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Chlorine in PDB 2vpm: Trypanothione Synthetase

Enzymatic activity of Trypanothione Synthetase

All present enzymatic activity of Trypanothione Synthetase:
6.3.1.9;

Protein crystallography data

The structure of Trypanothione Synthetase, PDB code: 2vpm was solved by P.K.Fyfe, S.L.Oza, A.H.Fairlamb, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.82 / 2.8
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.522, 167.082, 84.921, 90.00, 94.11, 90.00
R / Rfree (%) 20.3 / 25.3

Other elements in 2vpm:

The structure of Trypanothione Synthetase also contains other interesting chemical elements:

Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Trypanothione Synthetase (pdb code 2vpm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Trypanothione Synthetase, PDB code: 2vpm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 1 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1637

b:17.9
occ:1.00
 N A:LYS547 3.2 55.0 1.0
CB A:LYS547 3.8 55.7 1.0
CA A:ALA546 3.9 53.5 1.0
CA A:LYS547 4.0 55.8 1.0
C A:ALA546 4.0 53.9 1.0
O A:LYS547 4.3 56.7 1.0
CB A:ALA546 4.5 53.1 1.0
C A:LYS547 4.6 56.5 1.0
O A:TYR545 4.8 52.6 1.0

Chlorine binding site 2 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 2 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1638

b:45.5
occ:1.00
 NH1 A:ARG315 3.2 43.5 1.0
N A:PRO312 3.5 44.9 1.0
CG A:PRO312 3.5 44.7 1.0
CA A:PRO312 3.6 44.8 1.0
CD A:PRO312 3.8 45.0 1.0
C A:TRP311 3.8 45.1 1.0
CB A:TRP311 3.9 45.7 1.0
CB A:PRO312 3.9 44.8 1.0
CD A:ARG315 4.0 44.1 1.0
O A:TRP311 4.2 45.2 1.0
CZ A:ARG315 4.3 44.2 1.0
CA A:TRP311 4.5 45.3 1.0
NE A:ARG315 4.6 44.3 1.0
CE B:LYS616 4.7 42.2 1.0
OG B:SER617 4.7 42.7 1.0
CG B:LYS616 4.8 41.6 1.0

Chlorine binding site 3 out of 8 in 2vpm

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Chlorine binding site 3 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1639

b:21.9
occ:1.00
 O A:HOH2016 3.2 26.0 1.0
N A:PHE55 3.2 45.5 1.0
CB A:PHE55 3.8 44.8 1.0
N A:GLU61 3.8 43.5 1.0
CB A:GLN58 4.0 45.7 1.0
CB A:VAL60 4.0 43.8 1.0
CD2 A:PHE55 4.0 43.5 1.0
CA A:GLY54 4.0 46.1 1.0
CA A:PHE55 4.1 45.1 1.0
C A:GLY54 4.1 46.0 1.0
CB A:GLU61 4.3 43.4 1.0
CG A:PHE55 4.4 44.7 1.0
O A:PHE55 4.4 44.6 1.0
C A:VAL60 4.5 43.6 1.0
CA A:GLU61 4.5 43.5 1.0
CG1 A:VAL60 4.5 44.0 1.0
CA A:VAL60 4.5 43.8 1.0
N A:VAL60 4.6 43.9 1.0
CG A:GLN58 4.8 47.7 1.0
C A:PHE55 4.8 44.8 1.0
C A:GLN58 5.0 44.9 1.0
CA A:GLN58 5.0 45.4 1.0

Chlorine binding site 4 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 4 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1640

b:33.6
occ:1.00
 N A:SER122 3.4 47.4 1.0
CB A:SER122 3.8 48.3 1.0
CA A:PRO121 4.0 45.8 1.0
CB A:PRO121 4.2 45.7 1.0
CB A:CYS82 4.2 45.6 1.0
C A:PRO121 4.2 46.4 1.0
CD1 A:LEU186 4.2 39.2 1.0
CA A:SER122 4.3 48.2 1.0
SG A:CYS82 4.3 45.1 1.0
CD2 A:LEU186 4.7 37.8 1.0
CG A:LEU186 4.9 39.4 1.0
O A:CYS82 5.0 45.0 1.0

Chlorine binding site 5 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 5 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1641

b:20.5
occ:1.00
 N B:LYS547 3.3 59.6 1.0
CG A:ARG6 3.6 45.2 1.0
NE A:ARG6 3.7 44.6 1.0
CB A:ARG6 3.7 45.7 1.0
NH2 A:ARG452 3.8 41.0 1.0
CA B:ALA546 4.0 58.7 1.0
CB B:LYS547 4.0 60.1 1.0
CA B:LYS547 4.1 60.1 1.0
C B:ALA546 4.1 59.0 1.0
CD A:ARG6 4.2 45.2 1.0
CA A:ARG6 4.2 45.8 1.0
O B:LYS547 4.3 60.5 1.0
NH1 A:ARG452 4.3 41.4 1.0
O B:TYR545 4.6 57.3 1.0
CZ A:ARG452 4.6 40.0 1.0
C B:LYS547 4.6 60.5 1.0
CZ A:ARG6 4.7 44.8 1.0
CB B:ALA546 4.7 58.4 1.0
N A:ALA7 4.7 45.8 1.0
NH2 A:ARG6 4.8 45.5 1.0
OG1 A:THR395 4.9 43.0 1.0
C A:ARG6 5.0 45.6 1.0

Chlorine binding site 6 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 6 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1634

b:19.1
occ:1.00
 O B:HOH2015 3.2 31.8 1.0
N B:PHE55 3.3 46.9 1.0
CB B:GLN58 3.7 48.9 1.0
N B:GLU61 3.9 45.1 1.0
CA B:GLY54 4.0 47.5 1.0
CB B:PHE55 4.0 46.6 1.0
CB B:VAL60 4.0 45.9 1.0
CD2 B:PHE55 4.1 45.6 1.0
C B:GLY54 4.1 47.0 1.0
CA B:PHE55 4.2 46.9 1.0
CB B:GLU61 4.2 45.3 1.0
CG B:GLN58 4.2 50.2 1.0
CG1 B:VAL60 4.4 46.3 1.0
CA B:GLU61 4.5 45.0 1.0
O B:PHE55 4.5 46.1 1.0
C B:VAL60 4.5 45.5 1.0
CG B:PHE55 4.6 46.6 1.0
CA B:VAL60 4.6 46.1 1.0
N B:VAL60 4.6 46.8 1.0
CA B:GLN58 4.8 48.6 1.0
C B:PHE55 4.8 46.6 1.0
C B:GLN58 4.9 48.6 1.0

Chlorine binding site 7 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 7 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1635

b:45.7
occ:1.00
 N B:ARG397 3.5 43.2 1.0
CD B:ARG452 3.7 41.8 1.0
CA B:GLY396 3.7 42.8 1.0
C B:GLY396 4.1 43.0 1.0
CG1 B:VAL449 4.3 44.0 1.0
CB B:ARG397 4.3 43.5 1.0
NE B:ARG452 4.4 42.0 1.0
CA B:ARG397 4.5 43.4 1.0
CG B:ARG452 4.9 41.8 1.0

Chlorine binding site 8 out of 8 in 2vpm

Go back to Chlorine Binding Sites List in 2vpm
Chlorine binding site 8 out of 8 in the Trypanothione Synthetase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Trypanothione Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1636

b:35.4
occ:1.00
 OH B:TYR545 3.2 55.5 1.0
N A:ARG397 3.4 42.8 1.0
CZ B:ARG541 3.4 65.1 1.0
NH1 B:ARG541 3.7 65.4 1.0
NE B:ARG541 3.7 63.6 1.0
NH2 B:ARG541 3.7 64.4 1.0
CD A:ARG452 3.8 40.1 1.0
CA A:GLY396 3.8 42.8 1.0
CE1 B:TYR545 3.9 56.1 1.0
CZ B:TYR545 4.0 55.6 1.0
C A:GLY396 4.1 42.6 1.0
CD B:ARG541 4.2 62.2 1.0
CB A:ARG397 4.2 43.2 1.0
CG B:ARG541 4.3 61.4 1.0
O A:HOH2060 4.3 25.4 1.0
NE A:ARG452 4.4 39.3 1.0
CG1 A:VAL449 4.4 40.9 1.0
CA A:ARG397 4.4 43.0 1.0
CB B:ARG541 4.8 61.2 1.0
CD2 B:LEU536 4.8 51.5 1.0

Reference:

P.K.Fyfe, S.L.Oza, A.H.Fairlamb, W.N.Hunter. Leishmania Trypanothione Synthetase-Amidase Structure Reveals A Basis For Regulation of Conflicting Synthetic and Hydrolytic Activities. J.Biol.Chem. V. 283 17672 2008.
ISSN: ISSN 0021-9258
PubMed: 18420578
DOI: 10.1074/JBC.M801850200
Page generated: Fri Jul 11 00:56:50 2025

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