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Sodium in PDB 4dux: E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose, PDB code: 4dux 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) 86.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.648, 168.103, 201.881, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22.1

Other elements in 4dux:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose also contains other interesting chemical elements:

Magnesium (Mg) 8 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 (N460S) in Complex with L-Ribose (pdb code 4dux). 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 (N460S) in Complex with L-Ribose, PDB code: 4dux:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 4dux

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Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:28.4
occ:1.00
 O A:HOH4637 2.3 21.6 1.0
OD1 A:ASN604 2.4 24.0 1.0
O A:PHE601 2.4 30.6 1.0
OD2 A:ASP201 2.4 32.2 1.0
O4 A:0MK2001 2.7 19.4 1.0
CG A:ASN604 3.3 24.0 1.0
CD1 A:PHE601 3.3 38.6 1.0
CG A:ASP201 3.4 26.8 1.0
CE1 A:PHE601 3.4 27.5 1.0
C A:PHE601 3.5 30.7 1.0
ND2 A:ASN604 3.6 21.4 1.0
OH A:TYR100 3.8 32.2 1.0
O3 A:0MK2001 3.8 22.2 1.0
C4 A:0MK2001 3.8 20.6 1.0
C3 A:0MK2001 3.8 20.0 1.0
OD1 A:ASP201 3.9 29.6 1.0
CG A:PHE601 4.1 38.0 1.0
NE1 A:TRP568 4.2 22.3 1.0
CZ A:PHE601 4.2 38.3 1.0
CA A:CYS602 4.2 30.0 1.0
N A:CYS602 4.3 29.6 1.0
O A:HOH4045 4.3 21.8 1.0
CB A:ASP201 4.5 27.3 1.0
NE2 A:HIS540 4.6 22.0 1.0
CA A:PHE601 4.6 31.7 1.0
C A:CYS602 4.7 28.6 1.0
CB A:PHE601 4.7 32.0 1.0
O A:ASP201 4.7 21.3 1.0
CB A:ASN604 4.7 19.6 1.0
CD2 A:PHE601 4.7 37.4 1.0
CE2 A:PHE601 4.8 39.6 1.0
C5 A:0MK2001 4.9 20.2 1.0
CE1 A:HIS540 4.9 27.8 1.0
CZ A:TYR100 4.9 26.7 1.0
CE2 A:TRP568 5.0 24.3 1.0

Sodium binding site 2 out of 14 in 4dux

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Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:26.7
occ:1.00
 O A:PHE556 2.4 30.5 1.0
O A:TYR559 2.4 24.2 1.0
O A:LEU562 2.4 21.6 1.0
O A:HOH4482 2.5 51.2 1.0
O A:HOH4344 2.7 32.5 1.0
O A:PRO560 3.2 20.2 1.0
C A:LEU562 3.4 23.2 1.0
C A:TYR559 3.4 21.1 1.0
O A:HOH4550 3.5 43.3 1.0
C A:PHE556 3.5 27.3 1.0
C A:PRO560 3.7 21.4 1.0
CA A:PRO560 3.8 19.2 1.0
O A:HOH4254 4.0 32.4 1.0
N A:PRO560 4.0 20.7 1.0
N A:LEU562 4.1 21.9 1.0
CA A:PHE556 4.2 24.0 1.0
CA A:LEU562 4.3 21.0 1.0
CA A:GLN563 4.3 22.4 1.0
N A:GLN563 4.3 22.7 1.0
N A:ARG557 4.5 24.9 1.0
CG A:GLN563 4.6 22.1 1.0
CB A:LEU562 4.6 20.4 1.0
CA A:TYR559 4.6 20.5 1.0
N A:TYR559 4.6 22.7 1.0
N A:ARG561 4.6 18.0 1.0
CA A:ARG557 4.7 23.6 1.0
CD1 A:LEU350 4.7 18.7 1.0
C A:ARG557 4.8 27.2 1.0
CB A:PHE556 4.8 19.2 1.0
O A:ARG557 4.8 28.9 1.0
C A:ARG561 5.0 23.1 1.0

Sodium binding site 3 out of 14 in 4dux

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Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:45.6
occ:1.00
 O A:HOH4520 2.4 39.1 1.0
O A:LEU967 2.7 32.5 1.0
O A:PRO932 2.7 30.8 1.0
O A:THR970 2.9 37.6 1.0
O A:HOH4188 3.2 38.9 1.0
CZ A:PHE931 3.5 21.9 1.0
O A:HOH4429 3.6 37.5 1.0
C A:PRO932 3.7 30.3 1.0
CE1 A:PHE931 3.8 26.2 1.0
C A:LEU967 3.8 31.0 1.0
O A:MET968 3.8 36.8 1.0
CA A:MET968 3.8 34.7 1.0
C A:MET968 3.8 34.2 1.0
C A:THR970 3.8 37.3 1.0
CE2 A:PHE931 3.9 26.6 1.0
CD A:PRO932 4.0 27.8 1.0
CB A:PRO932 4.1 32.2 1.0
N A:PRO932 4.2 31.3 1.0
CA A:PRO932 4.3 30.0 1.0
N A:THR970 4.3 37.6 1.0
N A:MET968 4.3 31.0 1.0
CD1 A:PHE931 4.4 24.0 1.0
CD2 A:PHE931 4.5 28.0 1.0
N A:GLU969 4.5 37.5 1.0
CG A:PRO932 4.6 31.3 1.0
CA A:SER971 4.6 36.3 1.0
N A:SER971 4.6 36.2 1.0
CA A:THR970 4.7 37.0 1.0
CG A:PHE931 4.7 26.8 1.0
N A:SER933 4.8 26.6 1.0
C A:PHE931 5.0 30.9 1.0
C A:GLU969 5.0 39.2 1.0

Sodium binding site 4 out of 14 in 4dux

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Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:32.4
occ:1.00
 O B:HOH4251 2.2 19.4 1.0
O B:PHE601 2.4 28.7 1.0
OD2 B:ASP201 2.4 31.2 1.0
OD1 B:ASN604 2.5 33.7 1.0
O4 B:0MK2001 2.7 20.9 1.0
CG B:ASP201 3.3 29.4 1.0
CD1 B:PHE601 3.4 34.6 1.0
CG B:ASN604 3.4 33.3 1.0
CE1 B:PHE601 3.5 32.8 1.0
C B:PHE601 3.6 28.7 1.0
ND2 B:ASN604 3.7 25.4 1.0
OD1 B:ASP201 3.7 35.2 1.0
C4 B:0MK2001 3.8 25.4 1.0
C3 B:0MK2001 3.8 26.9 1.0
O3 B:0MK2001 3.8 25.9 1.0
OH B:TYR100 3.9 36.0 1.0
CG B:PHE601 4.1 36.1 1.0
CZ B:PHE601 4.2 30.7 1.0
NE1 B:TRP568 4.2 22.5 1.0
CA B:CYS602 4.3 26.5 1.0
N B:CYS602 4.4 27.3 1.0
O B:HOH4069 4.4 31.2 1.0
CB B:ASP201 4.5 28.9 1.0
NE2 B:HIS540 4.5 29.1 1.0
CA B:PHE601 4.6 31.5 1.0
O B:ASP201 4.7 27.1 1.0
CD2 B:PHE601 4.7 31.5 1.0
C B:CYS602 4.7 28.1 1.0
CE2 B:PHE601 4.8 33.5 1.0
CB B:PHE601 4.8 31.2 1.0
CB B:ASN604 4.8 31.0 1.0
CE2 B:TRP568 4.9 29.1 1.0
C5 B:0MK2001 5.0 23.1 1.0

Sodium binding site 5 out of 14 in 4dux

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Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:27.4
occ:1.00
 O B:PHE556 2.4 24.5 1.0
O B:LEU562 2.4 24.4 1.0
O B:TYR559 2.4 27.4 1.0
O B:HOH4431 2.7 46.8 1.0
O B:HOH4336 2.8 33.9 1.0
O B:PRO560 3.3 23.4 1.0
C B:TYR559 3.4 24.1 1.0
C B:LEU562 3.4 23.2 1.0
C B:PHE556 3.5 23.6 1.0
C B:PRO560 3.7 25.5 1.0
CA B:PRO560 3.7 23.2 1.0
O B:HOH4499 3.9 29.2 1.0
N B:PRO560 4.0 24.7 1.0
N B:LEU562 4.2 22.9 1.0
CA B:PHE556 4.2 21.8 1.0
N B:GLN563 4.3 22.4 1.0
CA B:GLN563 4.3 23.2 1.0
CA B:LEU562 4.3 23.2 1.0
N B:ARG557 4.5 23.9 1.0
CA B:TYR559 4.5 23.9 1.0
CB B:LEU562 4.5 21.3 1.0
N B:TYR559 4.5 21.1 1.0
N B:ARG561 4.6 24.4 1.0
CG B:GLN563 4.6 20.6 1.0
CA B:ARG557 4.7 23.7 1.0
CB B:PHE556 4.8 24.6 1.0
C B:ARG557 4.8 23.8 1.0
CD1 B:LEU350 4.8 25.5 1.0
O B:ARG557 4.9 25.4 1.0

Sodium binding site 6 out of 14 in 4dux

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Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:49.9
occ:1.00
 O B:LEU967 2.6 35.4 1.0
O B:THR970 2.7 45.2 1.0
O B:PRO932 2.9 33.5 1.0
O B:HOH4201 3.1 47.2 1.0
O B:HOH4395 3.2 46.7 1.0
CZ B:PHE931 3.5 26.5 1.0
C B:LEU967 3.7 36.8 1.0
CE1 B:PHE931 3.7 19.0 1.0
CA B:MET968 3.7 39.3 1.0
C B:THR970 3.8 42.1 1.0
C B:MET968 3.8 41.2 1.0
O B:MET968 3.8 42.5 1.0
C B:PRO932 3.9 35.6 1.0
CD B:PRO932 4.0 35.0 1.0
CE2 B:PHE931 4.0 25.6 1.0
N B:MET968 4.2 35.3 1.0
N B:THR970 4.2 41.7 1.0
CB B:PRO932 4.3 37.9 1.0
CD1 B:PHE931 4.3 25.1 1.0
N B:PRO932 4.3 35.9 1.0
N B:GLU969 4.4 42.3 1.0
CA B:PRO932 4.4 34.9 1.0
CG B:PRO932 4.5 33.4 1.0
CA B:SER971 4.6 41.5 1.0
N B:SER971 4.6 40.9 1.0
CA B:THR970 4.6 42.1 1.0
CD2 B:PHE931 4.6 25.6 1.0
CG B:PHE931 4.8 28.1 1.0
N B:SER933 4.9 35.1 1.0
CA B:LEU967 4.9 38.1 1.0
C B:GLU969 5.0 42.0 1.0
CB B:MET968 5.0 38.8 1.0

Sodium binding site 7 out of 14 in 4dux

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Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:50.5
occ:1.00
 O B:GLU650 2.7 36.0 1.0
O B:SER647 2.9 35.9 1.0
O B:HOH4588 3.0 47.0 1.0
O B:LEU670 3.1 42.0 1.0
O B:HOH4476 3.1 53.5 1.0
N B:GLU650 3.2 34.8 1.0
C B:GLU650 3.6 38.0 1.0
N B:ASN649 3.8 35.6 1.0
C B:ASP648 3.8 35.9 1.0
CA B:GLU650 3.9 36.2 1.0
C B:SER647 3.9 35.1 1.0
CA B:ASP648 3.9 34.8 1.0
C B:LEU670 4.2 41.4 1.0
C B:ASN649 4.2 35.0 1.0
N B:LEU670 4.3 43.7 1.0
CA B:ASN649 4.3 35.0 1.0
O B:ASP648 4.3 36.3 1.0
N B:ASP648 4.3 34.1 1.0
CB B:GLU650 4.4 35.4 1.0
CA B:LEU670 4.7 40.9 1.0
N B:LEU651 4.8 39.3 1.0
CB B:PRO669 4.8 45.6 1.0
OG B:SER647 4.9 33.8 1.0
CB B:LEU670 4.9 39.7 1.0
OE1 B:GLU650 4.9 37.3 1.0

Sodium binding site 8 out of 14 in 4dux

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Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:30.4
occ:1.00
 OD1 C:ASN604 2.4 30.7 1.0
O C:PHE601 2.4 27.3 1.0
OD2 C:ASP201 2.4 28.8 1.0
O C:HOH4265 2.5 26.5 1.0
O4 C:0MK2001 2.6 31.8 1.0
CG C:ASN604 3.3 27.9 1.0
CD1 C:PHE601 3.3 42.8 1.0
CG C:ASP201 3.4 33.2 1.0
CE1 C:PHE601 3.5 29.5 1.0
ND2 C:ASN604 3.5 24.3 1.0
C C:PHE601 3.6 30.1 1.0
C4 C:0MK2001 3.7 28.4 1.0
O3 C:0MK2001 3.7 25.0 1.0
C3 C:0MK2001 3.8 25.8 1.0
OH C:TYR100 3.8 33.9 1.0
OD1 C:ASP201 3.9 30.8 1.0
CG C:PHE601 4.0 35.5 1.0
NE1 C:TRP568 4.2 24.9 1.0
CZ C:PHE601 4.3 35.7 1.0
O C:HOH4066 4.3 25.7 1.0
CA C:CYS602 4.3 29.1 1.0
N C:CYS602 4.4 28.1 1.0
NE2 C:HIS540 4.5 25.7 1.0
CB C:ASP201 4.5 30.0 1.0
CA C:PHE601 4.6 31.9 1.0
CB C:PHE601 4.7 32.9 1.0
CB C:ASN604 4.7 29.5 1.0
CD2 C:PHE601 4.7 37.8 1.0
C C:CYS602 4.8 27.0 1.0
O C:ASP201 4.8 28.8 1.0
CE2 C:PHE601 4.8 39.7 1.0
C5 C:0MK2001 4.9 27.2 1.0
CE1 C:HIS540 4.9 29.2 1.0
CZ C:TYR100 5.0 32.4 1.0

Sodium binding site 9 out of 14 in 4dux

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Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:27.6
occ:1.00
 O C:PHE556 2.4 21.6 1.0
O C:LEU562 2.4 22.3 1.0
O C:HOH4355 2.4 34.9 1.0
O C:TYR559 2.4 24.4 1.0
O C:HOH4476 3.0 34.6 1.0
O C:PRO560 3.2 20.8 1.0
C C:LEU562 3.4 23.2 1.0
C C:TYR559 3.4 20.9 1.0
C C:PHE556 3.5 23.4 1.0
C C:PRO560 3.6 21.9 1.0
CA C:PRO560 3.8 19.7 1.0
O C:HOH4271 3.9 23.6 1.0
N C:LEU562 4.0 21.8 1.0
N C:PRO560 4.1 19.2 1.0
O C:HOH4608 4.1 52.4 1.0
CA C:LEU562 4.2 21.1 1.0
CA C:PHE556 4.2 23.9 1.0
N C:GLN563 4.3 21.9 1.0
CA C:GLN563 4.3 21.3 1.0
CB C:LEU562 4.4 20.2 1.0
N C:ARG557 4.5 23.6 1.0
N C:ARG561 4.6 20.7 1.0
CA C:TYR559 4.6 19.9 1.0
N C:TYR559 4.6 22.0 1.0
CA C:ARG557 4.7 22.1 1.0
CG C:GLN563 4.7 21.8 1.0
C C:ARG557 4.8 24.4 1.0
CD1 C:LEU350 4.8 25.7 1.0
CB C:PHE556 4.9 22.8 1.0
C C:ARG561 4.9 22.5 1.0
O C:ARG557 4.9 28.8 1.0
O C:ALA555 5.0 25.1 1.0

Sodium binding site 10 out of 14 in 4dux

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Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3103

b:42.6
occ:1.00
 O C:THR970 2.7 41.4 1.0
O C:LEU967 2.7 32.4 1.0
O C:PRO932 2.8 25.8 1.0
O C:HOH4207 3.0 40.3 1.0
CZ C:PHE931 3.5 36.7 1.0
O C:HOH4535 3.6 39.7 1.0
C C:THR970 3.6 41.0 1.0
C C:PRO932 3.8 28.5 1.0
CE1 C:PHE931 3.8 37.5 1.0
CE2 C:PHE931 3.8 35.2 1.0
C C:LEU967 3.9 33.1 1.0
C C:MET968 4.0 40.7 1.0
CA C:MET968 4.0 38.6 1.0
CD C:PRO932 4.0 27.9 1.0
O C:MET968 4.0 42.8 1.0
CB C:PRO932 4.0 29.8 1.0
N C:PRO932 4.1 30.1 1.0
CA C:SER971 4.2 39.3 1.0
N C:THR970 4.2 42.6 1.0
CA C:PRO932 4.2 28.4 1.0
N C:SER971 4.3 39.7 1.0
CD1 C:PHE931 4.3 33.1 1.0
CD2 C:PHE931 4.4 38.5 1.0
N C:MET968 4.4 35.5 1.0
CG C:PRO932 4.5 30.0 1.0
CA C:THR970 4.5 41.5 1.0
N C:GLU969 4.5 43.2 1.0
CG C:PHE931 4.6 37.6 1.0
C C:SER971 4.9 37.8 1.0
C C:GLU969 4.9 43.1 1.0
C C:PHE931 4.9 32.0 1.0
N C:SER933 4.9 25.8 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 15:00:30 2024

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