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Sodium in PDB 3czj: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One, PDB code: 3czj was solved by R.E.Huber, M.L.Dugdale, M.E.Fraser, S.D.Tammam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.05 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.443, 161.643, 202.155, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 3czj:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One (pdb code 3czj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One, PDB code: 3czj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 3czj

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Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:12.1
occ:1.00
 OD1 A:ASN604 2.3 9.5 1.0
O6 A:1492001 2.3 20.6 1.0
OD2 A:ASP201 2.4 13.2 1.0
O A:PHE601 2.4 17.3 1.0
O A:HOH8928 2.4 14.5 1.0
CG A:ASN604 3.3 12.3 1.0
CD1 A:PHE601 3.4 22.1 1.0
CG A:ASP201 3.4 14.4 1.0
CE1 A:PHE601 3.5 22.4 1.0
C6 A:1492001 3.5 20.1 1.0
C A:PHE601 3.6 17.2 1.0
ND2 A:ASN604 3.7 9.8 1.0
OH A:TYR100 3.9 13.5 1.0
OD1 A:ASP201 3.9 16.1 1.0
O4 A:1492001 4.0 16.5 1.0
CG A:PHE601 4.0 21.2 1.0
C4 A:1492001 4.0 18.5 1.0
NE1 A:TRP568 4.1 5.9 1.0
CZ A:PHE601 4.2 22.5 1.0
C5 A:1492001 4.3 18.4 1.0
CA A:CYS602 4.4 14.5 1.0
NE2 A:HIS540 4.4 9.9 1.0
N A:CYS602 4.4 14.8 1.0
O A:HOH8747 4.5 9.4 1.0
CB A:ASP201 4.6 13.2 1.0
CD2 A:PHE601 4.6 21.3 1.0
CA A:PHE601 4.6 17.1 1.0
CB A:PHE601 4.7 18.6 1.0
CB A:ASN604 4.7 9.9 1.0
CE2 A:PHE601 4.7 23.2 1.0
O A:ASP201 4.7 13.9 1.0
C A:CYS602 4.8 13.9 1.0
CE2 A:TRP568 4.9 6.1 1.0
CZ2 A:TRP568 5.0 6.8 1.0

Sodium binding site 2 out of 16 in 3czj

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Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:9.8
occ:1.00
 O A:TYR559 2.1 7.7 1.0
O A:LEU562 2.2 8.6 1.0
O A:PHE556 2.3 9.4 1.0
O A:HOH9127 2.8 19.4 1.0
O A:PRO560 3.1 7.8 1.0
C A:TYR559 3.2 8.1 1.0
C A:LEU562 3.3 6.9 1.0
C A:PHE556 3.5 8.9 1.0
C A:PRO560 3.5 8.0 1.0
CA A:PRO560 3.6 7.2 1.0
N A:PRO560 3.8 7.2 1.0
N A:LEU562 3.8 5.7 1.0
O A:HOH8934 4.0 15.3 1.0
CA A:LEU562 4.1 7.0 1.0
N A:GLN563 4.2 7.1 1.0
CA A:PHE556 4.2 8.8 1.0
CA A:GLN563 4.3 7.2 1.0
CB A:LEU562 4.3 5.9 1.0
O A:HOH8865 4.3 24.1 1.0
CA A:TYR559 4.4 9.0 1.0
N A:ARG561 4.4 6.5 1.0
N A:TYR559 4.5 9.8 1.0
N A:ARG557 4.5 10.3 1.0
CG A:GLN563 4.6 6.1 1.0
C A:ARG561 4.7 6.8 1.0
CA A:ARG557 4.7 9.9 1.0
CD1 A:LEU350 4.8 7.0 1.0
C A:ARG557 4.8 9.6 1.0
CB A:PHE556 4.8 6.4 1.0
O A:ALA555 4.9 7.9 1.0
O A:ARG557 4.9 8.2 1.0
CB A:TYR559 4.9 10.8 1.0

Sodium binding site 3 out of 16 in 3czj

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Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:20.2
occ:1.00
 O A:LEU967 2.5 17.2 1.0
O A:PRO932 2.5 10.7 1.0
O A:HOH9165 2.7 46.2 1.0
O A:THR970 2.7 23.0 1.0
O A:HOH8874 2.8 11.2 1.0
CZ A:PHE931 3.4 17.5 1.0
C A:PRO932 3.5 12.1 1.0
C A:LEU967 3.6 18.4 1.0
CE1 A:PHE931 3.6 17.5 1.0
CA A:MET968 3.7 22.8 1.0
O A:HOH9081 3.8 34.3 1.0
O A:MET968 3.8 23.8 1.0
C A:THR970 3.8 23.1 1.0
C A:MET968 3.8 23.4 1.0
CE2 A:PHE931 3.9 16.2 1.0
CB A:PRO932 4.0 13.2 1.0
CA A:PRO932 4.1 12.0 1.0
N A:MET968 4.1 19.9 1.0
N A:PRO932 4.2 13.8 1.0
CD1 A:PHE931 4.3 17.8 1.0
CD A:PRO932 4.3 12.6 1.0
N A:THR970 4.3 23.3 1.0
N A:SER933 4.5 10.0 1.0
CD2 A:PHE931 4.5 17.7 1.0
N A:GLU969 4.6 22.4 1.0
CA A:THR970 4.6 23.1 1.0
CG A:PHE931 4.7 16.8 1.0
CG A:PRO932 4.7 14.9 1.0
N A:SER971 4.8 21.8 1.0
CA A:LEU967 4.8 16.9 1.0
CA A:SER933 4.8 11.4 1.0
CA A:SER971 4.9 20.6 1.0
C A:PHE931 4.9 13.9 1.0
CB A:MET968 4.9 24.5 1.0

Sodium binding site 4 out of 16 in 3czj

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Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:27.0
occ:1.00
 O A:SER647 2.5 18.9 1.0
O A:GLU650 2.8 17.9 1.0
O A:LEU670 2.9 23.1 1.0
N A:GLU650 3.3 17.3 1.0
C A:ASP648 3.5 19.7 1.0
N A:ASN649 3.6 19.0 1.0
C A:SER647 3.6 19.6 1.0
CA A:ASP648 3.7 20.5 1.0
C A:GLU650 3.7 18.0 1.0
O A:ASP648 3.9 18.9 1.0
CA A:GLU650 4.0 17.5 1.0
C A:LEU670 4.1 23.4 1.0
N A:ASP648 4.1 19.6 1.0
CA A:ASN649 4.2 17.9 1.0
C A:ASN649 4.2 19.3 1.0
N A:LEU670 4.3 24.6 1.0
CB A:GLU650 4.6 15.9 1.0
CA A:LEU670 4.7 23.9 1.0
OG A:SER647 4.7 19.1 1.0
OE1 A:GLU650 4.7 14.3 1.0
CB A:LEU670 4.8 25.6 1.0
CA A:SER647 4.9 18.9 1.0
CB A:SER647 4.9 18.7 1.0
N A:LEU651 5.0 18.2 1.0

Sodium binding site 5 out of 16 in 3czj

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Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:14.3
occ:1.00
 OD1 B:ASN604 2.3 7.5 1.0
OD2 B:ASP201 2.4 13.1 1.0
O B:HOH9456 2.4 16.8 1.0
O B:PHE601 2.4 11.8 1.0
O6 B:1492001 2.4 14.6 1.0
CG B:ASN604 3.3 9.3 1.0
CG B:ASP201 3.3 11.3 1.0
CD2 B:PHE601 3.5 19.2 1.0
CE2 B:PHE601 3.6 20.1 1.0
C B:PHE601 3.6 13.6 1.0
C6 B:1492001 3.6 17.1 1.0
ND2 B:ASN604 3.7 6.3 1.0
OD1 B:ASP201 3.7 12.2 1.0
OH B:TYR100 3.9 14.6 1.0
O4 B:1492001 4.0 15.9 1.0
C4 B:1492001 4.0 15.9 1.0
CG B:PHE601 4.1 17.2 1.0
NE1 B:TRP568 4.2 4.8 1.0
CA B:CYS602 4.3 11.9 1.0
CZ B:PHE601 4.3 20.0 1.0
C5 B:1492001 4.4 17.2 1.0
N B:CYS602 4.4 13.0 1.0
O B:HOH9259 4.5 13.1 1.0
NE2 B:HIS540 4.5 7.3 1.0
CB B:ASP201 4.5 9.6 1.0
CA B:PHE601 4.7 14.4 1.0
CB B:ASN604 4.7 8.8 1.0
CB B:PHE601 4.7 15.1 1.0
C B:CYS602 4.7 10.5 1.0
O B:ASP201 4.7 8.9 1.0
CD1 B:PHE601 4.8 17.2 1.0
CE1 B:PHE601 4.9 18.0 1.0
CE2 B:TRP568 4.9 6.2 1.0

Sodium binding site 6 out of 16 in 3czj

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Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:11.2
occ:1.00
 O B:TYR559 2.1 9.8 1.0
O B:LEU562 2.2 7.3 1.0
O B:PHE556 2.3 7.6 1.0
O B:HOH9548 2.5 24.9 1.0
O B:HOH9663 2.8 24.2 1.0
C B:TYR559 3.2 9.2 1.0
O B:PRO560 3.2 8.3 1.0
C B:LEU562 3.3 6.7 1.0
C B:PHE556 3.4 7.0 1.0
C B:PRO560 3.5 7.6 1.0
CA B:PRO560 3.6 8.0 1.0
N B:PRO560 3.8 8.3 1.0
N B:LEU562 3.9 2.9 1.0
O B:HOH9463 4.0 15.2 1.0
CA B:LEU562 4.1 5.9 1.0
CA B:PHE556 4.2 6.0 1.0
N B:GLN563 4.2 4.1 1.0
CB B:LEU562 4.2 5.0 1.0
CA B:GLN563 4.3 5.5 1.0
CA B:TYR559 4.3 10.4 1.0
N B:ARG561 4.5 5.0 1.0
N B:TYR559 4.5 9.4 1.0
N B:ARG557 4.5 6.8 1.0
CA B:ARG557 4.7 7.3 1.0
CG B:GLN563 4.7 5.8 1.0
C B:ARG561 4.8 5.4 1.0
CD1 B:LEU350 4.8 7.1 1.0
C B:ARG557 4.8 6.4 1.0
CB B:PHE556 4.8 4.4 1.0
CB B:TYR559 4.9 9.4 1.0
O B:ALA555 4.9 7.8 1.0
O B:ARG557 4.9 5.9 1.0

Sodium binding site 7 out of 16 in 3czj

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Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:27.1
occ:1.00
 O B:PRO932 2.5 11.2 1.0
O B:LEU967 2.6 17.1 1.0
O B:THR970 2.7 19.6 1.0
O B:HOH9396 2.8 24.0 1.0
CZ B:PHE931 3.3 16.8 1.0
C B:PRO932 3.5 10.3 1.0
CE1 B:PHE931 3.6 16.7 1.0
O B:HOH9701 3.6 35.6 1.0
O B:HOH9624 3.7 34.2 1.0
C B:LEU967 3.7 15.2 1.0
C B:THR970 3.8 19.8 1.0
CA B:MET968 3.8 19.5 1.0
CE2 B:PHE931 3.9 13.8 1.0
CB B:PRO932 3.9 13.3 1.0
C B:MET968 4.0 19.0 1.0
O B:MET968 4.0 19.5 1.0
CA B:PRO932 4.0 12.5 1.0
N B:PRO932 4.2 12.6 1.0
CD B:PRO932 4.2 12.4 1.0
CD1 B:PHE931 4.2 15.6 1.0
N B:MET968 4.3 17.3 1.0
N B:THR970 4.3 20.6 1.0
CD2 B:PHE931 4.5 14.2 1.0
N B:SER933 4.5 11.0 1.0
CG B:PRO932 4.6 13.7 1.0
CA B:THR970 4.6 20.0 1.0
CG B:PHE931 4.6 14.2 1.0
N B:GLU969 4.6 19.3 1.0
N B:SER971 4.7 18.2 1.0
CA B:SER971 4.7 18.7 1.0
CA B:SER933 4.8 10.1 1.0
C B:PHE931 4.9 12.8 1.0
CA B:LEU967 4.9 14.9 1.0

Sodium binding site 8 out of 16 in 3czj

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Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:19.6
occ:1.00
 O B:SER647 2.4 12.7 1.0
O B:DMS8425 2.5 76.6 1.0
O B:GLU650 2.6 16.4 1.0
O B:LEU670 2.7 24.1 1.0
O B:HOH9706 3.1 27.4 1.0
C2 B:DMS8425 3.1 76.6 1.0
N B:GLU650 3.2 12.3 1.0
S B:DMS8425 3.2 77.1 1.0
C B:SER647 3.6 14.9 1.0
C B:GLU650 3.6 15.7 1.0
N B:ASN649 3.6 11.8 1.0
C B:ASP648 3.7 13.8 1.0
C1 B:DMS8425 3.7 76.9 1.0
CA B:ASP648 3.8 15.7 1.0
CA B:GLU650 3.9 14.4 1.0
C B:LEU670 3.9 23.8 1.0
N B:LEU670 4.1 24.8 1.0
N B:ASP648 4.1 14.1 1.0
C B:ASN649 4.2 12.7 1.0
CA B:ASN649 4.3 11.9 1.0
O B:ASP648 4.3 13.0 1.0
CB B:GLU650 4.3 12.3 1.0
CA B:LEU670 4.4 25.0 1.0
OG B:SER647 4.5 11.2 1.0
CB B:LEU670 4.6 25.2 1.0
OE1 B:GLU650 4.7 12.9 1.0
CB B:SER647 4.7 14.6 1.0
CA B:SER647 4.8 13.4 1.0
N B:LEU651 4.8 17.0 1.0
N B:ASP671 5.0 23.6 1.0

Sodium binding site 9 out of 16 in 3czj

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Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:12.8
occ:1.00
 OD2 C:ASP201 2.3 11.4 1.0
O6 C:1492001 2.4 16.9 1.0
OD1 C:ASN604 2.4 7.2 1.0
O C:HOH8766 2.5 15.8 1.0
O C:PHE601 2.5 9.7 1.0
CD1 C:PHE601 3.3 16.6 1.0
CE1 C:PHE601 3.3 17.0 1.0
CG C:ASP201 3.3 11.1 1.0
CG C:ASN604 3.4 8.6 1.0
C6 C:1492001 3.6 16.5 1.0
C C:PHE601 3.7 10.2 1.0
ND2 C:ASN604 3.8 10.9 1.0
OD1 C:ASP201 3.8 12.4 1.0
O4 C:1492001 3.9 11.4 1.0
OH C:TYR100 4.0 13.9 1.0
C4 C:1492001 4.0 13.9 1.0
CG C:PHE601 4.0 15.1 1.0
CZ C:PHE601 4.1 16.9 1.0
NE1 C:TRP568 4.2 5.1 1.0
C5 C:1492001 4.3 16.5 1.0
CA C:CYS602 4.4 10.9 1.0
NE2 C:HIS540 4.5 8.9 1.0
N C:CYS602 4.5 10.2 1.0
O C:HOH8568 4.5 7.4 1.0
CB C:ASP201 4.5 10.3 1.0
CD2 C:PHE601 4.6 14.4 1.0
CE2 C:PHE601 4.7 15.8 1.0
CA C:PHE601 4.7 12.0 1.0
CB C:PHE601 4.7 12.7 1.0
CB C:ASN604 4.8 9.6 1.0
O C:ASP201 4.8 9.9 1.0
C C:CYS602 4.9 10.2 1.0
CE2 C:TRP568 4.9 6.8 1.0

Sodium binding site 10 out of 16 in 3czj

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Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:10.0
occ:1.00
 O C:TYR559 2.2 9.2 1.0
O C:PHE556 2.2 9.2 1.0
O C:LEU562 2.3 5.6 1.0
O C:HOH8857 2.5 18.8 1.0
O C:HOH9202 2.7 24.3 1.0
C C:TYR559 3.2 9.1 1.0
O C:PRO560 3.2 10.8 1.0
C C:LEU562 3.3 5.1 1.0
C C:PHE556 3.4 8.7 1.0
C C:PRO560 3.6 9.0 1.0
CA C:PRO560 3.6 8.5 1.0
N C:PRO560 3.9 9.2 1.0
N C:LEU562 3.9 3.4 1.0
O C:HOH8772 4.1 16.4 1.0
CA C:PHE556 4.1 6.3 1.0
CA C:LEU562 4.1 4.9 1.0
O C:HOH8656 4.2 46.1 1.0
N C:GLN563 4.2 4.3 1.0
CB C:LEU562 4.3 4.1 1.0
CA C:GLN563 4.3 5.0 1.0
CA C:TYR559 4.3 9.2 1.0
N C:ARG557 4.4 7.5 1.0
N C:TYR559 4.5 7.3 1.0
N C:ARG561 4.5 5.7 1.0
CD1 C:LEU350 4.6 7.0 1.0
CA C:ARG557 4.6 7.7 1.0
C C:ARG557 4.8 6.5 1.0
CG C:GLN563 4.8 6.3 1.0
CB C:PHE556 4.8 6.0 1.0
C C:ARG561 4.8 6.1 1.0
O C:ALA555 4.8 6.3 1.0
O C:ARG557 4.9 6.7 1.0
CB C:TYR559 4.9 9.1 1.0

Reference:

J.C.Kappelhoff, S.Y.Liu, M.L.Dugdale, D.L.Dymianiw, L.R.Linton, R.E.Huber. Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-Beta-Galactosidase (E. Coli) As Examples. Protein J. V. 28 96 2009.
ISSN: ISSN 1572-3887
PubMed: 19229596
DOI: 10.1007/S10930-009-9168-1
Page generated: Mon Oct 7 08:08:43 2024

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