Bromine 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
Arsenic (As) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103A Mutant Co-Crystallized with NL2, PDB code: 7mdb:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 7mdb

Go back to Bromine Binding Sites List in 7mdb
Bromine 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 Bromine with other atoms in the Br 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:Br401

b:55.3
occ:0.38
 BR H:YXA401 0.0 55.3 0.4
C6 H:YXA401 1.9 44.4 0.4
O15 H:YXA402 2.5 47.1 0.3
C7 H:YXA401 2.8 45.5 0.4
C5 H:YXA401 2.8 46.1 0.4
C14 H:YXA402 3.4 45.9 0.3
C11 H:YXA402 3.4 45.7 0.3
CG H:ARG104 3.5 41.6 0.7
C16 H:YXA402 3.5 46.9 0.3
CA H:ARG104 3.7 33.7 1.0
N H:ARG104 3.8 30.7 1.0
C10 H:YXA402 3.8 49.2 0.3
OG1 H:THR107 3.9 32.2 1.0
C H:ALA103 4.1 30.6 1.0
CB H:ARG104 4.1 35.6 1.0
C8 H:YXA401 4.1 46.1 0.4
C4 H:YXA401 4.1 47.7 0.4
O H:ALA103 4.2 32.1 1.0
CB H:ALA103 4.4 33.1 1.0
O H:HOH843 4.5 48.5 1.0
C13 H:YXA402 4.5 45.4 0.3
C12 H:YXA402 4.6 46.2 0.3
N1 H:YXA402 4.6 49.4 0.3
C2 H:YXA402 4.6 45.2 0.3
C9 H:YXA401 4.6 45.5 0.4
O H:GLY100 4.7 33.7 1.0
CD H:ARG104 4.8 47.4 0.6
CG H:LYS108 4.8 36.0 1.0
CE H:LYS108 4.9 53.1 1.0
CA H:ALA103 4.9 31.3 1.0

Bromine binding site 2 out of 2 in 7mdb

Go back to Bromine Binding Sites List in 7mdb
Bromine 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 Bromine with other atoms in the Br 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:Br402

b:68.1
occ:0.31
 BR H:YXA402 0.0 68.1 0.3
C13 H:YXA401 1.2 52.2 0.4
C17 H:YXA401 1.4 54.5 0.4
C12 H:YXA401 1.5 51.8 0.4
O19 H:YXA401 1.7 58.1 0.4
C6 H:YXA402 1.9 51.9 0.3
O18 H:YXA401 2.5 54.0 0.4
C14 H:YXA401 2.7 52.2 0.4
C11 H:YXA401 2.8 51.9 0.4
C7 H:YXA402 2.8 53.3 0.3
C5 H:YXA402 2.8 53.2 0.3
O H:HOH654 3.2 50.7 1.0
O15 H:YXA401 3.3 52.7 0.4
O H:HOH790 3.9 44.6 1.0
C16 H:YXA401 3.9 54.7 0.4
C10 H:YXA401 4.0 46.0 0.4
CD2 H:HIS339 4.0 40.6 1.0
C4 H:YXA402 4.1 54.3 0.3
C8 H:YXA402 4.1 50.7 0.3
CD1 H:ILE342 4.2 47.1 1.0
NE2 H:HIS339 4.2 45.1 1.0
C2 H:YXA401 4.6 43.6 0.4
CG H:GLU350 4.6 53.0 1.0
N1 H:YXA401 4.6 46.5 0.4
C9 H:YXA402 4.6 52.7 0.3
CB H:GLU350 4.8 49.8 1.0
OE2 H:GLU350 4.9 65.8 1.0
CD H:GLU350 4.9 62.0 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 09:59:07 2021

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