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Sodium in PDB 4duv: E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex, PDB code: 4duv was solved by R.W.Wheatley, S.Lo, L.J.Janzcewicz, M.L.Dugdale, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.41 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.570, 167.731, 201.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 20.6

Other elements in 4duv:

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex (pdb code 4duv). 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex, PDB code: 4duv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 4duv

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Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:23.8
occ:1.00
 O A:HOH4254 2.2 20.9 1.0
OD1 A:ASN604 2.4 17.5 1.0
OD2 A:ASP201 2.4 19.0 1.0
O A:PHE601 2.5 22.9 1.0
O6 A:2DG2001 2.6 17.6 1.0
CG A:ASP201 3.3 25.1 1.0
CD2 A:PHE601 3.3 18.6 1.0
CE2 A:PHE601 3.4 18.5 1.0
CG A:ASN604 3.4 20.2 1.0
OD1 A:ASP201 3.6 19.1 1.0
C A:PHE601 3.7 22.0 1.0
ND2 A:ASN604 3.8 18.9 1.0
C6 A:2DG2001 3.8 20.3 1.0
OH A:TYR100 3.9 26.1 1.0
CG A:PHE601 4.0 22.3 1.0
NE1 A:TRP568 4.0 18.1 1.0
CZ A:PHE601 4.0 18.5 1.0
O4 A:2DG2001 4.1 17.7 1.0
C4 A:2DG2001 4.1 20.6 1.0
CA A:CYS602 4.4 21.3 1.0
NE2 A:HIS540 4.4 22.1 1.0
O A:HOH4049 4.4 17.1 1.0
N A:CYS602 4.4 21.9 1.0
C5 A:2DG2001 4.5 18.7 1.0
CB A:ASP201 4.5 15.9 1.0
CD1 A:PHE601 4.5 21.5 1.0
CE1 A:PHE601 4.6 22.0 1.0
CB A:PHE601 4.7 23.2 1.0
CA A:PHE601 4.7 22.6 1.0
CE2 A:TRP568 4.7 17.7 1.0
CB A:ASN604 4.7 16.8 1.0
O A:ASP201 4.8 17.4 1.0
CZ2 A:TRP568 4.9 18.8 1.0
CD1 A:TRP568 4.9 18.5 1.0
C A:CYS602 4.9 22.0 1.0
CE1 A:HIS540 4.9 28.2 1.0

Sodium binding site 2 out of 16 in 4duv

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Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:22.0
occ:1.00
 O A:HOH4514 2.4 39.0 1.0
O A:PHE556 2.4 21.4 1.0
O A:LEU562 2.4 21.5 1.0
O A:TYR559 2.4 19.8 1.0
O A:HOH4360 2.6 29.6 1.0
O A:PRO560 3.1 14.9 1.0
C A:TYR559 3.4 16.7 1.0
C A:LEU562 3.4 17.8 1.0
C A:PHE556 3.5 19.0 1.0
C A:PRO560 3.6 16.4 1.0
CA A:PRO560 3.7 16.5 1.0
O A:HOH4585 3.9 40.8 1.0
N A:PRO560 4.0 18.1 1.0
O A:HOH4261 4.0 28.4 1.0
N A:LEU562 4.1 12.9 1.0
CA A:LEU562 4.2 17.0 1.0
CA A:PHE556 4.3 17.4 1.0
N A:GLN563 4.3 18.6 1.0
CA A:GLN563 4.3 16.8 1.0
CA A:TYR559 4.5 18.6 1.0
CB A:LEU562 4.5 14.1 1.0
N A:TYR559 4.5 15.6 1.0
N A:ARG557 4.6 19.3 1.0
N A:ARG561 4.6 13.4 1.0
CG A:GLN563 4.6 18.3 1.0
CA A:ARG557 4.7 20.1 1.0
C A:ARG557 4.8 21.2 1.0
O A:ARG557 4.8 21.4 1.0
CD1 A:LEU350 4.8 18.3 1.0
CB A:PHE556 4.9 12.2 1.0
C A:ARG561 4.9 16.1 1.0
O A:ALA555 5.0 16.0 1.0

Sodium binding site 3 out of 16 in 4duv

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Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:33.7
occ:1.00
 O A:HOH4908 2.3 47.8 1.0
O A:LEU967 2.4 29.9 1.0
O A:PRO932 2.5 23.7 1.0
O A:THR970 2.6 30.4 1.0
O A:HOH4192 2.9 22.3 1.0
O A:HOH4455 3.4 44.5 1.0
CZ A:PHE931 3.5 23.8 1.0
C A:PRO932 3.5 20.6 1.0
C A:LEU967 3.6 26.7 1.0
C A:THR970 3.8 32.4 1.0
CE1 A:PHE931 3.8 26.8 1.0
CE2 A:PHE931 3.9 26.1 1.0
O A:MET968 3.9 30.8 1.0
C A:MET968 4.0 31.0 1.0
CA A:MET968 4.0 30.4 1.0
CB A:PRO932 4.1 23.4 1.0
CD A:PRO932 4.1 21.4 1.0
CA A:PRO932 4.2 22.8 1.0
N A:MET968 4.2 29.2 1.0
N A:THR970 4.2 32.1 1.0
N A:PRO932 4.2 24.2 1.0
CD1 A:PHE931 4.4 22.8 1.0
CD2 A:PHE931 4.5 24.5 1.0
N A:SER933 4.6 20.5 1.0
CA A:THR970 4.6 31.3 1.0
CG A:PRO932 4.6 24.6 1.0
N A:GLU969 4.7 31.2 1.0
CG A:PHE931 4.7 24.2 1.0
CA A:LEU967 4.7 29.7 1.0
N A:SER971 4.8 32.3 1.0
CA A:SER933 4.8 19.0 1.0
CA A:SER971 4.9 32.5 1.0
C A:PHE931 5.0 25.6 1.0

Sodium binding site 4 out of 16 in 4duv

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Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:45.3
occ:1.00
 O A:SER647 2.7 28.0 1.0
O A:GLU650 2.7 28.6 1.0
O A:LEU670 2.8 28.6 1.0
O A:HOH4570 2.8 52.4 1.0
O A:HOH4571 3.0 40.6 1.0
N A:GLU650 3.4 29.1 1.0
C A:GLU650 3.7 31.7 1.0
C A:SER647 3.8 27.9 1.0
C A:LEU670 3.9 32.5 1.0
C A:ASP648 3.9 31.6 1.0
N A:ASN649 3.9 27.5 1.0
CA A:GLU650 4.0 32.4 1.0
CA A:ASP648 4.0 30.5 1.0
N A:LEU670 4.1 35.6 1.0
N A:ASP648 4.3 27.2 1.0
CB A:GLU650 4.4 30.4 1.0
CA A:LEU670 4.4 33.3 1.0
C A:ASN649 4.4 27.8 1.0
O A:ASP648 4.5 30.6 1.0
CA A:ASN649 4.5 28.0 1.0
OG A:SER647 4.6 24.5 1.0
CB A:LEU670 4.7 34.0 1.0
N A:LEU651 4.9 31.2 1.0
C A:PRO669 4.9 33.8 1.0
OE1 A:GLU650 4.9 25.9 1.0
CB A:PRO669 5.0 40.4 1.0
CB A:SER647 5.0 26.1 1.0

Sodium binding site 5 out of 16 in 4duv

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Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:23.9
occ:1.00
 O B:HOH4288 2.2 19.3 1.0
OD1 B:ASN604 2.4 23.1 1.0
OD2 B:ASP201 2.4 21.4 1.0
O6 B:2DG2001 2.4 21.2 1.0
O B:PHE601 2.6 22.9 1.0
CG B:ASP201 3.2 25.4 1.0
CE2 B:PHE601 3.4 21.6 1.0
CG B:ASN604 3.4 20.2 1.0
CD2 B:PHE601 3.4 16.9 1.0
OD1 B:ASP201 3.5 24.9 1.0
C6 B:2DG2001 3.7 20.8 1.0
C B:PHE601 3.8 20.6 1.0
ND2 B:ASN604 3.8 23.1 1.0
NE1 B:TRP568 3.9 19.8 1.0
OH B:TYR100 4.0 23.2 1.0
CZ B:PHE601 4.0 14.1 1.0
C4 B:2DG2001 4.0 19.2 1.0
O4 B:2DG2001 4.0 14.7 1.0
CG B:PHE601 4.1 22.9 1.0
C5 B:2DG2001 4.4 18.0 1.0
CB B:ASP201 4.4 20.0 1.0
NE2 B:HIS540 4.4 20.2 1.0
O B:HOH4076 4.5 22.1 1.0
CA B:CYS602 4.5 18.2 1.0
CE1 B:PHE601 4.5 24.0 1.0
N B:CYS602 4.5 20.5 1.0
CD1 B:PHE601 4.6 21.9 1.0
O B:ASP201 4.6 19.5 1.0
CE2 B:TRP568 4.7 21.5 1.0
CB B:ASN604 4.8 20.8 1.0
CA B:PHE601 4.8 22.3 1.0
CB B:PHE601 4.8 19.5 1.0
CD1 B:TRP568 4.8 19.6 1.0
CZ2 B:TRP568 4.9 16.7 1.0
C B:CYS602 5.0 17.9 1.0

Sodium binding site 6 out of 16 in 4duv

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Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:24.1
occ:1.00
 O B:PHE556 2.4 15.1 1.0
O B:LEU562 2.4 20.6 1.0
O B:TYR559 2.4 23.5 1.0
O B:HOH4547 2.4 34.7 1.0
O B:HOH4393 2.6 30.8 1.0
O B:PRO560 3.3 18.2 1.0
C B:TYR559 3.4 20.2 1.0
C B:LEU562 3.4 19.2 1.0
C B:PHE556 3.5 16.8 1.0
C B:PRO560 3.6 17.7 1.0
CA B:PRO560 3.8 14.7 1.0
N B:PRO560 4.0 17.0 1.0
O B:HOH4295 4.0 24.3 1.0
N B:LEU562 4.1 14.1 1.0
CA B:LEU562 4.2 18.0 1.0
CA B:PHE556 4.2 13.9 1.0
O B:HOH4739 4.2 44.2 1.0
N B:GLN563 4.3 16.3 1.0
CA B:GLN563 4.4 16.2 1.0
CB B:LEU562 4.4 19.1 1.0
CA B:TYR559 4.5 19.5 1.0
N B:TYR559 4.5 17.1 1.0
N B:ARG561 4.6 16.1 1.0
N B:ARG557 4.6 18.4 1.0
CG B:GLN563 4.6 12.2 1.0
CA B:ARG557 4.7 19.4 1.0
CB B:PHE556 4.8 16.4 1.0
O B:ARG557 4.8 20.7 1.0
C B:ARG557 4.8 19.3 1.0
CD1 B:LEU350 4.8 16.4 1.0
C B:ARG561 4.9 14.9 1.0

Sodium binding site 7 out of 16 in 4duv

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Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:34.5
occ:1.00
 O B:LEU967 2.4 30.7 1.0
O B:PRO932 2.6 27.3 1.0
O B:THR970 2.6 36.1 1.0
O B:HOH4224 2.7 27.0 1.0
O B:HOH4604 2.9 53.2 1.0
CZ B:PHE931 3.5 26.7 1.0
C B:LEU967 3.5 28.4 1.0
C B:PRO932 3.6 27.6 1.0
O B:HOH4496 3.7 35.4 1.0
C B:THR970 3.7 32.9 1.0
CA B:MET968 3.8 32.4 1.0
CE1 B:PHE931 3.9 23.8 1.0
CE2 B:PHE931 3.9 20.4 1.0
C B:MET968 3.9 35.6 1.0
O B:MET968 4.0 36.6 1.0
CB B:PRO932 4.1 27.4 1.0
N B:MET968 4.1 27.7 1.0
CD B:PRO932 4.2 27.3 1.0
N B:THR970 4.2 32.4 1.0
CA B:PRO932 4.2 25.8 1.0
N B:PRO932 4.3 26.8 1.0
N B:GLU969 4.5 32.7 1.0
CD1 B:PHE931 4.5 29.7 1.0
CD2 B:PHE931 4.5 28.5 1.0
CA B:THR970 4.5 31.8 1.0
CG B:PRO932 4.6 25.0 1.0
N B:SER933 4.6 22.7 1.0
N B:SER971 4.7 31.2 1.0
CA B:LEU967 4.8 29.5 1.0
CA B:SER971 4.8 29.5 1.0
CG B:PHE931 4.8 28.3 1.0
CA B:SER933 4.9 23.4 1.0
C B:GLU969 5.0 32.2 1.0

Sodium binding site 8 out of 16 in 4duv

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Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:40.6
occ:1.00
 O B:GLU650 2.4 25.9 1.0
O B:LEU670 2.8 29.7 1.0
O B:SER647 2.8 29.3 1.0
O B:HOH4959 2.9 43.2 1.0
O B:HOH4610 3.0 39.3 1.0
N B:GLU650 3.2 25.5 1.0
C B:GLU650 3.3 28.1 1.0
CA B:GLU650 3.7 26.8 1.0
C B:LEU670 3.9 31.8 1.0
N B:ASN649 3.9 27.7 1.0
C B:SER647 3.9 30.3 1.0
N B:LEU670 3.9 35.0 1.0
C B:ASP648 4.0 30.9 1.0
CB B:GLU650 4.1 26.5 1.0
CA B:ASP648 4.2 31.7 1.0
C B:ASN649 4.2 28.8 1.0
CA B:LEU670 4.3 34.5 1.0
CA B:ASN649 4.4 29.0 1.0
N B:LEU651 4.5 29.6 1.0
N B:ASP648 4.5 29.8 1.0
O B:ASP648 4.6 30.7 1.0
CB B:LEU670 4.6 33.6 1.0
OG B:SER647 4.7 30.7 1.0
C B:PRO669 4.8 38.5 1.0
O B:HOH4807 4.9 45.2 1.0
CB B:PRO669 4.9 39.2 1.0
OE1 B:GLU650 5.0 25.5 1.0
CA B:PRO669 5.0 38.7 1.0

Sodium binding site 9 out of 16 in 4duv

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Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:22.4
occ:1.00
 O C:HOH4288 2.2 23.2 1.0
OD1 C:ASN604 2.4 23.4 1.0
O6 C:2DG2001 2.4 21.2 1.0
OD2 C:ASP201 2.4 25.6 1.0
O C:PHE601 2.5 23.5 1.0
CG C:ASP201 3.3 24.2 1.0
CE2 C:PHE601 3.4 24.8 1.0
CD2 C:PHE601 3.4 25.0 1.0
CG C:ASN604 3.4 21.8 1.0
OD1 C:ASP201 3.6 28.1 1.0
C6 C:2DG2001 3.6 20.8 1.0
C C:PHE601 3.7 25.1 1.0
ND2 C:ASN604 3.9 20.9 1.0
OH C:TYR100 3.9 23.4 1.0
NE1 C:TRP568 3.9 23.5 1.0
CZ C:PHE601 4.0 18.3 1.0
CG C:PHE601 4.0 27.4 1.0
C4 C:2DG2001 4.1 19.4 1.0
O4 C:2DG2001 4.1 17.9 1.0
C5 C:2DG2001 4.4 20.1 1.0
O C:HOH4079 4.4 17.1 1.0
NE2 C:HIS540 4.4 18.7 1.0
CA C:CYS602 4.4 22.8 1.0
CB C:ASP201 4.5 21.6 1.0
N C:CYS602 4.5 21.9 1.0
CD1 C:PHE601 4.5 19.1 1.0
CE1 C:PHE601 4.5 23.5 1.0
CE2 C:TRP568 4.7 22.2 1.0
CA C:PHE601 4.7 26.5 1.0
CB C:PHE601 4.7 24.9 1.0
O C:ASP201 4.8 19.9 1.0
CB C:ASN604 4.8 22.6 1.0
CD1 C:TRP568 4.8 17.9 1.0
CZ2 C:TRP568 4.8 18.4 1.0
C C:CYS602 5.0 19.8 1.0

Sodium binding site 10 out of 16 in 4duv

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Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex


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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:22.4
occ:1.00
 O C:PHE556 2.4 17.5 1.0
O C:LEU562 2.4 17.9 1.0
O C:TYR559 2.4 21.5 1.0
O C:HOH4396 2.5 26.3 1.0
O C:HOH4567 2.6 32.5 1.0
O C:PRO560 3.2 17.7 1.0
C C:LEU562 3.4 19.1 1.0
C C:TYR559 3.4 16.9 1.0
C C:PHE556 3.5 17.5 1.0
C C:PRO560 3.6 15.7 1.0
CA C:PRO560 3.7 16.0 1.0
N C:PRO560 4.0 14.5 1.0
O C:HOH4295 4.0 20.8 1.0
N C:LEU562 4.1 15.3 1.0
CA C:LEU562 4.2 15.0 1.0
CA C:PHE556 4.2 19.6 1.0
N C:GLN563 4.3 16.7 1.0
CA C:GLN563 4.4 16.0 1.0
CB C:LEU562 4.4 15.8 1.0
CA C:TYR559 4.5 18.6 1.0
N C:TYR559 4.5 17.7 1.0
N C:ARG561 4.5 14.1 1.0
N C:ARG557 4.6 18.6 1.0
CG C:GLN563 4.7 16.1 1.0
CA C:ARG557 4.7 17.6 1.0
CD1 C:LEU350 4.8 18.0 1.0
C C:ARG557 4.8 19.5 1.0
CB C:PHE556 4.9 19.8 1.0
O C:ARG557 4.9 22.5 1.0
C C:ARG561 4.9 16.0 1.0

Reference:

R.W.Wheatley, S.Lo, L.J.Janzcewicz, M.L.Dugdale, R.E.Huber. The Glucose Acceptor Site of Lacz Beta-Galactosidase For the Synthesis of Allolactose - the Natural Inducer of the Lac Operon To Be Published.
Page generated: Tue Dec 15 06:37:17 2020

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Zn in 8WD3
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