Chlorine in PDB 9ggj: Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate

Enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate

All present enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate:
4.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate, PDB code: 9ggj was solved by M.Nielipinski, A.J.Pietrzyk-Brzezinska, D.Krzeszewska, B.Sekula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.57 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.588, 230.848, 112.534, 90, 89.48, 90
R / Rfree (%) 17.5 / 22.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate (pdb code 9ggj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate, PDB code: 9ggj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 9ggj

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Chlorine binding site 1 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


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 Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:34.8
occ:1.00
 O B:HOH871 3.2 27.1 1.0
N A:TYR493 3.3 20.4 1.0
N B:ARG265 3.4 23.1 1.0
O B:ILE263 3.5 25.5 1.0
CG B:ARG265 3.7 21.7 1.0
CB A:TYR493 3.7 20.4 1.0
CB B:ARG265 3.8 22.1 1.0
CA A:SER492 4.0 21.3 1.0
CA B:ASP264 4.0 24.8 1.0
CA A:TYR493 4.1 20.1 1.0
C A:SER492 4.1 21.2 1.0
CA B:ARG265 4.2 22.3 1.0
CB A:SER492 4.2 20.6 1.0
C B:ASP264 4.2 25.0 1.0
C B:ILE263 4.2 24.9 1.0
CD B:ARG265 4.3 21.5 1.0
N B:ASP264 4.5 25.3 1.0
CG1 B:ILE263 4.6 23.6 1.0
CD1 B:PHE266 4.9 23.0 1.0

Chlorine binding site 2 out of 7 in 9ggj

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Chlorine binding site 2 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


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 Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:31.7
occ:1.00
 O A:HOH732 2.9 35.0 1.0
N B:TYR493 3.3 21.0 1.0
N A:ARG265 3.4 23.3 1.0
O A:ILE263 3.5 26.4 1.0
CG A:ARG265 3.7 20.4 1.0
CB B:TYR493 3.7 20.8 1.0
CB A:ARG265 3.9 20.9 1.0
CA B:SER492 3.9 22.5 1.0
O A:HOH951 4.0 46.4 1.0
CA A:ASP264 4.0 25.3 1.0
C B:SER492 4.1 22.0 1.0
CA B:TYR493 4.1 20.9 1.0
C A:ILE263 4.1 24.9 1.0
CB B:SER492 4.2 21.7 1.0
CG1 A:ILE263 4.2 23.9 1.0
C A:ASP264 4.2 24.3 1.0
CA A:ARG265 4.3 22.1 1.0
CD A:ARG265 4.3 19.9 1.0
N A:ASP264 4.4 25.7 1.0
O A:HOH728 4.8 32.2 1.0
CD1 A:ILE263 4.9 24.5 1.0

Chlorine binding site 3 out of 7 in 9ggj

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Chlorine binding site 3 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


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 Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl704

b:23.0
occ:1.00
 N D:ARG265 3.2 18.9 1.0
N C:TYR493 3.3 19.1 1.0
NE2 H:HIS103 3.4 25.3 1.0
CE1 H:HIS103 3.5 25.1 1.0
O D:ILE263 3.5 22.6 1.0
CB C:TYR493 3.6 19.6 1.0
CG D:ARG265 3.7 19.1 1.0
CA D:ASP264 3.9 22.2 1.0
CB D:ARG265 3.9 18.0 1.0
CA C:SER492 4.0 19.8 1.0
C D:ASP264 4.0 19.7 1.0
CA C:TYR493 4.1 19.0 1.0
C D:ILE263 4.2 22.6 1.0
C C:SER492 4.2 19.0 1.0
CA D:ARG265 4.2 18.2 1.0
CB C:SER492 4.3 18.6 1.0
N D:ASP264 4.3 21.9 1.0
CD D:ARG265 4.4 18.9 1.0
CD2 H:HIS103 4.6 24.1 1.0
CG1 D:ILE263 4.7 24.5 1.0
ND1 H:HIS103 4.7 23.6 1.0
CD2 D:PHE266 4.8 21.2 1.0
CE H:MET267 4.8 23.5 0.5
OD1 D:ASP264 4.8 26.1 1.0
N D:PHE266 4.9 17.1 1.0
CG C:TYR493 5.0 19.4 1.0

Chlorine binding site 4 out of 7 in 9ggj

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Chlorine binding site 4 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


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 Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl705

b:26.9
occ:1.00
 N D:TYR493 3.2 17.1 1.0
O G:HOH778 3.3 23.7 1.0
N C:ARG265 3.3 21.6 1.0
CG C:ARG265 3.6 20.4 1.0
CB D:TYR493 3.8 17.1 1.0
O3 G:GOL603 3.8 57.9 1.0
CA C:ASP264 3.8 24.4 1.0
CB C:ARG265 3.9 20.2 1.0
CA D:SER492 4.0 17.8 1.0
O C:ILE263 4.0 23.7 1.0
C C:ASP264 4.1 23.0 1.0
C D:SER492 4.1 17.6 1.0
CA D:TYR493 4.1 16.9 1.0
CB D:SER492 4.2 17.5 1.0
CA C:ARG265 4.2 21.8 1.0
CG1 C:ILE263 4.3 24.1 1.0
CD C:ARG265 4.3 19.9 1.0
C C:ILE263 4.3 23.5 1.0
C2 G:GOL603 4.4 55.0 1.0
N C:ASP264 4.4 24.7 1.0
C3 G:GOL603 4.6 56.8 1.0
CD1 C:ILE263 4.7 24.7 1.0
O1 G:GOL603 4.7 52.3 1.0
CG C:ASP264 4.8 28.4 1.0
CB C:ASP264 4.8 26.6 1.0
OD2 C:ASP264 4.9 30.4 1.0

Chlorine binding site 5 out of 7 in 9ggj

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Chlorine binding site 5 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl706

b:22.4
occ:1.00
 N H:TYR493 3.2 18.7 1.0
O C:HOH1126 3.2 24.7 1.0
NE2 C:HIS103 3.3 24.3 1.0
N G:ARG265 3.3 20.2 1.0
CE1 C:HIS103 3.3 23.7 1.0
O G:ILE263 3.6 23.9 1.0
CB H:TYR493 3.7 19.4 1.0
CG G:ARG265 3.7 20.4 1.0
CA G:ASP264 3.9 22.7 1.0
CB G:ARG265 3.9 19.3 1.0
CA H:SER492 3.9 18.6 1.0
CA H:TYR493 4.1 18.9 1.0
C H:SER492 4.1 18.4 1.0
C G:ASP264 4.1 21.6 1.0
CA G:ARG265 4.2 19.5 1.0
C G:ILE263 4.2 22.3 1.0
CB H:SER492 4.3 18.6 1.0
N G:ASP264 4.4 22.3 1.0
CD G:ARG265 4.5 19.9 1.0
CD2 C:HIS103 4.5 23.9 1.0
ND1 C:HIS103 4.5 24.4 1.0
CG1 G:ILE263 4.6 21.7 1.0
OD1 G:ASP264 4.8 24.3 1.0
CD2 G:PHE266 4.8 17.0 1.0
O H:HOH808 4.9 25.6 1.0
O H:SER491 4.9 18.5 1.0
N G:PHE266 5.0 18.2 1.0

Chlorine binding site 6 out of 7 in 9ggj

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Chlorine binding site 6 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl607

b:32.6
occ:1.00
 O E:HOH884 3.1 29.9 1.0
N F:TYR493 3.3 23.8 1.0
N E:ARG265 3.3 24.5 1.0
O E:ILE263 3.5 26.1 1.0
CG E:ARG265 3.7 24.1 1.0
CB F:TYR493 3.7 23.7 1.0
CB E:ARG265 3.8 23.3 1.0
CA E:ASP264 4.0 25.8 1.0
CA F:SER492 4.0 22.7 1.0
C E:ILE263 4.1 24.8 1.0
CA F:TYR493 4.2 23.4 1.0
C E:ASP264 4.2 24.8 1.0
CA E:ARG265 4.2 23.8 1.0
C F:SER492 4.2 23.3 1.0
CB F:SER492 4.2 23.0 1.0
CD E:ARG265 4.3 24.5 1.0
O E:HOH916 4.3 49.1 1.0
N E:ASP264 4.4 26.0 1.0
CG1 E:ILE263 4.4 21.8 1.0
CD1 E:ILE263 4.9 21.2 1.0

Chlorine binding site 7 out of 7 in 9ggj

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Chlorine binding site 7 out of 7 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) in Complex with Biological Substrate and Products - Argininosuccinate, Argnine and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl605

b:23.2
occ:1.00
 N G:TYR493 3.1 17.4 1.0
O H:HOH737 3.2 37.0 1.0
O H:HOH932 3.3 24.6 1.0
N H:ARG265 3.5 18.2 1.0
CB G:TYR493 3.6 18.9 1.0
CG H:ARG265 3.7 19.7 1.0
CA G:SER492 3.8 18.3 1.0
O H:ILE263 3.8 23.6 1.0
O G:HOH986 3.9 43.0 1.0
C G:SER492 3.9 17.8 1.0
CA H:ASP264 4.0 20.8 1.0
CA G:TYR493 4.0 18.1 1.0
CB H:ARG265 4.0 19.4 1.0
CB G:SER492 4.1 18.2 1.0
C H:ASP264 4.3 19.2 1.0
CD H:ARG265 4.3 19.2 1.0
CA H:ARG265 4.3 19.7 1.0
C H:ILE263 4.4 24.2 1.0
CG1 H:ILE263 4.5 26.9 1.0
N H:ASP264 4.5 22.8 1.0
O G:HOH1035 4.9 39.5 1.0
CG H:ASP264 4.9 22.5 1.0
OD2 H:ASP264 4.9 22.9 1.0
O H:HOH849 4.9 29.5 1.0
CB H:ASP264 5.0 21.0 1.0
O G:TYR493 5.0 17.5 1.0

Reference:

M.Nielipinski, D.Krzeszewska, A.J.Pietrzyk-Brzezinska, B.Sekula. Arabidopsis Thaliana Argininosuccinate Lyase Structure Uncovers the Role of Serine As the Catalytic Base. J.Struct.Biol. 08130 2024.
ISSN: ESSN 1095-8657
PubMed: 39384000
DOI: 10.1016/J.JSB.2024.108130
Page generated: Thu Oct 31 18:12:26 2024

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