5 1.0 O A:HOH652 3.6 42.9 1.0 OD1 A:ASP18 4.0 21.8 1.0 O A:HOH519 4.2 32.3 1.0 CA A:ASP18 4.3 19.8 1.0 OH A:TYR29 4.4 22.8 1.0 O A:HOH610 4.5 24.2 1.0 O A:GLU16 4.6 22.1 1.0 O A:HOH778 4.6 26.4 1.0 O A:HOH813 4.6 36.3 1.0 N A:ALA19 4.8 20.4 1.0 CB A:ASP18 4.9 18.7 1.0 CG A:ASP18 5.0 20.4 1.0 O A:ALA17 5.0 20.4 1.0 N A:ASP18 5.0 19.1 1.0

A.Zmich, L.J.Perkins, C.Bingman, A.R.Buller. Elucidation of the Stereochemical Mechanism of Cystathionine Gamma-Lyase Reveals How Substrate Specificity Constrains Catalysis. Acs Catalysis V. 14 11196 2024.
ISSN: ESSN 2155-5435
PubMed: 39391268
DOI: 10.1021/ACSCATAL.4C02281