Chlorine in PDB 9ggi: Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)

Enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)

All present enzymatic activity of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl):
4.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl), PDB code: 9ggi 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) 48.45 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.044, 229.542, 111.586, 90, 90.56, 90
R / Rfree (%) 14.7 / 17.1

Other elements in 9ggi:

The structure of Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl) (pdb code 9ggi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl), PDB code: 9ggi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 9ggi

Go back to Chlorine Binding Sites List in 9ggi
Chlorine binding site 1 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:15.6
occ:1.00
 O H:HOH819 3.2 20.3 1.0
O C:HOH720 3.2 25.0 1.0
N C:TYR493 3.2 20.2 1.0
N D:ARG265 3.3 19.2 1.0
CG D:ARG265 3.7 18.9 1.0
CB C:TYR493 3.7 20.9 1.0
CA D:ASP264 3.8 19.4 1.0
O D:ILE263 3.8 19.3 1.0
CB D:ARG265 3.9 19.0 1.0
CA C:SER492 3.9 19.9 1.0
C D:ASP264 4.0 19.3 1.0
CB C:SER492 4.0 19.9 1.0
C C:SER492 4.1 19.8 1.0
CA C:TYR493 4.1 20.2 1.0
CA D:ARG265 4.2 19.1 1.0
C D:ILE263 4.3 19.3 1.0
C1 C:GOL606 4.3 48.6 1.0
CD D:ARG265 4.3 18.8 1.0
N D:ASP264 4.4 19.3 1.0
CG1 D:ILE263 4.4 19.0 1.0
O3 C:GOL606 4.6 30.0 1.0
CG D:ASP264 4.7 19.5 1.0
OD2 D:ASP264 4.8 19.6 1.0
C3 C:GOL606 4.8 40.7 1.0
O2 C:GOL606 4.8 40.6 1.0
CB D:ASP264 4.9 19.5 1.0
C2 C:GOL606 4.9 47.1 1.0
CD1 D:ILE263 4.9 18.9 1.0

Chlorine binding site 2 out of 6 in 9ggi

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Chlorine binding site 2 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl602

b:16.5
occ:1.00
 N C:ARG265 3.2 19.2 1.0
N D:TYR493 3.2 20.1 1.0
O G:HOH1141 3.2 26.7 1.0
NE2 G:HIS103 3.3 20.4 1.0
CE1 G:HIS103 3.6 20.5 1.0
O C:ILE263 3.6 19.4 1.0
CG C:ARG265 3.6 19.0 1.0
CB D:TYR493 3.7 20.5 1.0
CB C:ARG265 3.8 19.1 1.0
CA C:ASP264 3.9 19.4 1.0
CA D:SER492 3.9 20.0 1.0
C C:ASP264 4.0 19.3 1.0
C D:SER492 4.1 19.9 1.0
CA D:TYR493 4.1 20.0 1.0
CA C:ARG265 4.1 19.1 1.0
C C:ILE263 4.2 19.3 1.0
CB D:SER492 4.2 19.9 1.0
CD C:ARG265 4.3 18.9 1.0
N C:ASP264 4.3 19.3 1.0
CD2 G:HIS103 4.4 19.6 1.0
CG1 C:ILE263 4.6 19.1 1.0
ND1 G:HIS103 4.7 19.9 1.0
CD2 C:PHE266 4.8 19.4 1.0
CE G:MET267 4.9 24.8 1.0
O D:HOH961 4.9 22.1 1.0
OD1 C:ASP264 4.9 19.5 1.0
CE2 C:PHE266 5.0 19.4 1.0
N C:PHE266 5.0 19.3 1.0

Chlorine binding site 3 out of 6 in 9ggi

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Chlorine binding site 3 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:16.1
occ:1.00
 O D:HOH1118 3.1 24.9 1.0
N G:TYR493 3.2 20.1 1.0
N H:ARG265 3.3 19.2 1.0
NE2 D:HIS103 3.3 19.5 1.0
O H:ILE263 3.6 19.3 1.0
CE1 D:HIS103 3.6 20.0 1.0
CB G:TYR493 3.7 20.5 1.0
CG H:ARG265 3.7 18.9 1.0
CB H:ARG265 3.8 19.0 1.0
CA H:ASP264 3.8 19.3 1.0
CA G:SER492 3.9 20.0 1.0
C G:SER492 4.1 19.8 1.0
C H:ASP264 4.1 19.3 1.0
CA G:TYR493 4.1 20.1 1.0
C H:ILE263 4.1 19.3 1.0
CA H:ARG265 4.2 19.1 1.0
CB G:SER492 4.2 19.9 1.0
N H:ASP264 4.3 19.3 1.0
CD H:ARG265 4.3 18.9 1.0
CD2 D:HIS103 4.5 19.3 1.0
CG1 H:ILE263 4.6 19.1 1.0
ND1 D:HIS103 4.8 19.5 1.0
CD2 H:PHE266 4.8 19.3 1.0
OD1 H:ASP264 4.9 19.4 1.0
O G:HOH846 4.9 23.5 1.0
O G:HOH768 4.9 26.0 1.0
N H:PHE266 5.0 19.2 1.0

Chlorine binding site 4 out of 6 in 9ggi

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Chlorine binding site 4 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl601

b:24.1
occ:1.00
 N F:ARG265 3.3 19.6 1.0
N E:TYR493 3.3 20.1 1.0
CB E:TYR493 3.6 20.7 1.0
O F:HOH834 3.6 32.6 1.0
CG F:ARG265 3.6 19.3 1.0
O F:ILE263 3.7 20.3 1.0
CB F:ARG265 3.8 19.4 1.0
CA F:ASP264 4.0 19.9 1.0
CA E:TYR493 4.1 20.1 1.0
CA F:ARG265 4.1 19.5 1.0
C F:ASP264 4.2 19.7 1.0
CA E:SER492 4.2 19.9 1.0
CD F:ARG265 4.2 19.2 1.0
C F:ILE263 4.3 19.8 1.0
C E:SER492 4.3 19.7 1.0
CB E:SER492 4.4 19.9 1.0
N F:ASP264 4.5 19.8 1.0
CD1 F:PHE266 4.6 19.9 1.0
CG1 F:ILE263 4.6 19.4 1.0
CE1 F:PHE266 4.6 19.8 1.0
CG E:TYR493 5.0 20.6 1.0
OD1 F:ASP264 5.0 20.0 1.0
N F:PHE266 5.0 19.7 1.0

Chlorine binding site 5 out of 6 in 9ggi

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Chlorine binding site 5 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl602

b:25.1
occ:1.00
 O E:HOH1161 2.7 47.9 1.0
N F:TYR493 3.2 21.3 1.0
O E:HOH850 3.3 33.4 1.0
N E:ARG265 3.4 19.4 1.0
O E:ILE263 3.6 21.1 1.0
CG E:ARG265 3.6 19.3 1.0
CB F:TYR493 3.6 21.9 1.0
CB E:ARG265 3.9 19.3 1.0
O F:HOH1207 3.9 61.0 1.0
CA F:SER492 4.0 21.2 1.0
CA E:ASP264 4.0 19.6 1.0
CA F:TYR493 4.1 21.1 1.0
CB F:SER492 4.1 21.2 1.0
C F:SER492 4.1 20.9 1.0
C E:ILE263 4.1 19.7 1.0
CD E:ARG265 4.2 19.2 1.0
C E:ASP264 4.2 19.5 1.0
CA E:ARG265 4.3 19.4 1.0
CG1 E:ILE263 4.3 19.5 1.0
N E:ASP264 4.4 19.7 1.0
O E:HOH1029 4.5 48.3 1.0
O F:TYR493 4.9 20.6 1.0
CD1 E:ILE263 4.9 19.4 1.0
C F:TYR493 5.0 20.5 1.0

Chlorine binding site 6 out of 6 in 9ggi

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Chlorine binding site 6 out of 6 in the Crystal Structure of Argininosuccinate Lyase From Arabidopsis Thaliana (Atasl)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl601

b:16.7
occ:1.00
 O C:HOH848 3.2 18.9 1.0
N H:TYR493 3.3 21.1 1.0
N G:ARG265 3.3 19.4 1.0
O H:HOH714 3.3 26.8 1.0
CG G:ARG265 3.7 19.1 1.0
O G:ILE263 3.8 19.6 1.0
CB H:TYR493 3.8 21.7 1.0
CA G:ASP264 3.8 19.6 1.0
CB G:ARG265 3.9 19.2 1.0
CA H:SER492 3.9 20.9 1.0
CB H:SER492 4.0 20.7 1.0
C G:ASP264 4.1 19.4 1.0
C H:SER492 4.1 20.7 1.0
CA H:TYR493 4.1 20.9 1.0
C2 H:GOL606 4.2 44.5 1.0
CA G:ARG265 4.2 19.3 1.0
CD G:ARG265 4.3 19.1 1.0
C G:ILE263 4.3 19.5 1.0
CG1 G:ILE263 4.3 19.2 1.0
N G:ASP264 4.4 19.5 1.0
O3 H:GOL606 4.6 36.6 1.0
O2 H:GOL606 4.7 51.0 1.0
C3 H:GOL606 4.7 40.8 1.0
CD1 G:ILE263 4.8 19.1 1.0
CG G:ASP264 4.9 19.8 1.0
CB G:ASP264 5.0 19.7 1.0
OD2 G:ASP264 5.0 19.9 1.0
O H:TYR493 5.0 20.4 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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