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Sodium in PDB 3vdb: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone, PDB code: 3vdb was solved by R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber, 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 (%) 15.7 / 20.5

Other elements in 3vdb:

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

Magnesium (Mg) 9 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone (pdb code 3vdb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone, PDB code: 3vdb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 3vdb

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Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:17.6
occ:1.00
 OD1 A:ASN604 2.3 14.8 1.0
OD2 A:ASP201 2.3 22.6 1.0
O A:HOH4218 2.3 18.3 1.0
O A:PHE601 2.4 23.6 1.0
O6 A:1492001 2.4 25.6 1.0
CG A:ASP201 3.3 21.2 1.0
CG A:ASN604 3.3 18.8 1.0
C6 A:1492001 3.5 28.1 1.0
CD1 A:PHE601 3.5 30.1 1.0
C A:PHE601 3.6 23.8 1.0
ND2 A:ASN604 3.7 17.2 1.0
CE1 A:PHE601 3.7 30.4 1.0
OD1 A:ASP201 3.7 24.9 1.0
OH A:TYR100 3.8 21.1 1.0
O4 A:1492001 4.0 20.7 1.0
C4 A:1492001 4.1 26.3 1.0
NE1 A:TRP568 4.1 17.3 1.0
CG A:PHE601 4.2 28.5 1.0
C5 A:1492001 4.3 25.6 1.0
CA A:CYS602 4.3 19.0 1.0
N A:CYS602 4.4 20.7 1.0
O A:HOH4038 4.4 15.7 1.0
CZ A:PHE601 4.4 31.9 1.0
CB A:ASP201 4.5 19.4 1.0
NE2 A:HIS540 4.5 15.5 1.0
CA A:PHE601 4.7 24.0 1.0
CB A:ASN604 4.7 14.8 1.0
O A:ASP201 4.7 20.1 1.0
CB A:PHE601 4.7 24.4 1.0
CD2 A:PHE601 4.8 24.6 1.0
C A:CYS602 4.8 19.3 1.0
CE2 A:TRP568 4.9 16.0 1.0
CE2 A:PHE601 4.9 33.5 1.0
CZ A:TYR100 4.9 24.4 1.0
CZ2 A:TRP568 5.0 16.5 1.0

Sodium binding site 2 out of 14 in 3vdb

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Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:19.2
occ:1.00
 O A:LEU562 2.4 16.9 1.0
O A:PHE556 2.4 18.5 1.0
O A:TYR559 2.4 18.5 1.0
O A:HOH4557 2.4 25.4 1.0
O A:HOH4403 2.5 27.8 1.0
O A:PRO560 3.1 14.2 1.0
C A:LEU562 3.4 13.6 1.0
C A:TYR559 3.4 15.9 1.0
C A:PHE556 3.5 16.1 1.0
C A:PRO560 3.6 16.9 1.0
CA A:PRO560 3.7 14.8 1.0
N A:PRO560 4.0 15.4 1.0
O A:HOH4223 4.0 19.2 1.0
N A:LEU562 4.0 12.3 1.0
O A:HOH4154 4.0 35.0 1.0
CA A:LEU562 4.2 14.6 1.0
N A:GLN563 4.3 14.5 1.0
CA A:PHE556 4.3 15.8 1.0
CA A:GLN563 4.3 12.3 1.0
CB A:LEU562 4.5 11.3 1.0
CA A:TYR559 4.5 15.7 1.0
N A:ARG561 4.5 12.8 1.0
N A:TYR559 4.6 15.7 1.0
N A:ARG557 4.6 19.5 1.0
CG A:GLN563 4.6 11.8 1.0
CD1 A:LEU350 4.6 13.0 1.0
CA A:ARG557 4.7 17.3 1.0
C A:ARG557 4.8 18.2 1.0
O A:ARG557 4.8 17.8 1.0
C A:ARG561 4.9 14.8 1.0
CB A:PHE556 4.9 13.4 1.0
O A:ALA555 5.0 14.8 1.0

Sodium binding site 3 out of 14 in 3vdb

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Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:25.6
occ:1.00
 O A:LEU967 2.4 23.1 1.0
O A:PRO932 2.4 19.4 1.0
O A:THR970 2.7 32.6 1.0
O A:HOH4164 2.7 22.2 1.0
C A:PRO932 3.4 19.5 1.0
C A:LEU967 3.5 25.1 1.0
CZ A:PHE931 3.6 29.9 1.0
O A:HOH4359 3.6 41.7 1.0
CA A:MET968 3.7 30.2 1.0
O A:MET968 3.8 32.8 1.0
CE1 A:PHE931 3.8 27.0 1.0
C A:THR970 3.8 33.1 1.0
C A:MET968 3.9 32.6 1.0
CE2 A:PHE931 4.0 24.6 1.0
CB A:PRO932 4.0 21.2 1.0
N A:MET968 4.1 25.6 1.0
CA A:PRO932 4.1 18.4 1.0
CD A:PRO932 4.2 20.3 1.0
N A:PRO932 4.2 22.6 1.0
N A:THR970 4.3 31.2 1.0
CD1 A:PHE931 4.4 28.5 1.0
N A:SER933 4.5 14.1 1.0
CD2 A:PHE931 4.5 27.5 1.0
CG A:PRO932 4.6 25.0 1.0
CA A:THR970 4.6 31.8 1.0
N A:GLU969 4.7 28.9 1.0
CA A:LEU967 4.7 23.4 1.0
CG A:PHE931 4.7 27.0 1.0
CA A:SER933 4.8 19.8 1.0
N A:SER971 4.8 31.2 1.0
CA A:SER971 4.9 29.3 1.0
C A:PHE931 5.0 22.0 1.0

Sodium binding site 4 out of 14 in 3vdb

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Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:20.0
occ:1.00
 OD1 B:ASN604 2.3 15.8 1.0
O B:HOH4263 2.3 18.9 1.0
OD2 B:ASP201 2.3 23.7 1.0
O B:PHE601 2.4 19.6 1.0
O6 B:1492001 2.4 22.0 1.0
CG B:ASP201 3.2 18.7 1.0
CG B:ASN604 3.3 17.5 1.0
C B:PHE601 3.6 20.8 1.0
CD2 B:PHE601 3.6 29.9 1.0
OD1 B:ASP201 3.6 19.5 1.0
C6 B:1492001 3.7 26.7 1.0
ND2 B:ASN604 3.7 12.6 1.0
OH B:TYR100 3.7 20.2 1.0
CE2 B:PHE601 3.8 29.2 1.0
C4 B:1492001 4.1 24.5 1.0
O4 B:1492001 4.1 21.6 1.0
NE1 B:TRP568 4.2 13.2 1.0
CA B:CYS602 4.2 18.2 1.0
CG B:PHE601 4.2 23.1 1.0
O B:HOH4068 4.3 18.1 1.0
N B:CYS602 4.3 19.0 1.0
C5 B:1492001 4.4 26.9 1.0
CB B:ASP201 4.4 16.3 1.0
CZ B:PHE601 4.5 32.1 1.0
NE2 B:HIS540 4.6 13.9 1.0
O B:ASP201 4.6 17.7 1.0
CB B:ASN604 4.7 17.1 1.0
C B:CYS602 4.7 16.8 1.0
CA B:PHE601 4.7 22.2 1.0
CB B:PHE601 4.8 21.3 1.0
CZ B:TYR100 4.9 24.1 1.0
CD1 B:PHE601 4.9 16.9 1.0
CE2 B:TRP568 4.9 15.9 1.0
O B:CYS602 5.0 15.9 1.0
CZ2 B:TRP568 5.0 14.7 1.0

Sodium binding site 5 out of 14 in 3vdb

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Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:19.6
occ:1.00
 O B:HOH4352 2.3 30.5 1.0
O B:LEU562 2.4 17.5 1.0
O B:PHE556 2.4 16.3 1.0
O B:TYR559 2.4 18.3 1.0
O B:HOH4461 2.5 33.1 1.0
O B:PRO560 3.2 18.2 1.0
C B:LEU562 3.3 15.0 1.0
C B:TYR559 3.4 17.5 1.0
C B:PHE556 3.5 14.5 1.0
C B:PRO560 3.6 17.6 1.0
CA B:PRO560 3.7 16.2 1.0
O B:HOH4270 3.9 23.8 1.0
N B:PRO560 4.0 16.8 1.0
N B:LEU562 4.0 8.1 1.0
O B:HOH4921 4.1 51.2 1.0
CA B:LEU562 4.1 13.9 1.0
N B:GLN563 4.2 10.8 1.0
CA B:PHE556 4.2 12.0 1.0
CA B:GLN563 4.3 13.4 1.0
CB B:LEU562 4.4 11.9 1.0
CA B:TYR559 4.5 17.3 1.0
N B:ARG561 4.6 13.2 1.0
N B:TYR559 4.6 14.9 1.0
N B:ARG557 4.6 13.7 1.0
CD1 B:LEU350 4.7 14.6 1.0
CG B:GLN563 4.7 12.1 1.0
CA B:ARG557 4.8 15.4 1.0
C B:ARG557 4.9 15.4 1.0
C B:ARG561 4.9 11.4 1.0
CB B:PHE556 4.9 12.8 1.0
O B:ARG557 4.9 14.1 1.0
O B:ALA555 5.0 15.0 1.0

Sodium binding site 6 out of 14 in 3vdb

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Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:31.9
occ:1.00
 O B:LEU967 2.5 24.9 1.0
O B:PRO932 2.6 19.0 1.0
O B:THR970 2.6 27.2 1.0
O B:HOH4203 2.9 27.2 1.0
O B:HOH4497 3.3 40.3 1.0
O B:HOH4422 3.5 42.0 1.0
CZ B:PHE931 3.5 30.0 1.0
C B:PRO932 3.7 17.1 1.0
C B:LEU967 3.7 21.5 1.0
C B:THR970 3.7 29.3 1.0
CE1 B:PHE931 3.7 27.7 1.0
O B:MET968 3.9 27.2 1.0
CA B:MET968 3.9 25.4 1.0
C B:MET968 3.9 24.2 1.0
CE2 B:PHE931 4.0 18.1 1.0
CB B:PRO932 4.1 21.7 1.0
CD B:PRO932 4.2 20.6 1.0
N B:THR970 4.2 27.5 1.0
N B:MET968 4.3 22.7 1.0
CA B:PRO932 4.3 19.2 1.0
N B:PRO932 4.3 21.2 1.0
CD1 B:PHE931 4.4 25.6 1.0
CG B:PRO932 4.5 25.4 1.0
CA B:THR970 4.6 28.2 1.0
N B:GLU969 4.6 24.7 1.0
CD2 B:PHE931 4.6 19.2 1.0
N B:SER971 4.6 26.3 1.0
N B:SER933 4.7 18.0 1.0
CA B:SER971 4.7 28.4 1.0
CG B:PHE931 4.8 20.6 1.0
O B:HOH4237 4.9 42.4 1.0
CA B:LEU967 4.9 21.2 1.0
C B:GLU969 4.9 28.8 1.0
CA B:SER933 5.0 17.1 1.0

Sodium binding site 7 out of 14 in 3vdb

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Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:31.1
occ:1.00
 O B:DMS8015 2.4 50.2 1.0
O B:SER647 2.4 21.1 1.0
O B:LEU670 2.6 25.8 1.0
O B:GLU650 2.7 24.0 1.0
O B:HOH4502 2.8 34.1 1.0
N B:GLU650 3.4 19.4 1.0
S B:DMS8015 3.5 62.6 1.0
C B:SER647 3.5 24.5 1.0
C2 B:DMS8015 3.7 53.9 1.0
C B:GLU650 3.7 23.6 1.0
C B:LEU670 3.7 26.7 1.0
N B:ASN649 3.8 19.2 1.0
CA B:ASP648 3.8 24.8 1.0
C B:ASP648 3.9 21.8 1.0
CA B:GLU650 3.9 20.7 1.0
N B:LEU670 4.1 30.9 1.0
N B:ASP648 4.1 21.9 1.0
C1 B:DMS8015 4.1 56.9 1.0
CB B:GLU650 4.2 16.6 1.0
OG B:SER647 4.3 18.5 1.0
CA B:LEU670 4.3 30.9 1.0
C B:ASN649 4.4 21.0 1.0
CA B:ASN649 4.5 18.9 1.0
O B:ASP648 4.5 22.1 1.0
CB B:LEU670 4.6 32.9 1.0
CB B:SER647 4.8 22.2 1.0
CA B:SER647 4.8 21.3 1.0
OE1 B:GLU650 4.8 20.8 1.0
N B:ASP671 4.9 26.6 1.0
N B:LEU651 4.9 23.7 1.0

Sodium binding site 8 out of 14 in 3vdb

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Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:19.8
occ:1.00
 OD2 C:ASP201 2.3 19.3 1.0
OD1 C:ASN604 2.3 17.1 1.0
O C:HOH4258 2.3 19.8 1.0
O C:PHE601 2.4 16.2 1.0
O6 C:1492001 2.4 25.5 1.0
CG C:ASP201 3.2 18.7 1.0
CG C:ASN604 3.3 14.4 1.0
CD1 C:PHE601 3.4 26.2 1.0
CE1 C:PHE601 3.6 27.2 1.0
C C:PHE601 3.6 17.4 1.0
OD1 C:ASP201 3.6 21.2 1.0
C6 C:1492001 3.7 28.6 1.0
ND2 C:ASN604 3.7 20.4 1.0
OH C:TYR100 3.8 20.5 1.0
O4 C:1492001 4.0 18.9 1.0
C4 C:1492001 4.1 21.6 1.0
CG C:PHE601 4.1 22.3 1.0
NE1 C:TRP568 4.1 13.7 1.0
CA C:CYS602 4.3 16.9 1.0
CZ C:PHE601 4.3 30.7 1.0
N C:CYS602 4.3 14.5 1.0
C5 C:1492001 4.4 29.6 1.0
O C:HOH4063 4.4 14.5 1.0
CB C:ASP201 4.5 16.1 1.0
NE2 C:HIS540 4.5 19.0 1.0
CA C:PHE601 4.6 18.9 1.0
CB C:ASN604 4.7 17.9 1.0
CB C:PHE601 4.7 17.8 1.0
CD2 C:PHE601 4.8 19.5 1.0
O C:ASP201 4.8 15.3 1.0
C C:CYS602 4.8 15.7 1.0
CE2 C:PHE601 4.8 28.4 1.0
CZ C:TYR100 4.9 19.3 1.0
CE2 C:TRP568 4.9 14.8 1.0

Sodium binding site 9 out of 14 in 3vdb

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Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:19.3
occ:1.00
 O C:PHE556 2.4 16.9 1.0
O C:LEU562 2.4 15.2 1.0
O C:TYR559 2.4 18.0 1.0
O C:HOH4626 2.4 35.8 1.0
O C:HOH4348 2.4 25.7 1.0
O C:PRO560 3.2 19.5 1.0
C C:LEU562 3.4 13.4 1.0
C C:TYR559 3.4 17.8 1.0
C C:PHE556 3.5 17.9 1.0
C C:PRO560 3.6 16.7 1.0
CA C:PRO560 3.7 16.3 1.0
N C:PRO560 4.0 16.6 1.0
N C:LEU562 4.1 9.9 1.0
O C:HOH4263 4.1 24.1 1.0
CA C:LEU562 4.2 11.4 1.0
CA C:PHE556 4.2 11.8 1.0
N C:GLN563 4.2 10.2 1.0
O C:HOH4150 4.3 51.3 1.0
CA C:GLN563 4.3 12.8 1.0
CB C:LEU562 4.4 11.0 1.0
CA C:TYR559 4.5 16.3 1.0
N C:ARG561 4.5 13.9 1.0
CD1 C:LEU350 4.5 15.1 1.0
N C:TYR559 4.5 12.8 1.0
N C:ARG557 4.6 14.9 1.0
O C:HOH4688 4.6 43.6 1.0
CG C:GLN563 4.7 14.4 1.0
CA C:ARG557 4.7 14.9 1.0
C C:ARG557 4.8 13.8 1.0
O C:ARG557 4.8 16.6 1.0
CB C:PHE556 4.8 13.2 1.0
C C:ARG561 4.9 14.0 1.0

Sodium binding site 10 out of 14 in 3vdb

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Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3103

b:29.1
occ:1.00
 O C:PRO932 2.4 21.0 1.0
O C:LEU967 2.4 22.0 1.0
O C:THR970 2.7 24.4 1.0
O C:HOH4199 2.9 22.2 1.0
O C:HOH4701 3.1 50.5 1.0
C C:PRO932 3.4 18.3 1.0
O C:HOH4421 3.5 33.6 1.0
C C:LEU967 3.5 20.4 1.0
CZ C:PHE931 3.7 19.9 1.0
C C:THR970 3.8 26.2 1.0
CA C:MET968 3.8 27.0 1.0
CE1 C:PHE931 3.9 21.6 1.0
C C:MET968 4.0 25.0 1.0
O C:MET968 4.0 24.6 1.0
CE2 C:PHE931 4.0 17.5 1.0
CB C:PRO932 4.0 21.7 1.0
CA C:PRO932 4.1 20.6 1.0
N C:PRO932 4.1 20.2 1.0
N C:MET968 4.2 22.7 1.0
CD C:PRO932 4.2 22.1 1.0
N C:THR970 4.3 22.7 1.0
CD1 C:PHE931 4.4 21.6 1.0
N C:SER933 4.4 18.4 1.0
CD2 C:PHE931 4.5 20.7 1.0
CG C:PRO932 4.6 21.7 1.0
CA C:THR970 4.6 24.2 1.0
N C:GLU969 4.7 23.6 1.0
CG C:PHE931 4.7 20.5 1.0
N C:SER971 4.7 23.3 1.0
CA C:LEU967 4.7 19.5 1.0
CA C:SER971 4.8 24.9 1.0
CA C:SER933 4.8 14.9 1.0
C C:PHE931 4.8 20.3 1.0

Reference:

R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber. Substitution For ASN460 Cripples {Beta}-Galactosidase (Escherichia Coli) By Increasing Substrate Affinity and Decreasing Transition State Stability. Arch.Biochem.Biophys. V. 521 51 2012.
ISSN: ISSN 0003-9861
PubMed: 22446164
DOI: 10.1016/J.ABB.2012.03.014
Page generated: Tue Dec 15 06:28:42 2020

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Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
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