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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 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 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 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

Go back to 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 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

Go back to 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

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