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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

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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)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 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 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

Go back to 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 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

Go back to 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

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