Chlorine in PDB 7rsm: Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp

Enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp

All present enzymatic activity of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp, PDB code: 7rsm was solved by K.Yang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.72 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.7, 135.2, 72.24, 90, 112.54, 90
R / Rfree (%) 24.7 / 30.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp (pdb code 7rsm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp, PDB code: 7rsm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7rsm

Go back to Chlorine Binding Sites List in 7rsm
Chlorine binding site 1 out of 4 in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:49.3
occ:1.00
 CL A:2L5502 0.0 49.3 1.0
C15 A:2L5502 1.8 46.0 1.0
OG A:SER348 2.4 33.1 1.0
C14 A:2L5502 2.7 45.6 1.0
OD1 A:ASP346 2.8 36.9 1.0
C19 A:2L5502 2.8 39.8 1.0
C13 A:2L5502 2.9 45.8 1.0
O A:PHE347 3.2 26.4 1.0
CA A:GLY419 3.5 31.9 1.0
CZ3 A:TRP417 3.5 38.5 1.0
CB A:SER348 3.6 30.1 1.0
C12 A:2L5502 3.6 50.0 1.0
CG A:ASP346 3.9 39.1 1.0
O4 A:2L5502 3.9 40.4 1.0
C A:PHE347 3.9 30.9 1.0
C16 A:2L5502 4.0 42.4 1.0
C18 A:2L5502 4.1 37.4 1.0
C A:GLY419 4.1 30.8 1.0
N A:ALA420 4.1 26.1 1.0
CA A:SER348 4.2 27.2 1.0
C11 A:2L5502 4.2 47.7 1.0
OD2 A:ASP346 4.2 40.2 1.0
CE3 A:TRP417 4.3 34.6 1.0
N A:SER348 4.3 29.1 1.0
CH2 A:TRP417 4.4 41.7 1.0
C17 A:2L5502 4.5 40.6 1.0
N A:GLY419 4.6 30.7 1.0
O A:ILE418 4.7 29.0 1.0
N A:PHE347 4.8 27.5 1.0
CD1 A:LEU305 4.9 29.0 1.0
N4 A:2L5502 4.9 39.3 1.0
CA A:PHE347 5.0 28.8 1.0

Chlorine binding site 2 out of 4 in 7rsm

Go back to Chlorine Binding Sites List in 7rsm
Chlorine binding site 2 out of 4 in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:54.5
occ:1.00
 CL B:2L5502 0.0 54.5 1.0
C15 B:2L5502 1.8 49.8 1.0
OG B:SER348 2.3 35.3 1.0
OD1 B:ASP346 2.7 33.2 1.0
C14 B:2L5502 2.7 46.1 1.0
C19 B:2L5502 2.8 44.6 1.0
C13 B:2L5502 3.0 48.0 1.0
O B:PHE347 3.3 29.9 1.0
CB B:SER348 3.5 28.2 1.0
CG B:ASP346 3.6 37.5 1.0
OD2 B:ASP346 3.8 36.5 1.0
CA B:GLY419 3.9 33.5 1.0
C B:PHE347 3.9 30.9 1.0
C12 B:2L5502 4.0 49.3 1.0
OXT B:2L5502 4.0 46.1 1.0
C16 B:2L5502 4.0 44.9 1.0
CZ3 B:TRP417 4.0 40.6 1.0
C18 B:2L5502 4.0 39.0 1.0
CA B:SER348 4.1 30.9 1.0
N B:SER348 4.2 33.0 1.0
C B:GLY419 4.4 32.9 1.0
N B:ALA420 4.4 30.3 1.0
C11 B:2L5502 4.5 52.5 1.0
C17 B:2L5502 4.5 43.5 1.0
CE3 B:TRP417 4.6 39.1 1.0
CD1 B:LEU305 4.6 26.9 1.0
N B:PHE347 4.8 22.4 1.0
CH2 B:TRP417 4.8 42.7 1.0
N B:GLY419 4.8 34.2 1.0
CB B:ASP346 4.9 30.4 1.0
CA B:PHE347 4.9 29.7 1.0
O B:ILE418 5.0 31.3 1.0

Chlorine binding site 3 out of 4 in 7rsm

Go back to Chlorine Binding Sites List in 7rsm
Chlorine binding site 3 out of 4 in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:53.2
occ:1.00
 CL C:2L5502 0.0 53.2 1.0
C15 C:2L5502 1.8 49.6 1.0
C14 C:2L5502 2.7 43.5 1.0
OG C:SER348 2.7 36.7 1.0
C19 C:2L5502 2.8 41.9 1.0
C13 C:2L5502 3.0 45.4 1.0
O C:PHE347 3.0 29.8 1.0
OXT C:2L5502 3.0 43.7 1.0
OD1 C:ASP346 3.1 35.6 1.0
CA C:GLY419 3.2 31.9 1.0
C12 C:2L5502 3.3 46.1 1.0
CZ3 C:TRP417 3.5 43.2 1.0
C11 C:2L5502 3.5 46.8 1.0
C C:GLY419 3.6 34.8 1.0
N C:ALA420 3.7 38.0 1.0
CB C:SER348 3.7 29.7 1.0
C C:PHE347 4.0 31.4 1.0
C16 C:2L5502 4.0 41.3 1.0
C18 C:2L5502 4.1 40.6 1.0
CE3 C:TRP417 4.1 37.1 1.0
N C:GLY419 4.1 36.1 1.0
CA C:SER348 4.1 32.0 1.0
CG C:ASP346 4.2 39.5 1.0
O C:ILE418 4.4 34.6 1.0
N C:SER348 4.5 28.3 1.0
O C:GLY419 4.5 33.1 1.0
OD2 C:ASP346 4.5 40.7 1.0
CH2 C:TRP417 4.5 39.4 1.0
C17 C:2L5502 4.5 40.5 1.0
C C:ILE418 4.6 36.5 1.0
O4 C:2L5502 4.7 45.6 1.0
N4 C:2L5502 4.7 45.1 1.0
O C:ALA420 4.8 36.3 1.0
CA C:ALA420 4.8 37.0 1.0
N C:PHE347 5.0 30.9 1.0

Chlorine binding site 4 out of 4 in 7rsm

Go back to Chlorine Binding Sites List in 7rsm
Chlorine binding site 4 out of 4 in the Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Pyrrolysyl-Trna Synthetase (N346D/C348S/Y384F) in Complex with O-Chlorophenylalanine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:54.8
occ:1.00
 CL D:2L5502 0.0 54.8 1.0
C15 D:2L5502 1.8 46.5 1.0
OG D:SER348 2.7 37.2 1.0
C14 D:2L5502 2.7 41.0 1.0
C19 D:2L5502 2.8 39.7 1.0
O4 D:2L5502 2.9 42.9 1.0
OD1 D:ASP346 2.9 39.7 1.0
C13 D:2L5502 3.0 46.3 1.0
O D:PHE347 3.2 29.6 1.0
CA D:GLY419 3.3 31.6 1.0
C12 D:2L5502 3.3 44.4 1.0
C11 D:2L5502 3.4 43.7 1.0
N D:ALA420 3.7 30.0 1.0
CG D:ASP346 3.8 38.5 1.0
C D:GLY419 3.8 32.6 1.0
CZ3 D:TRP417 3.8 34.9 1.0
OD2 D:ASP346 3.9 41.4 1.0
CB D:SER348 3.9 29.1 1.0
C16 D:2L5502 4.0 40.4 1.0
C D:PHE347 4.1 29.9 1.0
C18 D:2L5502 4.1 37.1 1.0
CA D:SER348 4.4 28.7 1.0
N D:GLY419 4.4 33.8 1.0
CE3 D:TRP417 4.4 35.1 1.0
C17 D:2L5502 4.5 37.3 1.0
N D:SER348 4.6 25.0 1.0
CH2 D:TRP417 4.6 36.4 1.0
OXT D:2L5502 4.6 46.1 1.0
O D:GLY419 4.7 33.3 1.0
O D:ALA420 4.7 34.6 1.0
N4 D:2L5502 4.8 49.3 1.0
O D:ILE418 4.8 28.3 1.0
CA D:ALA420 4.8 33.5 1.0
C D:ALA420 4.9 34.6 1.0
N D:PHE347 4.9 25.4 1.0
C D:ILE418 5.0 34.5 1.0

Reference:

E.C.Vatansever, K.S.Yang, Z.Z.Geng, Y.Qiao, P.Li, S.Xu, W.R.Liu. A Designed, Highly Efficient Pyrrolysyl-Trna Synthetase Mutant Binds O-Chlorophenylalanine Using Two Halogen Bonds. J.Mol.Biol. V. 434 67534 2022.
ISSN: ESSN 1089-8638
PubMed: 35278475
DOI: 10.1016/J.JMB.2022.167534
Page generated: Tue Apr 4 21:39:10 2023

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