Zinc in PDB 8thm: Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
Enzymatic activity of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
All present enzymatic activity of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001:
4.2.1.1;
Protein crystallography data
The structure of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001, PDB code: 8thm
was solved by
S.B.Pulsford,
C.J.Jackson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.51 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.314,
181.848,
190.057,
90,
90,
90
|
R / Rfree (%)
|
19.3 /
24.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
(pdb code 8thm). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001, PDB code: 8thm:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8thm
Go back to
Zinc Binding Sites List in 8thm
Zinc binding site 1 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:41.7
occ:1.00
|
O
|
A:HOH780
|
2.2
|
41.4
|
1.0
|
NE2
|
A:HIS312
|
2.2
|
33.3
|
1.0
|
SG
|
A:CYS323
|
2.3
|
40.9
|
1.0
|
SG
|
A:CYS244
|
2.3
|
38.1
|
1.0
|
CD2
|
A:HIS312
|
3.0
|
33.0
|
1.0
|
CB
|
A:CYS323
|
3.1
|
32.5
|
1.0
|
CE1
|
A:HIS312
|
3.3
|
45.5
|
1.0
|
CB
|
A:CYS244
|
3.3
|
31.2
|
1.0
|
O
|
A:HOH844
|
3.4
|
42.0
|
1.0
|
CA
|
A:CYS323
|
3.5
|
42.3
|
1.0
|
CB
|
A:ASP246
|
3.9
|
41.1
|
1.0
|
O
|
A:HOH843
|
4.0
|
40.7
|
1.0
|
OD2
|
A:ASP246
|
4.0
|
48.9
|
1.0
|
CG
|
A:HIS312
|
4.2
|
38.6
|
1.0
|
N
|
A:ALA324
|
4.2
|
51.7
|
1.0
|
C
|
A:CYS323
|
4.2
|
42.0
|
1.0
|
ND1
|
A:HIS312
|
4.3
|
37.8
|
1.0
|
N
|
A:GLY271
|
4.3
|
42.6
|
1.0
|
CG
|
A:ASP246
|
4.4
|
46.0
|
1.0
|
CA
|
A:GLY271
|
4.6
|
38.1
|
1.0
|
N
|
A:CYS323
|
4.7
|
40.3
|
1.0
|
CA
|
A:CYS244
|
4.7
|
43.3
|
1.0
|
N
|
A:ASP246
|
4.8
|
46.2
|
1.0
|
O
|
A:HOH845
|
4.9
|
53.6
|
1.0
|
N
|
A:ALA325
|
4.9
|
44.2
|
1.0
|
CA
|
A:ASP246
|
4.9
|
41.1
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 2 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn602
b:43.9
occ:1.00
|
O
|
D:HOH787
|
2.2
|
41.6
|
1.0
|
NE2
|
F:HIS155
|
2.2
|
38.2
|
1.0
|
O
|
D:HOH758
|
2.2
|
48.2
|
1.0
|
NE2
|
A:HIS155
|
2.2
|
40.8
|
1.0
|
NE2
|
D:HIS155
|
2.2
|
39.6
|
1.0
|
O
|
F:HOH809
|
2.3
|
50.6
|
1.0
|
CD2
|
D:HIS155
|
2.9
|
45.4
|
1.0
|
CD2
|
A:HIS155
|
3.1
|
47.3
|
1.0
|
CE1
|
F:HIS155
|
3.1
|
40.1
|
1.0
|
CD2
|
F:HIS155
|
3.2
|
35.2
|
1.0
|
CE1
|
A:HIS155
|
3.3
|
49.4
|
1.0
|
CE1
|
D:HIS155
|
3.4
|
44.8
|
1.0
|
O
|
A:HOH824
|
4.2
|
59.0
|
1.0
|
CG
|
D:HIS155
|
4.2
|
42.7
|
1.0
|
ND1
|
F:HIS155
|
4.3
|
41.1
|
1.0
|
OE1
|
D:GLN187
|
4.3
|
50.1
|
1.0
|
CG
|
A:HIS155
|
4.3
|
51.9
|
1.0
|
CG
|
F:HIS155
|
4.3
|
40.8
|
1.0
|
ND1
|
A:HIS155
|
4.3
|
49.6
|
1.0
|
ND1
|
D:HIS155
|
4.4
|
52.2
|
1.0
|
O
|
D:HOH797
|
4.8
|
52.6
|
1.0
|
CD
|
D:GLN187
|
4.8
|
60.3
|
1.0
|
CG
|
F:GLN154
|
4.9
|
37.9
|
1.0
|
CD
|
D:GLN154
|
5.0
|
40.4
|
1.0
|
CD
|
F:GLN154
|
5.0
|
43.1
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 3 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn601
b:51.7
occ:1.00
|
O
|
B:HOH746
|
1.9
|
46.6
|
1.0
|
NE2
|
B:HIS312
|
2.2
|
33.9
|
1.0
|
SG
|
B:CYS244
|
2.3
|
51.8
|
1.0
|
SG
|
B:CYS323
|
2.3
|
52.0
|
1.0
|
O
|
B:HOH811
|
3.1
|
48.4
|
1.0
|
CE1
|
B:HIS312
|
3.1
|
44.7
|
1.0
|
CD2
|
B:HIS312
|
3.2
|
35.2
|
1.0
|
CB
|
B:CYS323
|
3.2
|
41.0
|
1.0
|
CB
|
B:CYS244
|
3.4
|
40.2
|
1.0
|
CA
|
B:CYS323
|
3.6
|
48.9
|
1.0
|
O
|
B:HOH793
|
3.7
|
51.5
|
1.0
|
CB
|
B:ASP246
|
4.1
|
49.9
|
1.0
|
OD2
|
B:ASP246
|
4.2
|
58.0
|
1.0
|
N
|
B:GLY271
|
4.2
|
43.1
|
1.0
|
ND1
|
B:HIS312
|
4.2
|
45.9
|
1.0
|
C
|
B:CYS323
|
4.3
|
49.8
|
1.0
|
CG
|
B:HIS312
|
4.3
|
38.0
|
1.0
|
N
|
B:ALA324
|
4.4
|
46.5
|
1.0
|
CA
|
B:GLY271
|
4.4
|
39.0
|
1.0
|
CG
|
B:ASP246
|
4.7
|
57.5
|
1.0
|
CA
|
B:CYS244
|
4.8
|
45.5
|
1.0
|
O
|
B:HOH813
|
4.8
|
51.9
|
1.0
|
N
|
B:CYS323
|
4.8
|
53.7
|
1.0
|
N
|
B:ALA325
|
4.8
|
54.3
|
1.0
|
CB
|
B:ALA325
|
4.9
|
55.0
|
1.0
|
N
|
B:ASP246
|
5.0
|
49.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 4 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn602
b:46.1
occ:1.00
|
O
|
E:HOH780
|
2.0
|
41.2
|
1.0
|
O
|
E:HOH736
|
2.2
|
48.3
|
1.0
|
O
|
C:HOH782
|
2.2
|
45.2
|
1.0
|
NE2
|
B:HIS155
|
2.2
|
46.0
|
1.0
|
NE2
|
C:HIS155
|
2.2
|
38.4
|
1.0
|
NE2
|
E:HIS155
|
2.3
|
42.9
|
1.0
|
CD2
|
B:HIS155
|
3.0
|
36.5
|
1.0
|
CD2
|
E:HIS155
|
3.1
|
41.9
|
1.0
|
CD2
|
C:HIS155
|
3.1
|
44.5
|
1.0
|
CE1
|
C:HIS155
|
3.3
|
49.4
|
1.0
|
CE1
|
B:HIS155
|
3.3
|
41.1
|
1.0
|
CE1
|
E:HIS155
|
3.3
|
41.1
|
1.0
|
NE2
|
E:GLN187
|
3.9
|
70.1
|
1.0
|
CG
|
B:HIS155
|
4.3
|
47.6
|
1.0
|
CG
|
E:HIS155
|
4.3
|
46.1
|
1.0
|
CG
|
C:HIS155
|
4.3
|
44.4
|
1.0
|
ND1
|
B:HIS155
|
4.3
|
47.0
|
1.0
|
ND1
|
C:HIS155
|
4.4
|
42.8
|
1.0
|
ND1
|
E:HIS155
|
4.4
|
45.7
|
1.0
|
O
|
C:HOH721
|
4.7
|
61.8
|
1.0
|
CD
|
B:GLN154
|
4.8
|
48.5
|
1.0
|
OE1
|
B:GLN154
|
4.9
|
45.1
|
1.0
|
CD
|
C:GLN154
|
4.9
|
46.5
|
1.0
|
CG
|
B:GLN154
|
5.0
|
42.3
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 5 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn601
b:55.6
occ:1.00
|
CE1
|
C:HIS312
|
1.8
|
58.6
|
1.0
|
SG
|
C:CYS323
|
2.3
|
51.6
|
1.0
|
SG
|
C:CYS244
|
2.3
|
48.1
|
1.0
|
NE2
|
C:HIS312
|
2.4
|
53.6
|
1.0
|
ND1
|
C:HIS312
|
3.0
|
62.9
|
1.0
|
O
|
C:HOH735
|
3.0
|
65.7
|
1.0
|
CB
|
C:CYS323
|
3.2
|
47.0
|
1.0
|
CB
|
C:CYS244
|
3.3
|
54.4
|
1.0
|
O1
|
C:CO2606
|
3.3
|
56.1
|
1.0
|
CA
|
C:CYS323
|
3.4
|
55.0
|
1.0
|
CD2
|
C:HIS312
|
3.6
|
49.5
|
1.0
|
OD2
|
C:ASP246
|
3.6
|
63.1
|
1.0
|
CB
|
C:ASP246
|
3.7
|
54.1
|
1.0
|
O
|
C:HOH788
|
3.7
|
47.1
|
1.0
|
CG
|
C:HIS312
|
3.9
|
55.5
|
1.0
|
C
|
C:CO2606
|
4.0
|
67.2
|
1.0
|
C
|
C:CYS323
|
4.2
|
58.5
|
1.0
|
CG
|
C:ASP246
|
4.2
|
53.9
|
1.0
|
N
|
C:ALA324
|
4.2
|
60.4
|
1.0
|
N
|
C:GLY271
|
4.6
|
44.9
|
1.0
|
N
|
C:CYS323
|
4.7
|
53.9
|
1.0
|
CA
|
C:CYS244
|
4.7
|
56.5
|
1.0
|
N
|
C:ALA325
|
4.8
|
61.5
|
1.0
|
CB
|
C:ALA325
|
4.8
|
57.8
|
1.0
|
O2
|
C:CO2606
|
4.9
|
62.3
|
1.0
|
CA
|
C:GLY271
|
4.9
|
51.1
|
1.0
|
N
|
C:ASP246
|
4.9
|
44.1
|
1.0
|
CA
|
C:ASP246
|
4.9
|
52.2
|
1.0
|
O
|
C:GLY322
|
5.0
|
62.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 6 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn601
b:47.6
occ:1.00
|
NE2
|
D:HIS312
|
2.2
|
44.4
|
1.0
|
SG
|
D:CYS323
|
2.3
|
45.2
|
1.0
|
SG
|
D:CYS244
|
2.3
|
45.9
|
1.0
|
O
|
D:HOH704
|
2.5
|
46.8
|
1.0
|
CB
|
D:CYS323
|
3.1
|
61.0
|
1.0
|
CD2
|
D:HIS312
|
3.1
|
43.6
|
1.0
|
CE1
|
D:HIS312
|
3.2
|
46.7
|
1.0
|
CB
|
D:CYS244
|
3.4
|
41.4
|
1.0
|
O2
|
D:CO2607
|
3.4
|
55.6
|
1.0
|
CA
|
D:CYS323
|
3.5
|
52.2
|
1.0
|
O
|
D:HOH804
|
3.8
|
41.6
|
1.0
|
CB
|
D:ASP246
|
4.0
|
43.1
|
1.0
|
OD2
|
D:ASP246
|
4.1
|
47.1
|
1.0
|
C
|
D:CYS323
|
4.2
|
53.7
|
1.0
|
N
|
D:ALA324
|
4.2
|
55.0
|
1.0
|
CG
|
D:HIS312
|
4.3
|
42.2
|
1.0
|
ND1
|
D:HIS312
|
4.3
|
47.0
|
1.0
|
N
|
D:GLY271
|
4.3
|
37.8
|
1.0
|
CG
|
D:ASP246
|
4.5
|
52.2
|
1.0
|
CA
|
D:GLY271
|
4.6
|
39.5
|
1.0
|
C
|
D:CO2607
|
4.6
|
70.0
|
1.0
|
N
|
D:ALA325
|
4.7
|
53.1
|
1.0
|
N
|
D:CYS323
|
4.7
|
54.7
|
1.0
|
CA
|
D:CYS244
|
4.8
|
40.8
|
1.0
|
CB
|
D:ALA325
|
4.8
|
52.5
|
1.0
|
N
|
D:ASP246
|
4.9
|
45.1
|
1.0
|
CA
|
D:ASP246
|
5.0
|
43.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8thm
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Zinc Binding Sites List in 8thm
Zinc binding site 7 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_07.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn601
b:46.5
occ:1.00
|
NE2
|
E:HIS312
|
2.2
|
37.5
|
1.0
|
O
|
E:HOH792
|
2.3
|
47.4
|
1.0
|
SG
|
E:CYS244
|
2.3
|
48.2
|
1.0
|
SG
|
E:CYS323
|
2.3
|
48.2
|
1.0
|
CE1
|
E:HIS312
|
3.1
|
45.1
|
1.0
|
CB
|
E:CYS323
|
3.1
|
47.9
|
1.0
|
CD2
|
E:HIS312
|
3.2
|
38.0
|
1.0
|
CB
|
E:CYS244
|
3.3
|
38.7
|
1.0
|
CA
|
E:CYS323
|
3.4
|
53.5
|
1.0
|
O
|
E:HOH806
|
3.6
|
53.5
|
1.0
|
O
|
E:HOH803
|
3.8
|
47.6
|
1.0
|
CB
|
E:ASP246
|
3.9
|
43.8
|
1.0
|
C
|
E:CYS323
|
4.1
|
52.3
|
1.0
|
OD2
|
E:ASP246
|
4.1
|
48.3
|
1.0
|
N
|
E:ALA324
|
4.2
|
55.2
|
1.0
|
ND1
|
E:HIS312
|
4.2
|
51.8
|
1.0
|
N
|
E:GLY271
|
4.3
|
44.5
|
1.0
|
CG
|
E:HIS312
|
4.3
|
44.7
|
1.0
|
CA
|
E:GLY271
|
4.5
|
45.5
|
1.0
|
CG
|
E:ASP246
|
4.5
|
47.1
|
1.0
|
O
|
E:HOH778
|
4.6
|
58.2
|
1.0
|
N
|
E:CYS323
|
4.7
|
51.4
|
1.0
|
N
|
E:ALA325
|
4.7
|
52.4
|
1.0
|
CA
|
E:CYS244
|
4.8
|
39.7
|
1.0
|
N
|
E:ASP246
|
4.8
|
45.2
|
1.0
|
CA
|
E:ASP246
|
4.9
|
45.1
|
1.0
|
O
|
E:CYS323
|
4.9
|
54.1
|
1.0
|
CB
|
E:ALA325
|
4.9
|
50.7
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8thm
Go back to
Zinc Binding Sites List in 8thm
Zinc binding site 8 out
of 8 in the Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_08.jpg) Mono view
![](/pictures/ZN/pdb/th/8thm-ZN-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Beta Carbonic Anhydrase From the Carboxysome of Cyanobium Pcc 7001 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn601
b:45.6
occ:1.00
|
NE2
|
F:HIS312
|
2.3
|
45.4
|
1.0
|
SG
|
F:CYS323
|
2.3
|
39.9
|
1.0
|
SG
|
F:CYS244
|
2.3
|
41.7
|
1.0
|
O
|
F:HOH783
|
2.3
|
42.6
|
1.0
|
CD2
|
F:HIS312
|
2.9
|
46.2
|
1.0
|
CB
|
F:CYS323
|
3.1
|
42.4
|
1.0
|
CB
|
F:CYS244
|
3.3
|
38.6
|
1.0
|
CE1
|
F:HIS312
|
3.4
|
49.5
|
1.0
|
O
|
F:HOH826
|
3.4
|
47.5
|
1.0
|
CA
|
F:CYS323
|
3.5
|
49.5
|
1.0
|
O
|
F:HOH828
|
3.8
|
41.9
|
1.0
|
CB
|
F:ASP246
|
3.9
|
36.8
|
1.0
|
CG
|
F:HIS312
|
4.2
|
43.7
|
1.0
|
N
|
F:ALA324
|
4.2
|
51.4
|
1.0
|
OD2
|
F:ASP246
|
4.2
|
42.8
|
1.0
|
C
|
F:CYS323
|
4.2
|
57.3
|
1.0
|
ND1
|
F:HIS312
|
4.3
|
42.3
|
1.0
|
N
|
F:GLY271
|
4.4
|
36.9
|
1.0
|
CG
|
F:ASP246
|
4.6
|
49.7
|
1.0
|
CA
|
F:GLY271
|
4.6
|
42.7
|
1.0
|
N
|
F:CYS323
|
4.7
|
45.6
|
1.0
|
CA
|
F:CYS244
|
4.7
|
43.2
|
1.0
|
N
|
F:ASP246
|
4.8
|
37.7
|
1.0
|
N
|
F:ALA325
|
4.9
|
51.7
|
1.0
|
CA
|
F:ASP246
|
4.9
|
45.2
|
1.0
|
|
Reference:
S.B.Pulsford,
M.A.Outram,
B.Forster,
C.J.Jackson,
T.Rhodes,
S.J.Williams,
G.D.Price,
M.R.Badger,
B.M.Long.
Alpha-Cyanobacterial Carbonic Anhydrase Is Allosterically Regulated By the Rubisco Substrate Ribulose 1,5-Bisphosphate (Rubp) To Be Published.
Page generated: Thu Dec 28 13:42:25 2023
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