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 Sites List in 9ggj
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 Sites List in 9ggj
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 Sites List in 9ggj
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 Sites List in 9ggj
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 Sites List in 9ggj
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 Sites List in 9ggj
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
Go back to
Chlorine Binding Sites List in 9ggj
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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