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Sodium in PDB 4duw: E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose, PDB code: 4duw 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) 24.81 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.826, 162.635, 203.692, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21.3

Other elements in 4duw:

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose also contains other interesting chemical elements:

Magnesium (Mg) 10 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) in Complex with Allolactose (pdb code 4duw). 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) in Complex with Allolactose, PDB code: 4duw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 4duw

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Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:34.9
occ:1.00
 OD1 A:ASN604 2.4 35.1 1.0
O A:HOH4253 2.4 33.4 1.0
O A:PHE601 2.4 38.6 1.0
OD2 A:ASP201 2.4 40.4 1.0
O6 A:LAK2001 2.4 35.6 1.0
CG A:ASP201 3.3 33.5 1.0
C6 A:LAK2001 3.4 43.7 1.0
CG A:ASN604 3.4 33.0 1.0
CD2 A:PHE601 3.5 31.5 1.0
C A:PHE601 3.6 36.8 1.0
CE2 A:PHE601 3.6 35.2 1.0
OD1 A:ASP201 3.8 37.2 1.0
ND2 A:ASN604 3.8 35.2 1.0
OH A:TYR100 3.9 38.0 1.0
O4 A:LAK2001 4.1 30.0 1.0
C4 A:LAK2001 4.1 42.5 1.0
NE1 A:TRP568 4.2 28.8 1.0
CG A:PHE601 4.2 32.8 1.0
C5 A:LAK2001 4.2 44.2 1.0
CA A:CYS602 4.3 34.3 1.0
CZ A:PHE601 4.3 35.2 1.0
N A:CYS602 4.4 37.2 1.0
O A:HOH4050 4.4 29.6 1.0
CB A:ASP201 4.5 29.9 1.0
NE2 A:HIS540 4.5 30.2 1.0
O A:ASP201 4.7 25.4 1.0
CA A:PHE601 4.7 34.9 1.0
CB A:ASN604 4.7 27.6 1.0
C A:CYS602 4.8 31.9 1.0
CD1 A:PHE601 4.8 22.8 1.0
CB A:PHE601 4.8 33.9 1.0
CE1 A:PHE601 4.9 36.9 1.0
CE2 A:TRP568 4.9 21.1 1.0
CE1 A:HIS540 5.0 28.6 1.0
CZ2 A:TRP568 5.0 28.6 1.0

Sodium binding site 2 out of 16 in 4duw

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Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:30.2
occ:1.00
 O A:PHE556 2.4 26.9 1.0
O A:LEU562 2.4 25.7 1.0
O A:TYR559 2.4 30.6 1.0
O A:HOH4355 2.5 38.4 1.0
O A:HOH4489 2.5 35.8 1.0
O A:PRO560 3.3 21.8 1.0
C A:TYR559 3.4 24.5 1.0
C A:LEU562 3.5 22.5 1.0
C A:PHE556 3.5 25.3 1.0
C A:PRO560 3.7 25.1 1.0
CA A:PRO560 3.8 22.2 1.0
O A:HOH4258 3.9 34.7 1.0
N A:PRO560 4.0 26.0 1.0
N A:LEU562 4.2 23.1 1.0
CA A:PHE556 4.3 23.9 1.0
CA A:LEU562 4.3 22.1 1.0
N A:GLN563 4.4 22.1 1.0
CA A:GLN563 4.4 24.2 1.0
CA A:TYR559 4.5 23.8 1.0
CB A:LEU562 4.5 15.4 1.0
N A:TYR559 4.5 23.9 1.0
N A:ARG557 4.6 25.1 1.0
N A:ARG561 4.6 21.8 1.0
CD1 A:LEU350 4.6 25.3 1.0
CG A:GLN563 4.7 23.9 1.0
CA A:ARG557 4.7 26.7 1.0
C A:ARG557 4.8 26.9 1.0
CB A:PHE556 4.8 23.8 1.0
O A:ARG557 5.0 27.5 1.0
C A:ARG561 5.0 25.0 1.0

Sodium binding site 3 out of 16 in 4duw

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Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:49.9
occ:1.00
 O A:HOH4711 2.3 49.7 1.0
O A:LEU967 2.4 43.0 1.0
O A:PRO932 2.6 26.5 1.0
O A:HOH4195 2.7 30.7 1.0
O A:THR970 2.7 44.5 1.0
C A:LEU967 3.6 37.7 1.0
C A:PRO932 3.6 31.5 1.0
CZ A:PHE931 3.6 41.8 1.0
O A:HOH4433 3.8 51.0 1.0
C A:THR970 3.8 41.6 1.0
O A:MET968 3.8 45.1 1.0
CE2 A:PHE931 3.8 36.6 1.0
C A:MET968 3.9 44.5 1.0
CA A:MET968 4.0 43.5 1.0
CE1 A:PHE931 4.0 37.4 1.0
CB A:PRO932 4.1 35.2 1.0
N A:THR970 4.2 42.2 1.0
N A:MET968 4.2 40.0 1.0
CA A:PRO932 4.2 33.7 1.0
CD A:PRO932 4.2 35.7 1.0
N A:PRO932 4.3 36.0 1.0
CD2 A:PHE931 4.4 41.0 1.0
N A:GLU969 4.6 42.1 1.0
CA A:THR970 4.6 40.4 1.0
N A:SER933 4.6 31.2 1.0
CD1 A:PHE931 4.6 36.2 1.0
CG A:PRO932 4.6 37.4 1.0
O A:HOH4537 4.6 45.7 1.0
N A:SER971 4.7 39.5 1.0
CA A:LEU967 4.7 37.8 1.0
CG A:PHE931 4.8 39.5 1.0
CA A:SER971 4.8 37.1 1.0
CA A:SER933 4.8 32.5 1.0

Sodium binding site 4 out of 16 in 4duw

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Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:50.6
occ:1.00
 O A:HOH4771 2.7 54.4 1.0
O A:GLU650 2.8 31.1 1.0
O A:SER647 3.0 37.6 1.0
O A:HOH4544 3.0 51.6 1.0
O A:LEU670 3.0 37.3 1.0
O A:HOH4545 3.1 42.0 1.0
N A:GLU650 3.3 30.8 1.0
C A:ASP648 3.7 38.7 1.0
C A:GLU650 3.7 32.3 1.0
N A:ASN649 3.8 34.3 1.0
O A:ASP648 3.9 38.2 1.0
C A:SER647 4.0 37.2 1.0
CA A:ASP648 4.0 39.4 1.0
CA A:GLU650 4.0 30.5 1.0
C A:LEU670 4.1 40.3 1.0
N A:LEU670 4.2 41.4 1.0
CA A:ASN649 4.3 31.5 1.0
C A:ASN649 4.3 32.1 1.0
N A:ASP648 4.4 37.7 1.0
CB A:GLU650 4.5 32.5 1.0
CA A:LEU670 4.6 39.7 1.0
CB A:PRO669 4.8 48.6 1.0
N A:LEU651 4.9 36.0 1.0
OG A:SER647 4.9 37.2 1.0
CB A:LEU670 4.9 40.9 1.0
OE1 A:GLU650 4.9 32.2 1.0
C A:PRO669 5.0 44.0 1.0

Sodium binding site 5 out of 16 in 4duw

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Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:27.9
occ:1.00
 O B:HOH4290 2.3 27.2 1.0
OD1 B:ASN604 2.4 25.6 1.0
O B:PHE601 2.4 24.3 1.0
O6 B:LAK2001 2.4 32.7 1.0
OD2 B:ASP201 2.4 25.2 1.0
CG B:ASP201 3.4 23.0 1.0
CG B:ASN604 3.4 25.3 1.0
CD2 B:PHE601 3.4 28.6 1.0
C B:PHE601 3.5 27.4 1.0
C6 B:LAK2001 3.6 28.7 1.0
CE2 B:PHE601 3.6 25.2 1.0
OD1 B:ASP201 3.7 22.8 1.0
ND2 B:ASN604 3.8 26.5 1.0
OH B:TYR100 3.8 28.5 1.0
CG B:PHE601 4.1 30.1 1.0
O4 B:LAK2001 4.1 25.3 1.0
C4 B:LAK2001 4.1 33.4 1.0
NE1 B:TRP568 4.2 22.9 1.0
CA B:CYS602 4.3 27.4 1.0
CZ B:PHE601 4.3 29.8 1.0
C5 B:LAK2001 4.3 37.6 1.0
N B:CYS602 4.3 27.8 1.0
O B:HOH4072 4.3 25.2 1.0
NE2 B:HIS540 4.5 22.3 1.0
CB B:ASP201 4.6 18.4 1.0
CA B:PHE601 4.6 29.4 1.0
CB B:PHE601 4.7 27.9 1.0
CD1 B:PHE601 4.7 21.5 1.0
O B:ASP201 4.7 25.9 1.0
CB B:ASN604 4.8 20.5 1.0
C B:CYS602 4.8 27.2 1.0
CE1 B:PHE601 4.8 28.3 1.0
CE2 B:TRP568 4.9 18.9 1.0
CZ B:TYR100 4.9 29.4 1.0
CZ2 B:TRP568 4.9 17.6 1.0

Sodium binding site 6 out of 16 in 4duw

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Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:31.4
occ:1.00
 O B:HOH4565 2.2 40.2 1.0
O B:PHE556 2.4 27.3 1.0
O B:TYR559 2.4 30.4 1.0
O B:LEU562 2.4 28.2 1.0
O B:HOH4398 2.5 37.0 1.0
O B:PRO560 3.1 24.4 1.0
C B:TYR559 3.3 28.6 1.0
C B:LEU562 3.4 23.0 1.0
C B:PHE556 3.5 25.7 1.0
C B:PRO560 3.6 25.8 1.0
CA B:PRO560 3.6 27.1 1.0
O B:HOH4296 3.8 35.0 1.0
N B:PRO560 3.9 26.3 1.0
O B:HOH4828 4.0 49.2 1.0
N B:LEU562 4.1 18.5 1.0
CA B:LEU562 4.2 24.0 1.0
CA B:PHE556 4.3 26.3 1.0
N B:GLN563 4.3 24.4 1.0
O B:HOH4838 4.3 39.4 1.0
CA B:GLN563 4.4 22.6 1.0
CB B:LEU562 4.5 19.0 1.0
CA B:TYR559 4.5 26.9 1.0
N B:TYR559 4.5 26.3 1.0
N B:ARG561 4.5 25.8 1.0
N B:ARG557 4.6 24.4 1.0
CG B:GLN563 4.7 22.7 1.0
CA B:ARG557 4.7 22.8 1.0
C B:ARG557 4.8 23.8 1.0
O B:ARG557 4.8 20.9 1.0
CD1 B:LEU350 4.8 23.2 1.0
CB B:PHE556 4.9 25.6 1.0
C B:ARG561 4.9 23.6 1.0

Sodium binding site 7 out of 16 in 4duw

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Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:46.4
occ:1.00
 O B:LEU967 2.4 38.7 1.0
O B:PRO932 2.6 27.4 1.0
O B:HOH4222 2.7 32.9 1.0
O B:THR970 2.8 35.8 1.0
O B:HOH4504 3.5 50.2 1.0
CZ B:PHE931 3.5 29.3 1.0
C B:LEU967 3.5 33.4 1.0
C B:PRO932 3.7 28.1 1.0
O B:HOH4637 3.8 54.8 1.0
CE1 B:PHE931 3.8 32.3 1.0
O B:MET968 3.8 37.6 1.0
C B:THR970 3.9 35.0 1.0
C B:MET968 3.9 36.9 1.0
CE2 B:PHE931 3.9 24.2 1.0
CA B:MET968 4.0 35.9 1.0
N B:THR970 4.1 32.0 1.0
N B:MET968 4.2 34.0 1.0
CB B:PRO932 4.3 29.7 1.0
CA B:PRO932 4.3 29.0 1.0
CD B:PRO932 4.4 30.4 1.0
N B:PRO932 4.4 29.0 1.0
N B:GLU969 4.5 35.8 1.0
CD1 B:PHE931 4.5 30.3 1.0
CD2 B:PHE931 4.5 26.4 1.0
CA B:THR970 4.6 34.3 1.0
N B:SER933 4.7 27.6 1.0
CA B:LEU967 4.8 33.2 1.0
N B:SER971 4.8 35.3 1.0
CG B:PRO932 4.8 29.2 1.0
CG B:PHE931 4.8 25.0 1.0
CA B:SER971 4.9 35.6 1.0
C B:GLU969 4.9 34.2 1.0
CA B:SER933 4.9 28.2 1.0

Sodium binding site 8 out of 16 in 4duw

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Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:56.0
occ:1.00
 O B:GLU650 2.7 33.2 1.0
O B:HOH4646 2.8 45.8 1.0
O B:LEU670 2.8 39.9 1.0
O B:HOH4974 2.8 43.9 1.0
O B:SER647 2.8 38.0 1.0
N B:GLU650 3.4 28.6 1.0
C B:GLU650 3.7 32.8 1.0
C B:LEU670 3.9 39.7 1.0
C B:ASP648 3.9 34.5 1.0
CA B:GLU650 4.0 32.2 1.0
C B:SER647 4.0 36.8 1.0
N B:ASN649 4.0 31.8 1.0
N B:LEU670 4.0 42.2 1.0
CA B:ASP648 4.1 37.1 1.0
O B:ASP648 4.3 36.6 1.0
CB B:GLU650 4.4 31.3 1.0
CA B:LEU670 4.4 41.5 1.0
C B:ASN649 4.4 28.2 1.0
CA B:ASN649 4.5 30.8 1.0
N B:ASP648 4.5 35.4 1.0
OG B:SER647 4.6 33.8 1.0
CB B:LEU670 4.7 37.9 1.0
C B:PRO669 4.9 45.6 1.0
N B:LEU651 4.9 37.7 1.0
CB B:PRO669 5.0 48.4 1.0

Sodium binding site 9 out of 16 in 4duw

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Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:27.7
occ:1.00
 O C:HOH4303 2.3 25.7 1.0
OD1 C:ASN604 2.4 27.7 1.0
OD2 C:ASP201 2.4 25.9 1.0
O6 C:LAK2001 2.4 27.0 1.0
O C:PHE601 2.5 25.4 1.0
CG C:ASP201 3.3 28.3 1.0
CG C:ASN604 3.4 25.0 1.0
C6 C:LAK2001 3.6 31.3 1.0
CD2 C:PHE601 3.6 29.4 1.0
CE2 C:PHE601 3.7 27.5 1.0
C C:PHE601 3.7 24.2 1.0
ND2 C:ASN604 3.7 21.0 1.0
OD1 C:ASP201 3.7 25.8 1.0
OH C:TYR100 3.8 34.1 1.0
O4 C:LAK2001 4.0 29.5 1.0
C4 C:LAK2001 4.1 33.0 1.0
CG C:PHE601 4.2 26.4 1.0
NE1 C:TRP568 4.2 21.7 1.0
CA C:CYS602 4.3 26.3 1.0
CZ C:PHE601 4.3 25.0 1.0
C5 C:LAK2001 4.3 35.4 1.0
O C:HOH4088 4.4 20.9 1.0
N C:CYS602 4.4 25.2 1.0
CB C:ASP201 4.5 21.4 1.0
NE2 C:HIS540 4.6 19.9 1.0
CD1 C:PHE601 4.7 27.6 1.0
CB C:ASN604 4.7 24.8 1.0
O C:ASP201 4.7 24.1 1.0
CA C:PHE601 4.7 26.6 1.0
C C:CYS602 4.8 25.4 1.0
CE1 C:PHE601 4.8 25.0 1.0
CB C:PHE601 4.8 27.6 1.0
CZ C:TYR100 4.9 29.7 1.0
CE2 C:TRP568 4.9 25.9 1.0
CZ2 C:TRP568 5.0 24.2 1.0

Sodium binding site 10 out of 16 in 4duw

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Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G974A) in Complex with Allolactose


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) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:31.9
occ:1.00
 O C:PHE556 2.4 29.2 1.0
O C:TYR559 2.4 28.5 1.0
O C:LEU562 2.4 23.8 1.0
O C:HOH4416 2.7 35.6 1.0
O C:HOH4592 2.7 41.6 1.0
O C:PRO560 3.2 25.4 1.0
C C:TYR559 3.4 25.7 1.0
C C:LEU562 3.4 23.8 1.0
C C:PHE556 3.5 27.0 1.0
C C:PRO560 3.6 25.1 1.0
CA C:PRO560 3.7 22.6 1.0
O C:HOH4310 3.8 35.1 1.0
N C:PRO560 4.0 25.2 1.0
N C:LEU562 4.1 19.0 1.0
CA C:PHE556 4.2 26.0 1.0
N C:GLN563 4.3 25.5 1.0
CA C:LEU562 4.3 20.5 1.0
CA C:GLN563 4.3 23.2 1.0
N C:ARG561 4.5 22.2 1.0
CA C:TYR559 4.6 23.9 1.0
N C:ARG557 4.6 23.6 1.0
CB C:LEU562 4.6 19.1 1.0
CD1 C:LEU350 4.6 21.8 1.0
N C:TYR559 4.6 24.5 1.0
CG C:GLN563 4.7 21.6 1.0
CA C:ARG557 4.8 25.5 1.0
O C:ARG557 4.8 25.1 1.0
C C:ARG557 4.8 26.3 1.0
CB C:PHE556 4.8 22.1 1.0
C C:ARG561 5.0 23.3 1.0
O C:ALA555 5.0 25.9 1.0

Reference:

R.W.Wheatley, S.Lo, L.J.Jancewicz, M.L.Dugdale, R.E.Huber. Structural Explanation For Allolactose (Lac Operon Inducer) Synthesis By Lacz Beta-Galactosidase and the Evolutionary Relationship Between Allolactose Synthesis and the Lac Repressor J.Biol.Chem. V. 288 12993 2013.
ISSN: ISSN 0021-9258
PubMed: 23486479
DOI: 10.1074/JBC.M113.455436
Page generated: Mon Oct 7 15:00:22 2024

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