Sodium in PDB 6rlu: Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
All present enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine:
6.1.1.11;
Protein crystallography data
The structure of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine, PDB code: 6rlu
was solved by
L.Pang,
S.De Graef,
S.V.Strelkov,
S.D.Weeks,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.57 /
1.88
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
178.357,
178.357,
246.688,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.9 /
19.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
(pdb code 6rlu). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine, PDB code: 6rlu:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6rlu
Go back to
Sodium Binding Sites List in 6rlu
Sodium binding site 1 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:23.8
occ:1.00
|
O
|
A:HOH898
|
2.3
|
26.1
|
1.0
|
OE2
|
A:GLU384
|
2.3
|
25.8
|
1.0
|
OG
|
A:SER387
|
2.3
|
23.9
|
1.0
|
O
|
A:HOH901
|
2.3
|
45.6
|
1.0
|
O
|
A:HOH676
|
2.4
|
27.2
|
1.0
|
O2S
|
A:FZQ507
|
2.4
|
22.4
|
1.0
|
CD
|
A:GLU384
|
3.2
|
33.6
|
1.0
|
CB
|
A:SER387
|
3.4
|
18.4
|
1.0
|
OE1
|
A:GLU384
|
3.6
|
29.9
|
1.0
|
S
|
A:FZQ507
|
3.7
|
23.2
|
1.0
|
NZ
|
A:LYS369
|
3.9
|
50.1
|
1.0
|
O
|
A:HOH913
|
3.9
|
40.1
|
1.0
|
O3'
|
A:FZQ507
|
4.2
|
22.1
|
1.0
|
O
|
A:HOH810
|
4.3
|
25.0
|
1.0
|
OD2
|
A:ASP371
|
4.3
|
25.8
|
1.0
|
OD1
|
A:ASP371
|
4.3
|
22.0
|
1.0
|
CG
|
A:GLU384
|
4.4
|
24.1
|
1.0
|
O1S
|
A:FZQ507
|
4.4
|
20.6
|
1.0
|
N3S
|
A:FZQ507
|
4.4
|
22.3
|
1.0
|
C3'
|
A:FZQ507
|
4.6
|
21.0
|
1.0
|
CG
|
A:ASP371
|
4.6
|
23.9
|
1.0
|
CA
|
A:SER387
|
4.7
|
16.9
|
1.0
|
O5'
|
A:FZQ507
|
4.7
|
22.7
|
1.0
|
CE
|
A:LYS369
|
4.9
|
36.2
|
1.0
|
N
|
A:SER387
|
5.0
|
17.6
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6rlu
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Sodium Binding Sites List in 6rlu
Sodium binding site 2 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:50.1
occ:1.00
|
OG
|
A:SER379
|
3.0
|
31.8
|
1.0
|
ND2
|
A:ASN170
|
3.2
|
31.2
|
1.0
|
CB
|
A:SER379
|
3.7
|
31.6
|
1.0
|
CB
|
A:ASN170
|
3.7
|
20.1
|
1.0
|
CG
|
A:ASN170
|
3.9
|
29.3
|
1.0
|
CA
|
A:SER379
|
4.0
|
30.3
|
1.0
|
NH2
|
A:ARG383
|
4.3
|
47.6
|
1.0
|
NH1
|
A:ARG383
|
4.4
|
56.2
|
1.0
|
OE2
|
A:GLU438
|
4.8
|
17.7
|
1.0
|
N
|
A:SER379
|
4.8
|
29.4
|
1.0
|
CZ
|
A:ARG383
|
4.9
|
71.7
|
1.0
|
NE2
|
A:HIS171
|
5.0
|
20.7
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6rlu
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Sodium Binding Sites List in 6rlu
Sodium binding site 3 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:25.5
occ:1.00
|
OE2
|
B:GLU384
|
2.2
|
26.1
|
1.0
|
O
|
B:HOH822
|
2.3
|
26.8
|
1.0
|
O2S
|
B:FZQ510
|
2.3
|
21.1
|
1.0
|
OG
|
B:SER387
|
2.4
|
23.2
|
1.0
|
O
|
B:HOH619
|
2.4
|
29.6
|
1.0
|
O
|
B:HOH821
|
2.5
|
58.4
|
1.0
|
CD
|
B:GLU384
|
3.2
|
36.4
|
1.0
|
CB
|
B:SER387
|
3.4
|
17.8
|
1.0
|
OE1
|
B:GLU384
|
3.6
|
24.6
|
1.0
|
S
|
B:FZQ510
|
3.6
|
22.4
|
1.0
|
NZ
|
B:LYS369
|
3.8
|
47.0
|
1.0
|
O
|
B:HOH902
|
3.9
|
36.2
|
1.0
|
O3'
|
B:FZQ510
|
4.2
|
24.5
|
1.0
|
O
|
B:HOH808
|
4.3
|
23.5
|
1.0
|
O1S
|
B:FZQ510
|
4.3
|
21.7
|
1.0
|
CG
|
B:GLU384
|
4.3
|
26.1
|
1.0
|
OD1
|
B:ASP371
|
4.3
|
23.5
|
1.0
|
N3S
|
B:FZQ510
|
4.3
|
20.7
|
1.0
|
OD2
|
B:ASP371
|
4.3
|
18.7
|
1.0
|
O
|
B:HOH909
|
4.4
|
62.0
|
1.0
|
O5'
|
B:FZQ510
|
4.7
|
22.8
|
1.0
|
CG
|
B:ASP371
|
4.7
|
21.7
|
1.0
|
C3'
|
B:FZQ510
|
4.7
|
24.5
|
1.0
|
CA
|
B:SER387
|
4.7
|
16.1
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6rlu
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Sodium Binding Sites List in 6rlu
Sodium binding site 4 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na507
b:32.8
occ:1.00
|
O
|
B:THR410
|
2.3
|
29.7
|
1.0
|
O
|
B:GLN413
|
2.4
|
31.5
|
1.0
|
O
|
B:HOH915
|
2.4
|
42.7
|
1.0
|
O
|
B:HOH685
|
2.4
|
35.0
|
1.0
|
O
|
B:LEU407
|
2.4
|
37.6
|
1.0
|
O
|
B:HOH898
|
2.5
|
37.0
|
1.0
|
C
|
B:THR410
|
3.4
|
32.9
|
1.0
|
C
|
B:LEU407
|
3.4
|
37.8
|
1.0
|
O
|
B:HOH973
|
3.5
|
50.3
|
1.0
|
C
|
B:GLN413
|
3.5
|
32.8
|
1.0
|
CA
|
B:LEU407
|
4.0
|
34.0
|
1.0
|
O
|
B:ALA411
|
4.1
|
36.4
|
1.0
|
N
|
B:GLN413
|
4.1
|
29.1
|
1.0
|
CA
|
B:GLN413
|
4.2
|
27.8
|
1.0
|
N
|
B:ALA411
|
4.2
|
30.5
|
1.0
|
CA
|
B:ALA411
|
4.2
|
31.5
|
1.0
|
CB
|
B:GLN413
|
4.3
|
27.5
|
1.0
|
C
|
B:ALA411
|
4.3
|
35.0
|
1.0
|
N
|
B:THR410
|
4.3
|
35.8
|
1.0
|
CA
|
B:THR410
|
4.3
|
33.5
|
1.0
|
CB
|
B:LEU407
|
4.3
|
35.1
|
1.0
|
OD1
|
B:ASN414
|
4.4
|
39.5
|
1.0
|
N
|
B:ARG408
|
4.5
|
35.1
|
1.0
|
N
|
B:ASN414
|
4.6
|
31.8
|
1.0
|
CB
|
B:THR410
|
4.7
|
36.6
|
1.0
|
CA
|
B:ASN414
|
4.8
|
33.4
|
1.0
|
CD2
|
B:LEU407
|
4.9
|
45.8
|
1.0
|
CA
|
B:ARG408
|
5.0
|
35.4
|
1.0
|
N
|
B:ALA412
|
5.0
|
29.6
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6rlu
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Sodium Binding Sites List in 6rlu
Sodium binding site 5 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na508
b:49.2
occ:1.00
|
O
|
B:HOH823
|
2.3
|
44.4
|
1.0
|
OG1
|
B:THR164
|
2.4
|
25.2
|
1.0
|
OD1
|
B:ASN162
|
2.6
|
28.3
|
1.0
|
O
|
B:HOH861
|
2.8
|
52.1
|
1.0
|
CB
|
B:THR164
|
3.5
|
27.6
|
1.0
|
CG2
|
B:THR164
|
3.6
|
29.4
|
1.0
|
CG
|
B:ASN162
|
3.7
|
35.4
|
1.0
|
N
|
B:THR164
|
4.0
|
22.2
|
1.0
|
CA
|
B:THR164
|
4.2
|
21.4
|
1.0
|
ND2
|
B:ASN162
|
4.4
|
28.5
|
1.0
|
N
|
B:THR163
|
4.5
|
22.0
|
1.0
|
CA
|
B:ASN162
|
4.6
|
24.0
|
1.0
|
CB
|
B:ASN162
|
4.7
|
26.1
|
1.0
|
C
|
B:ASN162
|
4.8
|
25.6
|
1.0
|
C
|
B:THR164
|
4.9
|
24.5
|
1.0
|
C
|
B:THR163
|
4.9
|
25.2
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6rlu
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Sodium Binding Sites List in 6rlu
Sodium binding site 6 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Cytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na509
b:49.6
occ:1.00
|
ND2
|
B:ASN170
|
3.1
|
33.4
|
1.0
|
OG
|
B:SER379
|
3.2
|
26.8
|
1.0
|
CB
|
B:ASN170
|
3.7
|
21.2
|
1.0
|
CB
|
B:SER379
|
3.8
|
30.3
|
1.0
|
CG
|
B:ASN170
|
3.8
|
31.1
|
1.0
|
CA
|
B:SER379
|
4.1
|
29.4
|
1.0
|
NH2
|
B:ARG383
|
4.4
|
67.2
|
1.0
|
O
|
B:HOH771
|
4.5
|
40.4
|
1.0
|
N
|
B:SER379
|
4.9
|
30.0
|
1.0
|
OD1
|
B:ASN170
|
5.0
|
23.2
|
1.0
|
|
Reference:
L.Pang,
M.Nautiyal,
S.De Graef,
B.Gadakh,
V.Zorzini,
A.Economou,
S.V.Strelkov,
A.Van Aerschot,
S.D.Weeks.
Structural Insights Into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-Trna Synthetases. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31869198
DOI: 10.1021/ACSCHEMBIO.9B00887
Page generated: Tue Oct 8 13:15:29 2024
|