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Bromine in PDB 7md6: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1:
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 Y103N Mutant Co-Crystallized with NL1, PDB code: 7md6 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) 29.77 / 2.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.379, 104.379, 287.729, 90, 90, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 7md6:

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 (pdb code 7md6). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1, PDB code: 7md6:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 1 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


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 Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br401

b:78.8
occ:0.42
 BR H:LB6401 0.0 78.8 0.4
C6 H:LB6401 1.9 57.7 0.4
C7 H:LB6401 2.8 56.6 0.4
C5 H:LB6401 2.8 53.7 0.4
CG H:GLU350 3.4 56.5 1.0
CB H:GLU350 3.6 47.3 1.0
CD H:GLU350 3.8 61.0 1.0
CD2 H:HIS339 4.1 53.1 1.0
CD1 H:ILE342 4.1 60.0 1.0
C8 H:LB6401 4.1 55.7 0.4
C4 H:LB6401 4.1 54.9 0.4
OE1 H:GLU350 4.2 60.6 1.0
OE2 H:GLU350 4.3 71.5 1.0
CG1 H:ILE352 4.5 40.2 1.0
NE2 H:HIS339 4.5 56.3 1.0
C9 H:LB6401 4.7 53.5 0.4

Bromine binding site 2 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 2 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


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 Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br402

b:64.3
occ:0.48
 BR H:LB6402 0.0 64.3 0.5
C6 H:LB6402 1.9 52.4 0.5
C7 H:LB6402 2.8 51.6 0.5
C5 H:LB6402 2.9 47.0 0.5
N H:SER1 3.3 67.1 1.0
CA H:LYS6 3.9 38.6 1.0
N H:LYS6 4.1 38.3 1.0
C8 H:LB6402 4.1 51.9 0.5
C4 H:LB6402 4.2 50.0 0.5
CG2 H:THR5 4.2 35.7 1.0
CB H:HIS9 4.2 39.1 1.0
CB H:LYS6 4.3 42.1 1.0
C H:THR5 4.3 39.8 1.0
O H:THR5 4.4 37.7 1.0
C9 H:LB6402 4.7 51.1 0.5
CA H:SER1 4.7 59.6 1.0
CB H:THR5 4.8 35.6 1.0
C H:HIS9 4.8 41.9 1.0
N H:GLY10 4.9 39.4 1.0
CG H:LYS6 4.9 53.0 1.0

Bromine binding site 3 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 3 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br403

b:61.0
occ:0.55
 BR H:LB6403 0.0 61.0 0.6
C6 H:LB6403 1.9 43.4 0.6
C7 H:LB6403 2.8 40.6 0.6
C5 H:LB6403 2.8 40.0 0.6
O H:SER54 3.8 32.7 1.0
O H:HOH536 3.8 42.8 1.0
C H:SER54 3.9 29.7 1.0
CB H:SER54 3.9 30.9 1.0
CD2 H:HIS12 4.1 47.0 1.0
C8 H:LB6403 4.1 44.1 0.6
C4 H:LB6403 4.1 42.6 0.6
CB H:HIS12 4.2 44.3 1.0
N H:SER55 4.2 30.9 1.0
CA H:SER55 4.4 29.8 1.0
CG H:HIS12 4.4 51.0 1.0
CB H:SER58 4.4 32.8 1.0
CA H:SER54 4.6 32.6 1.0
C9 H:LB6403 4.7 40.8 0.6
OG H:SER58 4.7 39.7 1.0
OH H:TYR43 4.8 38.3 1.0
CG H:FLC408 4.8 51.1 1.0

Bromine binding site 4 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 4 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br404

b:42.9
occ:0.18
 CA H:TYR178 3.6 32.3 1.0
CD2 H:LEU7 3.7 30.4 1.0
CD2 H:LEU63 3.7 34.9 1.0
CD1 H:TYR178 3.8 31.1 1.0
O H:PRO177 3.8 37.5 1.0
CG H:LEU7 3.9 38.1 1.0
N H:TYR178 3.9 33.1 1.0
C H:PRO177 4.0 36.8 1.0
CB H:TYR178 4.2 30.9 1.0
CD1 H:LEU7 4.4 34.1 1.0
CG H:TYR178 4.4 30.7 1.0
CG H:LEU63 4.5 38.8 1.0
CB H:PRO177 4.5 33.5 1.0
CB H:LEU63 4.6 32.3 1.0
CD1 H:LEU63 4.6 31.0 1.0
CB H:LYS3 4.7 45.0 1.0
O H:LYS3 4.7 35.4 1.0
CE1 H:TYR178 4.7 36.1 1.0
CD2 H:LEU246 4.7 24.9 1.0
O H:LEU63 4.8 37.2 1.0
C H:TYR178 4.8 33.4 1.0
CA H:PRO177 4.9 32.6 1.0

Bromine binding site 5 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 5 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br405

b:49.3
occ:0.21
 ND1 H:HIS68 3.5 49.7 1.0
CZ H:PHE70 3.7 30.1 1.0
O H:HOH569 3.8 51.9 1.0
OA1 H:FLC408 3.9 61.8 1.0
OB1 H:FLC408 4.1 53.3 0.4
CG H:HIS68 4.1 45.4 1.0
CE2 H:PHE70 4.1 28.8 1.0
O H:HOH656 4.1 51.4 1.0
CB H:HIS68 4.2 39.1 1.0
CB H:ALA217 4.3 35.3 1.0
CE1 H:HIS68 4.3 45.2 1.0
O H:ALA217 4.5 34.8 1.0
CE1 H:PHE70 4.6 34.9 1.0
CB H:ALA221 4.8 30.4 1.0
C H:ALA217 4.8 39.0 1.0
CAC H:FLC408 5.0 46.6 0.2

Bromine binding site 6 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 6 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br406

b:83.3
occ:0.54
 BR H:LB6406 0.0 83.3 0.5
C6 H:LB6406 1.9 48.8 0.5
C5 H:LB6406 2.9 48.1 0.5
C7 H:LB6406 2.9 53.9 0.5
OE1 H:GLU218 4.2 80.3 1.0
C8 H:LB6406 4.2 51.9 0.5
CB H:PHE222 4.2 38.8 1.0
C4 H:LB6406 4.2 42.2 0.5
CG H:ARG219 4.2 44.2 1.0
O H:GLU218 4.3 38.9 1.0
CG H:PHE222 4.3 40.3 1.0
CA H:ARG219 4.3 39.7 1.0
CG H:GLU218 4.4 55.6 1.0
CD2 H:PHE222 4.4 39.4 1.0
C H:GLU218 4.6 36.7 1.0
N H:ARG219 4.6 35.0 1.0
C9 H:LB6406 4.7 48.7 0.5
CD H:GLU218 4.8 71.1 1.0
CB H:ARG219 4.8 38.6 1.0
O H:HOH602 4.9 47.8 1.0

Bromine binding site 7 out of 7 in 7md6

Go back to Bromine Binding Sites List in 7md6
Bromine binding site 7 out of 7 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme Y103N Mutant Co-Crystallized with NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br407

b:75.7
occ:0.49
 BR H:LB6407 0.0 75.7 0.5
C6 H:LB6407 1.9 45.0 0.5
C5 H:LB6407 2.8 40.9 0.5
C7 H:LB6407 2.9 43.0 0.5
NH1 H:ARG219 3.0 53.5 1.0
CB H:LYS215 3.7 39.5 1.0
CD2 H:LEU216 3.9 35.0 1.0
CD H:ARG219 4.0 50.6 1.0
C4 H:LB6407 4.1 39.5 0.5
CZ H:ARG219 4.1 60.2 1.0
C8 H:LB6407 4.2 42.5 0.5
CD H:LYS215 4.3 61.2 1.0
N H:LEU216 4.4 35.5 1.0
C H:LYS215 4.4 36.5 1.0
CG H:LYS215 4.5 52.5 1.0
CG H:LEU216 4.5 39.0 1.0
NE H:ARG219 4.5 63.9 1.0
C9 H:LB6407 4.7 37.5 0.5
CA H:LYS215 4.7 41.7 1.0
O H:LYS215 4.7 39.9 1.0
CA H:LEU216 4.9 39.0 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: Thu Jul 11 04:05:47 2024

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