Arsenic in PDB 7mdb: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2:
2.5.1.48; 4.4.1.1; 4.4.1.8;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2, PDB code: 7mdb was solved by A.Nuthanakanti, A.Serganov, A.Kaushik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 1.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.119, 105.119, 287.79, 90, 90, 90
R / Rfree (%) 17 / 18.9

Other elements in 7mdb:

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Bromine (Br) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 (pdb code 7mdb). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2, PDB code: 7mdb:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 7mdb

Go back to Arsenic Binding Sites List in 7mdb
Arsenic binding site 1 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As404

b:50.8
occ:0.38
 AS H:CAC404 0.0 50.8 0.4
O1 H:CAC404 1.9 44.4 0.8
O2 H:CAC404 1.9 43.4 0.4
C2 H:CAC404 2.0 47.7 0.2
C1 H:CAC404 2.0 31.9 1.0
OH H:TYR99 3.2 39.0 1.0
CE1 H:TYR99 3.9 38.3 1.0
O H:HOH507 3.9 36.8 1.0
CZ H:TYR99 4.1 37.3 1.0
OE2 H:GLU322 4.1 56.0 1.0
O H:HOH701 4.1 50.7 1.0
O H:HOH518 4.4 40.2 1.0
CD H:GLU322 5.0 49.7 1.0

Arsenic binding site 2 out of 2 in 7mdb

Go back to Arsenic Binding Sites List in 7mdb
Arsenic binding site 2 out of 2 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As405

b:54.5
occ:0.45
 AS H:CAC405 0.0 54.5 0.5
O2 H:CAC405 1.9 53.7 0.5
O1 H:CAC405 1.9 46.2 0.7
C1 H:CAC405 2.0 55.8 0.7
C2 H:CAC405 2.0 42.2 0.8
NA H:NA409 3.9 47.5 0.7
CE1 H:HIS124 3.9 37.8 1.0
ND1 H:HIS124 4.1 33.6 1.0
OG1 H:THR125 4.1 35.0 1.0
O H:HOH573 4.2 50.9 1.0
O H:HOH524 4.2 41.3 1.0
NZ H:LYS156 4.3 72.3 1.0
NE2 H:HIS124 4.5 35.9 1.0
N H:THR125 4.7 29.2 1.0
CG H:HIS124 4.7 31.7 1.0
CD H:LYS156 4.8 51.2 1.0
O H:HOH572 4.9 42.8 1.0
CD2 H:HIS124 5.0 34.1 1.0

Reference:

K.Shatalin, A.Nuthanakanti, A.Kaushik, D.Shishov, A.Peselis, I.Shamovsky, B.Pani, M.Lechpammer, N.Vasilyev, E.Shatalina, D.Rebatchouk, A.Mironov, P.Fedichev, A.Serganov, E.Nudler. Inhibitors of Bacterial H 2 S Biogenesis Targeting Antibiotic Resistance and Tolerance. Science V. 372 1169 2021.
ISSN: ESSN 1095-9203
PubMed: 34112687
DOI: 10.1126/SCIENCE.ABD8377
Page generated: Sat Jul 10 09:47:31 2021

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