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Chlorine in PDB 2zy4: Dodecameric L-Aspartate Beta-Decarboxylase

Enzymatic activity of Dodecameric L-Aspartate Beta-Decarboxylase

All present enzymatic activity of Dodecameric L-Aspartate Beta-Decarboxylase:
4.1.1.12;

Protein crystallography data

The structure of Dodecameric L-Aspartate Beta-Decarboxylase, PDB code: 2zy4 was solved by H.-J.Chen, T.-P.Ko, C.-Y.Lee, N.-C.Wang, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 149.953, 217.149, 207.154, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dodecameric L-Aspartate Beta-Decarboxylase (pdb code 2zy4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Dodecameric L-Aspartate Beta-Decarboxylase, PDB code: 2zy4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 2zy4

Go back to Chlorine Binding Sites List in 2zy4
Chlorine binding site 1 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl4001

b:18.1
occ:1.00
 N A:GLY99 3.2 20.0 1.0
NE A:ARG53 3.3 12.1 1.0
NH1 A:ARG49 3.4 17.8 1.0
N A:GLU98 3.8 21.4 1.0
CG A:ARG53 3.9 12.9 1.0
CA A:GLY99 3.9 17.9 1.0
CD A:ARG49 3.9 13.2 1.0
CB A:ARG49 3.9 12.2 1.0
NH2 A:ARG53 3.9 10.7 1.0
CB A:GLN97 4.0 21.3 1.0
O A:HOH593 4.0 43.1 1.0
O A:HOH599 4.1 44.9 1.0
CZ A:ARG53 4.1 12.6 1.0
C A:GLN97 4.1 19.9 1.0
CG A:ARG49 4.2 13.4 1.0
CD A:ARG53 4.2 13.0 1.0
C A:GLU98 4.2 21.0 1.0
CA A:GLN97 4.3 20.4 1.0
CA A:GLU98 4.3 23.1 1.0
CZ A:ARG49 4.3 15.5 1.0
CB A:GLU98 4.5 25.4 1.0
NE A:ARG49 4.5 16.0 1.0
O A:HOH594 4.6 31.3 1.0
CD2 B:LEU56 4.7 14.8 1.0
O A:ARG49 4.7 11.0 1.0
O A:GLN97 4.8 22.1 1.0
N A:VAL100 4.8 17.2 1.0
C A:GLY99 4.9 16.7 1.0
CG A:GLN97 4.9 19.4 1.0
CA A:ARG49 4.9 12.7 1.0
C A:ARG49 5.0 12.2 1.0

Chlorine binding site 2 out of 6 in 2zy4

Go back to Chlorine Binding Sites List in 2zy4
Chlorine binding site 2 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4002

b:20.9
occ:1.00
 N B:GLY99 3.2 22.3 1.0
NE B:ARG53 3.2 13.1 1.0
NH1 B:ARG49 3.5 18.2 1.0
O B:HOH792 3.6 49.6 1.0
O B:HOH794 3.7 40.9 1.0
N B:GLU98 3.7 22.0 1.0
CG B:ARG53 3.8 11.7 1.0
NH2 B:ARG53 3.8 12.0 1.0
CD B:ARG49 3.9 15.1 1.0
CA B:GLY99 3.9 21.1 1.0
CB B:GLN97 3.9 21.4 1.0
CB B:ARG49 4.0 12.0 1.0
CZ B:ARG53 4.0 14.7 1.0
C B:GLN97 4.1 21.9 1.0
CD B:ARG53 4.1 13.2 1.0
C B:GLU98 4.2 23.5 1.0
CG B:ARG49 4.2 12.5 1.0
CA B:GLN97 4.2 22.7 1.0
CA B:GLU98 4.3 24.7 1.0
CB B:GLU98 4.3 26.2 1.0
CZ B:ARG49 4.5 19.1 1.0
CD2 A:LEU56 4.5 14.4 1.0
NE B:ARG49 4.6 16.3 1.0
O B:ARG49 4.7 12.1 1.0
O B:GLN97 4.8 21.5 1.0
CG B:GLN97 4.8 22.3 1.0
N B:VAL100 4.8 19.4 1.0
CA B:ARG49 4.9 12.1 1.0
C B:GLY99 4.9 20.5 1.0
C B:ARG49 5.0 10.8 1.0

Chlorine binding site 3 out of 6 in 2zy4

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Chlorine binding site 3 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl4003

b:19.0
occ:1.00
 N C:GLY99 3.2 16.3 1.0
NE C:ARG53 3.3 10.3 1.0
NH1 C:ARG49 3.4 18.0 1.0
O C:HOH2271 3.4 41.6 1.0
CA C:GLY99 3.8 16.0 1.0
CG C:ARG53 3.8 10.3 1.0
CD C:ARG49 3.8 14.7 1.0
CB C:ARG49 3.9 9.7 1.0
O C:HOH853 3.9 53.6 1.0
N C:GLU98 3.9 21.1 1.0
CB C:GLN97 3.9 23.8 1.0
NH2 C:ARG53 3.9 14.4 1.0
CZ C:ARG53 4.1 13.7 1.0
C C:GLN97 4.1 21.6 1.0
CG C:ARG49 4.1 10.6 1.0
CD C:ARG53 4.1 11.5 1.0
C C:GLU98 4.3 18.8 1.0
CA C:GLN97 4.3 22.9 1.0
CZ C:ARG49 4.3 20.2 1.0
CA C:GLU98 4.4 20.9 1.0
NE C:ARG49 4.5 17.2 1.0
CD2 D:LEU56 4.5 11.3 1.0
CB C:GLU98 4.6 22.1 1.0
O C:HOH839 4.6 54.5 1.0
O C:HOH855 4.7 34.6 1.0
O C:GLN97 4.7 20.6 1.0
O C:ARG49 4.7 10.2 1.0
N C:VAL100 4.8 15.9 1.0
C C:GLY99 4.8 16.5 1.0
CA C:ARG49 4.9 10.7 1.0
CG C:GLN97 4.9 21.3 1.0
C C:ARG49 5.0 11.4 1.0

Chlorine binding site 4 out of 6 in 2zy4

Go back to Chlorine Binding Sites List in 2zy4
Chlorine binding site 4 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl4004

b:21.9
occ:1.00
 N D:GLY99 3.1 25.4 1.0
NE D:ARG53 3.2 16.4 1.0
NH1 D:ARG49 3.4 23.7 1.0
CG D:ARG53 3.7 13.1 1.0
CA D:GLY99 3.8 24.0 1.0
N D:GLU98 3.8 22.9 1.0
O D:HOH886 3.8 44.9 1.0
CB D:ARG49 3.8 12.2 1.0
CD D:ARG49 3.8 20.4 1.0
NH2 D:ARG53 3.9 15.9 1.0
CB D:GLN97 3.9 21.8 1.0
CZ D:ARG53 4.0 15.2 1.0
CD D:ARG53 4.0 12.9 1.0
C D:GLN97 4.0 21.7 1.0
CG D:ARG49 4.1 14.1 1.0
C D:GLU98 4.2 24.9 1.0
CA D:GLN97 4.3 21.3 1.0
CA D:GLU98 4.3 24.8 1.0
CZ D:ARG49 4.4 23.5 1.0
CB D:GLU98 4.5 26.2 1.0
O D:HOH884 4.5 48.1 1.0
CD2 C:LEU56 4.5 14.3 1.0
NE D:ARG49 4.5 20.3 1.0
O D:ARG49 4.6 13.1 1.0
N D:VAL100 4.7 24.3 1.0
O D:GLN97 4.7 22.7 1.0
C D:GLY99 4.8 24.9 1.0
CA D:ARG49 4.8 11.7 1.0
C D:ARG49 4.9 12.4 1.0
CG D:GLN97 4.9 19.7 1.0

Chlorine binding site 5 out of 6 in 2zy4

Go back to Chlorine Binding Sites List in 2zy4
Chlorine binding site 5 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl4005

b:20.8
occ:1.00
 N E:GLY99 3.2 19.6 1.0
NE E:ARG53 3.2 14.0 1.0
NH1 E:ARG49 3.3 18.7 1.0
O E:HOH552 3.6 36.8 1.0
CG E:ARG53 3.8 12.3 1.0
N E:GLU98 3.8 21.0 1.0
O E:HOH553 3.8 43.4 1.0
CD E:ARG49 3.8 17.9 1.0
CA E:GLY99 3.9 19.2 1.0
CB E:ARG49 3.9 13.1 1.0
NH2 E:ARG53 3.9 13.3 1.0
CB E:GLN97 4.0 20.2 1.0
CZ E:ARG53 4.1 15.7 1.0
C E:GLN97 4.1 19.8 1.0
CD E:ARG53 4.1 11.7 1.0
CG E:ARG49 4.2 13.1 1.0
C E:GLU98 4.2 20.7 1.0
CZ E:ARG49 4.3 22.6 1.0
CA E:GLN97 4.3 21.5 1.0
CA E:GLU98 4.4 20.7 1.0
CB E:GLU98 4.4 23.8 1.0
NE E:ARG49 4.5 17.8 1.0
O E:HOH1986 4.7 43.8 1.0
O E:ARG49 4.7 10.8 1.0
O E:GLN97 4.8 19.1 1.0
N E:VAL100 4.8 17.1 1.0
CA E:ARG49 4.9 12.3 1.0
C E:GLY99 4.9 18.4 1.0
C E:ARG49 4.9 11.8 1.0
CG E:GLN97 5.0 20.4 1.0

Chlorine binding site 6 out of 6 in 2zy4

Go back to Chlorine Binding Sites List in 2zy4
Chlorine binding site 6 out of 6 in the Dodecameric L-Aspartate Beta-Decarboxylase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Dodecameric L-Aspartate Beta-Decarboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl4006

b:24.3
occ:1.00
 N F:GLY99 3.2 23.6 1.0
NE F:ARG53 3.3 12.8 1.0
NH1 F:ARG49 3.4 22.7 1.0
O F:HOH2893 3.5 52.0 1.0
O F:HOH551 3.5 45.3 1.0
CD F:ARG49 3.7 16.7 1.0
N F:GLU98 3.8 23.9 1.0
CG F:ARG53 3.8 12.9 1.0
CA F:GLY99 3.9 23.3 1.0
CB F:ARG49 3.9 11.6 1.0
CB F:GLN97 4.0 20.4 1.0
CG F:ARG49 4.0 13.8 1.0
NH2 F:ARG53 4.0 12.1 1.0
C F:GLN97 4.1 20.8 1.0
CZ F:ARG53 4.1 13.5 1.0
CD F:ARG53 4.2 13.4 1.0
C F:GLU98 4.2 24.4 1.0
CA F:GLN97 4.3 21.5 1.0
CA F:GLU98 4.3 26.0 1.0
CZ F:ARG49 4.4 23.1 1.0
CB F:GLU98 4.5 29.0 1.0
NE F:ARG49 4.5 17.8 1.0
O F:GLN97 4.7 22.1 1.0
O F:ARG49 4.8 9.8 1.0
N F:VAL100 4.8 21.8 1.0
CA F:ARG49 4.9 10.7 1.0
C F:GLY99 4.9 23.0 1.0
CG F:GLN97 4.9 21.2 1.0
C F:ARG49 5.0 9.6 1.0

Reference:

H.-J.Chen, T.-P.Ko, C.-Y.Lee, N.-C.Wang, A.H.-J.Wang. Structure, Assembly, and Mechanism of A Plp-Dependent Dodecameric L-Aspartate Beta-Decarboxylase Structure V. 17 517 2009.
ISSN: ISSN 0969-2126
PubMed: 19368885
DOI: 10.1016/J.STR.2009.02.013
Page generated: Sat Jul 20 15:38:27 2024

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