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:
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
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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
|