Sodium in PDB 6vut: Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392
Protein crystallography data
The structure of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392, PDB code: 6vut
was solved by
A.Punetha,
C.Hou,
H.X.Ngo,
S.Garneau-Tsodikova,
O.V.Tsodikov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.96 /
2.73
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
175.190,
175.190,
122.191,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.3 /
22.7
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392
(pdb code 6vut). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392, PDB code: 6vut:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 6vut
Go back to
Sodium Binding Sites List in 6vut
Sodium binding site 1 out
of 3 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na508
b:39.5
occ:1.00
|
OG1
|
A:THR70
|
2.7
|
25.0
|
1.0
|
O
|
A:ARG68
|
2.8
|
25.5
|
1.0
|
NH1
|
A:ARG183
|
3.0
|
38.4
|
1.0
|
N
|
A:THR70
|
3.3
|
27.1
|
1.0
|
O
|
A:GLY189
|
3.3
|
26.4
|
1.0
|
CD
|
A:ARG183
|
3.5
|
36.0
|
1.0
|
C
|
A:ARG68
|
3.5
|
26.3
|
1.0
|
C
|
A:LEU69
|
3.7
|
27.4
|
1.0
|
N
|
A:LEU191
|
3.8
|
30.1
|
1.0
|
C
|
A:GLY189
|
3.8
|
25.1
|
1.0
|
CB
|
A:THR70
|
3.8
|
25.2
|
1.0
|
CG1
|
A:VAL76
|
3.9
|
33.0
|
1.0
|
CZ
|
A:ARG183
|
4.0
|
37.9
|
1.0
|
CA
|
A:THR70
|
4.0
|
25.5
|
1.0
|
CA
|
A:LEU190
|
4.0
|
26.4
|
1.0
|
CA
|
A:LEU69
|
4.0
|
25.9
|
1.0
|
CG2
|
A:VAL76
|
4.0
|
32.3
|
1.0
|
N
|
A:LEU69
|
4.0
|
25.2
|
1.0
|
O
|
A:ARG183
|
4.1
|
29.7
|
1.0
|
C
|
A:LEU190
|
4.1
|
27.3
|
1.0
|
NE
|
A:ARG183
|
4.2
|
37.1
|
1.0
|
N
|
A:LEU190
|
4.2
|
25.3
|
1.0
|
CB
|
A:ARG68
|
4.3
|
28.4
|
1.0
|
O
|
A:LEU69
|
4.4
|
30.5
|
1.0
|
CB
|
A:VAL76
|
4.5
|
32.7
|
1.0
|
CA
|
A:ARG68
|
4.5
|
27.5
|
1.0
|
C
|
A:ARG183
|
4.6
|
31.9
|
1.0
|
CA
|
A:LEU191
|
4.7
|
30.3
|
1.0
|
CA
|
A:GLY189
|
4.8
|
24.8
|
1.0
|
CG
|
A:ARG183
|
4.8
|
35.0
|
1.0
|
CB
|
A:ARG183
|
4.8
|
33.5
|
1.0
|
CB
|
A:LEU191
|
4.8
|
31.6
|
1.0
|
O
|
A:HOH640
|
5.0
|
31.2
|
1.0
|
O
|
A:LEU190
|
5.0
|
26.3
|
1.0
|
|
Sodium binding site 2 out
of 3 in 6vut
Go back to
Sodium Binding Sites List in 6vut
Sodium binding site 2 out
of 3 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na509
b:54.0
occ:1.00
|
OD2
|
A:ASP273
|
2.5
|
35.9
|
1.0
|
O2
|
A:PEG503
|
2.9
|
52.7
|
1.0
|
C1
|
A:PEG503
|
3.4
|
53.0
|
1.0
|
CE1
|
A:HIS249
|
3.4
|
35.9
|
1.0
|
CG
|
A:ASP273
|
3.5
|
34.5
|
1.0
|
NE1
|
A:TRP253
|
3.5
|
36.2
|
1.0
|
C2
|
A:PEG503
|
3.6
|
54.4
|
1.0
|
OG1
|
A:THR269
|
3.7
|
28.0
|
1.0
|
CD1
|
A:ILE267
|
3.7
|
32.2
|
1.0
|
OD1
|
A:ASP273
|
3.7
|
32.0
|
1.0
|
C3
|
A:PEG503
|
3.9
|
52.2
|
1.0
|
CD1
|
A:LEU241
|
4.0
|
33.6
|
1.0
|
ND1
|
A:HIS249
|
4.0
|
35.6
|
1.0
|
CD2
|
A:LEU241
|
4.1
|
33.3
|
1.0
|
O1
|
A:PEG503
|
4.1
|
47.0
|
1.0
|
CZ2
|
A:TRP253
|
4.2
|
35.8
|
1.0
|
CE2
|
A:TRP253
|
4.2
|
34.7
|
1.0
|
CB
|
A:THR269
|
4.4
|
27.8
|
1.0
|
CG
|
A:LEU241
|
4.4
|
33.3
|
1.0
|
C4
|
A:PEG503
|
4.4
|
51.9
|
1.0
|
CB
|
A:LEU241
|
4.5
|
32.9
|
1.0
|
NE2
|
A:HIS249
|
4.6
|
36.1
|
1.0
|
CD1
|
A:TRP253
|
4.6
|
35.1
|
1.0
|
CB
|
A:ASP273
|
4.9
|
34.3
|
1.0
|
CG1
|
A:ILE267
|
5.0
|
32.0
|
1.0
|
CG2
|
A:THR269
|
5.0
|
27.6
|
1.0
|
|
Sodium binding site 3 out
of 3 in 6vut
Go back to
Sodium Binding Sites List in 6vut
Sodium binding site 3 out
of 3 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT392 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na510
b:41.7
occ:1.00
|
O
|
A:ARG353
|
2.5
|
32.6
|
1.0
|
O
|
A:GLY130
|
2.9
|
31.1
|
1.0
|
N
|
A:ILE298
|
3.1
|
29.8
|
1.0
|
C
|
A:ARG353
|
3.2
|
31.4
|
1.0
|
CG
|
A:ARG353
|
3.3
|
30.2
|
1.0
|
N
|
A:GLY357
|
3.4
|
28.2
|
1.0
|
O
|
A:LEU296
|
3.4
|
30.2
|
1.0
|
CA
|
A:ARG297
|
3.5
|
30.9
|
1.0
|
CA
|
A:GLY357
|
3.7
|
27.9
|
1.0
|
CA
|
A:ASP354
|
3.7
|
32.6
|
1.0
|
N
|
A:ASP354
|
3.8
|
31.8
|
1.0
|
C
|
A:ARG297
|
3.8
|
29.4
|
1.0
|
CG1
|
A:ILE298
|
3.8
|
31.0
|
1.0
|
CB
|
A:ILE298
|
3.9
|
31.4
|
1.0
|
CA
|
A:ILE298
|
4.1
|
31.1
|
1.0
|
O
|
A:ASP354
|
4.1
|
32.1
|
1.0
|
C
|
A:LEU296
|
4.1
|
30.8
|
1.0
|
C
|
A:ASP354
|
4.1
|
30.4
|
1.0
|
C
|
A:GLY130
|
4.1
|
29.2
|
1.0
|
CA
|
A:ARG353
|
4.3
|
30.6
|
1.0
|
CD
|
A:ARG353
|
4.3
|
32.3
|
1.0
|
N
|
A:ARG297
|
4.3
|
30.6
|
1.0
|
CB
|
A:ARG353
|
4.3
|
30.1
|
1.0
|
C
|
A:LEU356
|
4.4
|
28.1
|
1.0
|
CG
|
A:ARG297
|
4.5
|
32.0
|
1.0
|
O
|
A:ILE298
|
4.6
|
31.3
|
1.0
|
CB
|
A:ARG297
|
4.6
|
31.6
|
1.0
|
CB
|
A:LEU356
|
4.6
|
28.3
|
1.0
|
N
|
A:GLY132
|
4.8
|
26.4
|
1.0
|
C
|
A:ILE298
|
4.8
|
31.2
|
1.0
|
N
|
A:LEU356
|
4.8
|
26.2
|
1.0
|
CD1
|
A:ILE298
|
4.9
|
30.8
|
1.0
|
CA
|
A:LEU356
|
4.9
|
27.8
|
1.0
|
CA
|
A:TYR131
|
5.0
|
26.1
|
1.0
|
N
|
A:TYR131
|
5.0
|
27.9
|
1.0
|
|
Reference:
A.Punetha,
H.X.Ngo,
S.Y.L.Holbrook,
K.D.Green,
M.J.Willby,
S.A.Bonnett,
K.Krieger,
E.K.Dennis,
J.E.Posey,
T.Parish,
O.V.Tsodikov,
S.Garneau-Tsodikova.
Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis Frommycobacterium Tuberculosis. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 32421305
DOI: 10.1021/ACSCHEMBIO.0C00184
Page generated: Tue Oct 8 14:26:22 2024
|