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Bromine in PDB 7mct: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL1

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL1

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1, PDB code: 7mct 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) 29.71 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.115, 105.115, 288.104, 90, 90, 90
R / Rfree (%) 16.2 / 17.2

Other elements in 7mct:

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

Bromine binding site 1 out of 5 in 7mct

Go back to Bromine Binding Sites List in 7mct
Bromine binding site 1 out of 5 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br401

b:113.4
occ:0.71
 BR H:LB6401 0.0 113.4 0.7
C6 H:LB6401 1.9 53.8 0.7
C7 H:LB6401 2.8 52.1 0.7
C5 H:LB6401 2.9 51.3 0.7
CG H:GLU350 3.3 40.9 1.0
CB H:GLU350 3.4 35.7 1.0
CG1 H:ILE352 3.9 31.4 1.0
CD2 H:HIS339 4.0 42.1 1.0
C8 H:LB6401 4.1 50.5 0.7
CD1 H:ILE342 4.1 49.3 1.0
O H:HOH823 4.2 55.0 1.0
C4 H:LB6401 4.2 47.4 0.7
CD H:GLU350 4.3 53.2 1.0
OE1 H:GLU350 4.5 52.9 1.0
C9 H:LB6401 4.7 42.9 0.7
CG2 H:ILE342 4.7 42.1 1.0
NE2 H:HIS339 4.7 42.2 1.0
O H:HOH652 4.7 44.0 1.0
CA H:ARG347 4.8 31.4 1.0
O H:ILE346 4.8 30.3 1.0
O H:HOH848 4.9 34.0 1.0
CB H:ILE352 4.9 29.0 1.0
CA H:GLU350 4.9 30.7 1.0
CD1 H:ILE352 5.0 28.1 1.0
CG H:HIS339 5.0 39.7 1.0

Bromine binding site 2 out of 5 in 7mct

Go back to Bromine Binding Sites List in 7mct
Bromine binding site 2 out of 5 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br402

b:45.2
occ:0.29
 BR H:LB6402 0.0 45.2 0.3
O3 H:PLP406 0.5 44.1 0.4
C3 H:PLP406 1.3 45.3 0.4
C6 H:LB6402 1.9 43.7 0.3
C2 H:PLP406 2.2 42.9 0.4
C4 H:PLP406 2.5 45.8 0.4
C2A H:PLP406 2.6 37.2 0.4
C5 H:LB6402 2.8 43.1 0.3
C7 H:LB6402 2.8 46.2 0.3
C4A H:PLP406 3.1 47.5 0.4
N H:SER1 3.2 49.4 1.0
N1 H:PLP406 3.4 44.1 0.4
C5 H:PLP406 3.7 47.8 0.4
CA H:LYS6 3.7 27.2 1.0
CG2 H:THR5 3.7 26.1 1.0
N H:LYS6 3.7 25.1 1.0
C H:THR5 4.0 25.4 1.0
C6 H:PLP406 4.0 45.4 0.4
O H:THR5 4.1 26.4 1.0
C4 H:LB6402 4.1 43.1 0.3
C8 H:LB6402 4.1 47.1 0.3
CB H:LYS6 4.2 26.0 1.0
CB H:THR5 4.3 26.5 1.0
CB H:HIS9 4.6 24.3 1.0
CA H:SER1 4.7 46.5 1.0
C9 H:LB6402 4.7 45.0 0.3
CG H:LYS6 4.7 35.5 1.0
CA H:THR5 4.8 25.2 1.0
C H:LYS6 5.0 24.9 1.0

Bromine binding site 3 out of 5 in 7mct

Go back to Bromine Binding Sites List in 7mct
Bromine binding site 3 out of 5 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br403

b:45.5
occ:0.31
 O H:HOH925 3.1 49.2 1.0
O H:HOH700 3.6 34.8 1.0
O H:SER54 3.8 23.6 1.0
CB H:SER58 4.0 22.5 1.0
O H:HOH709 4.1 34.8 1.0
CB H:HIS12 4.1 30.4 1.0
O H:HOH612 4.1 45.9 1.0
C H:SER54 4.2 22.6 1.0
CB H:SER54 4.2 23.4 1.0
CD2 H:HIS12 4.2 30.3 1.0
OG H:SER58 4.4 27.8 1.0
CG H:HIS12 4.5 29.7 1.0
N H:SER55 4.5 20.1 1.0
CA H:SER55 4.7 20.0 1.0
O3 H:GOL409 4.8 46.1 0.7
CA H:SER54 4.8 23.2 1.0
O H:HIS12 4.9 26.7 1.0

Bromine binding site 4 out of 5 in 7mct

Go back to Bromine Binding Sites List in 7mct
Bromine binding site 4 out of 5 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br404

b:28.4
occ:0.11
 O H:PRO177 3.5 23.5 1.0
CA H:TYR178 3.5 22.3 1.0
C H:PRO177 3.6 24.4 1.0
N H:TYR178 3.6 21.6 1.0
O H:HOH639 3.6 45.2 1.0
CD2 H:LEU63 3.7 26.5 1.0
CD2 H:LEU7 3.7 27.1 1.0
CD1 H:TYR178 3.9 23.1 1.0
CG H:LEU7 4.1 26.4 1.0
CB H:PRO177 4.1 23.6 1.0
CB H:TYR178 4.1 22.7 1.0
CB H:LEU63 4.2 22.2 1.0
CG H:LEU63 4.2 23.7 1.0
CD1 H:LEU63 4.2 26.3 1.0
CA H:PRO177 4.5 23.8 1.0
CG H:TYR178 4.5 23.1 1.0
CD2 H:LEU246 4.6 22.3 1.0
CD1 H:LEU7 4.6 27.6 1.0
O H:LEU63 4.6 23.3 1.0
C H:TYR178 4.8 22.4 1.0
CA H:LEU63 4.8 22.5 1.0
O H:HOH604 4.8 35.0 1.0
CE1 H:TYR178 5.0 25.2 1.0

Bromine binding site 5 out of 5 in 7mct

Go back to Bromine Binding Sites List in 7mct
Bromine binding site 5 out of 5 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound 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 with Bound NL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br405

b:41.9
occ:0.18
 O H:HOH879 2.9 46.6 1.0
O H:HOH599 3.1 37.8 1.0
O H:HOH942 3.2 48.3 1.0
O H:HOH673 3.5 44.2 1.0
CZ H:PHE70 3.6 25.7 1.0
ND1 H:HIS68 3.8 33.9 1.0
CE2 H:PHE70 3.8 27.7 1.0
CB H:ALA217 4.2 24.9 1.0
O H:ALA217 4.2 24.7 1.0
CG H:HIS68 4.3 30.1 1.0
CB H:HIS68 4.3 27.5 1.0
CB H:ALA221 4.3 24.1 1.0
C H:ALA217 4.5 27.0 1.0
CE1 H:HIS68 4.6 36.6 1.0
O H:HOH783 4.6 44.9 1.0
CE1 H:PHE70 4.6 23.6 1.0
O H:HOH922 4.9 46.2 1.0
CA H:ALA217 4.9 25.4 1.0
CD2 H:PHE70 5.0 23.8 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 04:05:36 2024

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