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Sodium in PDB 6rlt: Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine

Enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine

All present enzymatic activity of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine:
6.1.1.11;

Protein crystallography data

The structure of Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine, PDB code: 6rlt 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) 21.20 / 1.84
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 177.609, 177.609, 246.109, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 23.9

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)Uridine (pdb code 6rlt). 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)Uridine, PDB code: 6rlt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6rlt

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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)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:18.5
occ:1.00
 O A:HOH742 2.2 17.0 1.0
OE2 A:GLU384 2.3 16.6 1.0
O1S A:FZK507 2.4 19.6 1.0
OG A:SER387 2.4 20.9 1.0
O A:HOH907 2.4 44.7 1.0
O A:HOH701 2.6 18.6 1.0
CD A:GLU384 3.2 30.1 1.0
CB A:SER387 3.5 13.2 1.0
OE1 A:GLU384 3.6 26.7 1.0
S A:FZK507 3.7 18.6 1.0
O3' A:FZK507 4.1 12.6 1.0
OD2 A:ASP371 4.3 21.4 1.0
O A:HOH739 4.3 20.9 1.0
O2S A:FZK507 4.4 16.9 1.0
CG A:GLU384 4.4 24.0 1.0
N3S A:FZK507 4.4 17.8 1.0
OD1 A:ASP371 4.4 12.4 1.0
NZ A:LYS369 4.5 57.0 1.0
C3' A:FZK507 4.5 13.4 1.0
CG A:ASP371 4.7 15.8 1.0
CA A:SER387 4.7 10.7 1.0
O5' A:FZK507 4.7 17.4 1.0
CE A:LYS369 4.8 37.2 1.0

Sodium binding site 2 out of 6 in 6rlt

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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)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:40.0
occ:1.00
 O9 A:MLI508 2.7 29.4 1.0
OG A:SER379 2.9 25.6 1.0
ND2 A:ASN170 3.1 27.0 1.0
O7 A:MLI508 3.2 40.9 1.0
C3 A:MLI508 3.6 36.6 1.0
C2 A:MLI508 3.6 40.7 1.0
CB A:SER379 3.6 24.7 1.0
CB A:ASN170 3.6 14.0 1.0
C1 A:MLI508 3.6 39.1 1.0
CA A:SER379 3.8 24.4 1.0
CG A:ASN170 3.8 28.8 1.0
NH2 A:ARG383 4.4 36.6 1.0
O6 A:MLI508 4.5 39.8 1.0
N A:SER379 4.7 24.6 1.0
O8 A:MLI508 4.8 38.9 1.0
OE2 A:GLU438 4.8 13.7 1.0
O A:SER379 4.9 27.6 1.0
C A:SER379 4.9 26.9 1.0

Sodium binding site 3 out of 6 in 6rlt

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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)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:20.7
occ:1.00
 OE2 B:GLU384 2.2 20.0 1.0
O B:HOH899 2.2 20.8 1.0
O1S B:FZK510 2.3 18.9 1.0
OG B:SER387 2.4 16.3 1.0
O B:HOH697 2.5 25.2 1.0
O B:HOH900 2.5 42.1 1.0
CD B:GLU384 3.2 27.0 1.0
CB B:SER387 3.4 11.8 1.0
OE1 B:GLU384 3.6 23.9 1.0
S B:FZK510 3.6 17.7 1.0
NZ B:LYS369 3.9 39.5 1.0
O B:HOH930 4.1 35.1 1.0
O B:HOH769 4.2 19.1 1.0
OD1 B:ASP371 4.3 18.1 1.0
O3' B:FZK510 4.3 18.7 1.0
N3S B:FZK510 4.3 15.5 1.0
OD2 B:ASP371 4.3 11.7 1.0
O2S B:FZK510 4.3 12.4 1.0
CG B:GLU384 4.4 18.5 1.0
O5' B:FZK510 4.6 15.8 1.0
C3' B:FZK510 4.6 17.0 1.0
CA B:SER387 4.6 11.6 1.0
CG B:ASP371 4.6 17.0 1.0
CE B:LYS369 4.9 31.5 1.0
N B:SER387 5.0 12.8 1.0
CD B:LYS369 5.0 20.2 1.0

Sodium binding site 4 out of 6 in 6rlt

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Sodium binding site 4 out of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:25.2
occ:1.00
 O B:GLN413 2.3 26.3 1.0
O B:LEU407 2.4 30.6 1.0
O B:THR410 2.4 25.6 1.0
O B:HOH710 2.4 32.8 1.0
O B:HOH913 2.4 31.3 1.0
O B:HOH889 2.5 29.1 1.0
C B:LEU407 3.4 30.9 1.0
C B:GLN413 3.4 28.1 1.0
C B:THR410 3.4 28.1 1.0
CA B:LEU407 3.9 28.4 1.0
N B:GLN413 4.1 24.4 1.0
CA B:GLN413 4.1 23.6 1.0
CB B:GLN413 4.2 23.6 1.0
N B:THR410 4.2 27.7 1.0
O B:ALA411 4.2 31.3 1.0
CB B:LEU407 4.3 28.8 1.0
N B:ALA411 4.3 26.2 1.0
CA B:THR410 4.3 26.2 1.0
CA B:ALA411 4.4 26.5 1.0
C B:ALA411 4.4 30.8 1.0
N B:ASN414 4.5 27.6 1.0
O B:HOH946 4.5 49.4 1.0
OD1 B:ASN414 4.5 34.7 1.0
N B:ARG408 4.5 26.9 1.0
CB B:THR410 4.7 33.1 1.0
CA B:ASN414 4.7 28.9 1.0
CA B:ARG408 4.9 27.1 1.0
O B:HOH791 5.0 40.7 1.0

Sodium binding site 5 out of 6 in 6rlt

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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)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:43.3
occ:1.00
 OG1 B:THR164 2.3 18.7 1.0
OD1 B:ASN162 2.6 29.8 1.0
O B:HOH786 2.8 35.9 1.0
CB B:THR164 3.4 19.8 1.0
CG2 B:THR164 3.5 17.8 1.0
CG B:ASN162 3.7 25.1 1.0
N B:THR164 3.9 15.1 1.0
CA B:THR164 4.2 14.1 1.0
ND2 B:ASN162 4.4 16.0 1.0
N B:THR163 4.6 16.7 1.0
CA B:ASN162 4.7 17.8 1.0
CB B:ASN162 4.7 21.1 1.0
C B:THR164 4.9 18.2 1.0
C B:ASN162 4.9 20.1 1.0
C B:THR163 5.0 15.9 1.0

Sodium binding site 6 out of 6 in 6rlt

Go back to Sodium Binding Sites List in 6rlt
Sodium binding site 6 out of 6 in the Trypanosoma Brucei Seryl-Trna Synthetase in Complex with 5'-O-(N-(L- Seryl)-Sulfamoyl)Uridine


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)Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na509

b:36.4
occ:1.00
 O8 B:MLI511 2.4 26.2 1.0
ND2 B:ASN170 3.0 29.0 1.0
OG B:SER379 3.1 19.5 1.0
C3 B:MLI511 3.3 30.3 1.0
O6 B:MLI511 3.3 31.9 1.0
C1 B:MLI511 3.5 32.2 1.0
C2 B:MLI511 3.5 32.6 1.0
CB B:SER379 3.7 16.4 1.0
CB B:ASN170 3.7 12.6 1.0
CG B:ASN170 3.8 29.9 1.0
CA B:SER379 3.9 18.3 1.0
O7 B:MLI511 4.4 30.4 1.0
O9 B:MLI511 4.5 30.9 1.0
NH2 B:ARG383 4.6 37.4 1.0
N B:SER379 4.8 18.3 1.0
O B:SER379 4.9 27.7 1.0
OE2 B:GLU438 5.0 14.8 1.0
OD1 B:ASN170 5.0 17.8 1.0
C B:SER379 5.0 25.9 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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