Sodium in PDB 6rlv: Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
Enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
All present enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine:
6.1.1.11;
Protein crystallography data
The structure of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine, PDB code: 6rlv
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)
|
27.54 /
1.90
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.666,
177.666,
246.767,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.3 /
20.4
|
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)N3-Methyluridine
(pdb code 6rlv). 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)N3-Methyluridine, PDB code: 6rlv:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 1 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:27.6
occ:1.00
|
O
|
A:HOH890
|
2.3
|
51.0
|
1.0
|
O
|
A:HOH880
|
2.3
|
28.8
|
1.0
|
OE2
|
A:GLU384
|
2.3
|
25.8
|
1.0
|
OG
|
A:SER387
|
2.3
|
25.8
|
1.0
|
O2S
|
A:FZT507
|
2.4
|
25.2
|
1.0
|
O
|
A:HOH732
|
2.5
|
30.6
|
1.0
|
CD
|
A:GLU384
|
3.2
|
31.2
|
1.0
|
CB
|
A:SER387
|
3.4
|
21.3
|
1.0
|
OE1
|
A:GLU384
|
3.6
|
31.2
|
1.0
|
S
|
A:FZT507
|
3.7
|
24.1
|
1.0
|
NZ
|
A:LYS369
|
3.9
|
55.2
|
1.0
|
O3'
|
A:FZT507
|
4.1
|
23.1
|
1.0
|
O
|
A:HOH925
|
4.1
|
42.6
|
1.0
|
O
|
A:HOH793
|
4.2
|
25.9
|
1.0
|
OD2
|
A:ASP371
|
4.3
|
29.7
|
1.0
|
OD1
|
A:ASP371
|
4.4
|
24.2
|
1.0
|
O1S
|
A:FZT507
|
4.4
|
22.7
|
1.0
|
C3'
|
A:FZT507
|
4.4
|
22.6
|
1.0
|
CG
|
A:GLU384
|
4.5
|
27.4
|
1.0
|
N3S
|
A:FZT507
|
4.5
|
22.1
|
1.0
|
CG
|
A:ASP371
|
4.6
|
25.9
|
1.0
|
CA
|
A:SER387
|
4.6
|
19.7
|
1.0
|
O5'
|
A:FZT507
|
4.7
|
22.9
|
1.0
|
CE
|
A:LYS369
|
4.9
|
37.5
|
1.0
|
N
|
A:SER387
|
5.0
|
20.7
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 2 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:60.9
occ:1.00
|
OG
|
A:SER379
|
3.1
|
29.9
|
1.0
|
ND2
|
A:ASN170
|
3.2
|
32.9
|
1.0
|
CB
|
A:SER379
|
3.7
|
30.4
|
1.0
|
CB
|
A:ASN170
|
3.7
|
21.1
|
1.0
|
NH1
|
A:ARG383
|
3.8
|
60.9
|
1.0
|
CG
|
A:ASN170
|
3.9
|
35.0
|
1.0
|
CA
|
A:SER379
|
4.1
|
29.6
|
1.0
|
NE2
|
A:HIS171
|
4.8
|
22.2
|
1.0
|
OE2
|
A:GLU438
|
4.9
|
19.4
|
1.0
|
CZ
|
A:ARG383
|
4.9
|
78.0
|
1.0
|
OD1
|
A:ASN170
|
4.9
|
26.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 3 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:26.9
occ:1.00
|
O
|
B:HOH758
|
2.3
|
29.6
|
1.0
|
OE2
|
B:GLU384
|
2.3
|
26.3
|
1.0
|
O2S
|
B:FZT510
|
2.3
|
22.3
|
1.0
|
OG
|
B:SER387
|
2.3
|
25.4
|
1.0
|
O
|
B:HOH877
|
2.3
|
50.2
|
1.0
|
O
|
B:HOH619
|
2.4
|
35.3
|
1.0
|
CD
|
B:GLU384
|
3.2
|
34.8
|
1.0
|
CB
|
B:SER387
|
3.4
|
20.0
|
1.0
|
S
|
B:FZT510
|
3.6
|
22.9
|
1.0
|
OE1
|
B:GLU384
|
3.7
|
28.4
|
1.0
|
NZ
|
B:LYS369
|
3.7
|
55.2
|
1.0
|
O
|
B:HOH901
|
4.0
|
38.2
|
1.0
|
O3'
|
B:FZT510
|
4.2
|
24.0
|
1.0
|
O
|
B:HOH810
|
4.3
|
25.5
|
1.0
|
OD1
|
B:ASP371
|
4.3
|
24.7
|
1.0
|
OD2
|
B:ASP371
|
4.3
|
20.3
|
1.0
|
O1S
|
B:FZT510
|
4.3
|
22.3
|
1.0
|
O
|
B:HOH925
|
4.4
|
66.1
|
1.0
|
N3S
|
B:FZT510
|
4.4
|
22.3
|
1.0
|
CG
|
B:GLU384
|
4.4
|
25.2
|
1.0
|
C3'
|
B:FZT510
|
4.5
|
24.8
|
1.0
|
CG
|
B:ASP371
|
4.6
|
23.7
|
1.0
|
CA
|
B:SER387
|
4.7
|
19.2
|
1.0
|
O5'
|
B:FZT510
|
4.7
|
23.3
|
1.0
|
CE
|
B:LYS369
|
4.9
|
36.4
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 4 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na507
b:34.0
occ:1.00
|
O
|
B:THR410
|
2.3
|
35.2
|
1.0
|
O
|
B:GLN413
|
2.3
|
36.4
|
1.0
|
O
|
B:LEU407
|
2.3
|
39.9
|
1.0
|
O
|
B:HOH692
|
2.4
|
37.4
|
1.0
|
O
|
B:HOH898
|
2.5
|
46.5
|
1.0
|
O
|
B:HOH888
|
2.6
|
41.7
|
1.0
|
C
|
B:THR410
|
3.4
|
38.5
|
1.0
|
C
|
B:LEU407
|
3.4
|
40.9
|
1.0
|
O
|
B:HOH957
|
3.4
|
58.8
|
1.0
|
C
|
B:GLN413
|
3.4
|
37.2
|
1.0
|
CA
|
B:LEU407
|
3.9
|
37.5
|
1.0
|
N
|
B:GLN413
|
4.1
|
33.1
|
1.0
|
CA
|
B:GLN413
|
4.1
|
32.0
|
1.0
|
N
|
B:ALA411
|
4.2
|
36.4
|
1.0
|
O
|
B:ALA411
|
4.2
|
40.1
|
1.0
|
CA
|
B:ALA411
|
4.2
|
36.5
|
1.0
|
CB
|
B:GLN413
|
4.2
|
32.0
|
1.0
|
CA
|
B:THR410
|
4.3
|
39.0
|
1.0
|
C
|
B:ALA411
|
4.3
|
39.6
|
1.0
|
N
|
B:THR410
|
4.3
|
41.8
|
1.0
|
CB
|
B:LEU407
|
4.4
|
38.5
|
1.0
|
OD1
|
B:ASN414
|
4.4
|
43.7
|
1.0
|
N
|
B:ASN414
|
4.5
|
36.1
|
1.0
|
N
|
B:ARG408
|
4.5
|
38.9
|
1.0
|
O
|
B:HOH920
|
4.6
|
64.3
|
1.0
|
CB
|
B:THR410
|
4.7
|
40.4
|
1.0
|
CA
|
B:ASN414
|
4.8
|
37.4
|
1.0
|
O
|
B:HOH946
|
4.8
|
63.6
|
1.0
|
CD2
|
B:LEU407
|
4.8
|
49.0
|
1.0
|
CA
|
B:ARG408
|
4.9
|
39.6
|
1.0
|
O
|
B:HOH770
|
4.9
|
51.0
|
1.0
|
N
|
B:ALA412
|
5.0
|
34.8
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 5 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na508
b:51.4
occ:1.00
|
OG1
|
B:THR164
|
2.3
|
27.0
|
1.0
|
O
|
B:HOH871
|
2.6
|
48.9
|
1.0
|
OD1
|
B:ASN162
|
2.7
|
30.4
|
1.0
|
CB
|
B:THR164
|
3.4
|
29.2
|
1.0
|
CG2
|
B:THR164
|
3.5
|
29.3
|
1.0
|
CG
|
B:ASN162
|
3.8
|
33.7
|
1.0
|
N
|
B:THR164
|
3.9
|
24.4
|
1.0
|
CA
|
B:THR164
|
4.2
|
24.0
|
1.0
|
ND2
|
B:ASN162
|
4.5
|
32.5
|
1.0
|
N
|
B:THR163
|
4.6
|
24.8
|
1.0
|
CA
|
B:ASN162
|
4.6
|
24.9
|
1.0
|
CB
|
B:ASN162
|
4.8
|
29.6
|
1.0
|
C
|
B:ASN162
|
4.8
|
27.7
|
1.0
|
C
|
B:THR164
|
4.9
|
26.6
|
1.0
|
C
|
B:THR163
|
4.9
|
27.1
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6rlv
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Sodium Binding Sites List in 6rlv
Sodium binding site 6 out
of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)N3-Methyluridine
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)N3-Methyluridine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na509
b:51.9
occ:1.00
|
ND2
|
B:ASN170
|
3.1
|
32.9
|
1.0
|
OG
|
B:SER379
|
3.2
|
26.8
|
1.0
|
CB
|
B:ASN170
|
3.7
|
24.5
|
1.0
|
CB
|
B:SER379
|
3.7
|
29.8
|
1.0
|
CG
|
B:ASN170
|
3.8
|
33.9
|
1.0
|
CA
|
B:SER379
|
4.0
|
28.8
|
1.0
|
O
|
B:HOH747
|
4.3
|
48.3
|
1.0
|
NH2
|
B:ARG383
|
4.4
|
61.1
|
1.0
|
N
|
B:SER379
|
4.9
|
28.9
|
1.0
|
OD1
|
B:ASN170
|
4.9
|
26.5
|
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 13:15:30 2024
|