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Sodium in PDB 3t0d: E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone, PDB code: 3t0d was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.56 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.930, 162.710, 203.910, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.9

Other elements in 3t0d:

The structure of E.Coli (Lacz) Beta-Galactosidase (S796T) 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 - 16;

Binding sites:

The binding sites of Sodium atom in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone (pdb code 3t0d). 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 (S796T) in Complex with Galactonolactone, PDB code: 3t0d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 3t0d

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Sodium binding site 1 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:18.2
occ:1.00
 O A:HOH4267 2.3 17.8 1.0
OD1 A:ASN604 2.4 18.4 1.0
O A:PHE601 2.4 18.9 1.0
O6 A:1492001 2.4 17.5 1.0
OD2 A:ASP201 2.4 18.3 1.0
CG A:ASP201 3.3 19.8 1.0
CG A:ASN604 3.4 16.1 1.0
C6 A:1492001 3.6 17.5 1.0
C A:PHE601 3.6 21.5 1.0
CD2 A:PHE601 3.6 27.8 1.0
OD1 A:ASP201 3.7 18.6 1.0
ND2 A:ASN604 3.7 15.4 1.0
CE2 A:PHE601 3.8 29.0 1.0
OH A:TYR100 3.8 20.2 1.0
O4 A:1492001 4.0 14.7 1.0
NE1 A:TRP568 4.1 14.2 1.0
C4 A:1492001 4.1 18.4 1.0
CG A:PHE601 4.2 22.2 1.0
CA A:CYS602 4.3 18.8 1.0
C5 A:1492001 4.4 17.2 1.0
N A:CYS602 4.4 21.3 1.0
CZ A:PHE601 4.5 29.4 1.0
NE2 A:HIS540 4.5 13.3 1.0
O A:HOH4051 4.5 22.3 1.0
CB A:ASP201 4.5 16.7 1.0
O A:ASP201 4.6 15.3 1.0
CA A:PHE601 4.6 19.5 1.0
CB A:ASN604 4.7 13.7 1.0
CB A:PHE601 4.8 19.9 1.0
C A:CYS602 4.8 19.1 1.0
CD1 A:PHE601 4.8 20.4 1.0
CE2 A:TRP568 4.9 13.4 1.0
CE1 A:PHE601 4.9 27.3 1.0
CZ2 A:TRP568 5.0 12.7 1.0
CZ A:TYR100 5.0 21.7 1.0

Sodium binding site 2 out of 16 in 3t0d

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Sodium binding site 2 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:14.2
occ:1.00
 O A:LEU562 2.4 11.4 1.0
O A:PHE556 2.4 14.1 1.0
O A:TYR559 2.4 14.3 1.0
O A:HOH4384 2.5 27.5 1.0
O A:HOH4571 2.5 22.0 1.0
O A:PRO560 3.2 12.8 1.0
C A:LEU562 3.4 10.6 1.0
C A:TYR559 3.4 13.1 1.0
C A:PHE556 3.5 12.3 1.0
C A:PRO560 3.6 12.2 1.0
CA A:PRO560 3.8 13.3 1.0
O A:HOH4274 3.9 20.8 1.0
N A:PRO560 4.0 10.9 1.0
N A:LEU562 4.1 11.0 1.0
O A:HOH4677 4.1 35.5 1.0
CA A:LEU562 4.2 12.7 1.0
CA A:PHE556 4.2 12.0 1.0
N A:GLN563 4.2 10.7 1.0
CA A:GLN563 4.3 9.6 1.0
CB A:LEU562 4.5 9.1 1.0
CA A:TYR559 4.5 12.6 1.0
N A:ARG561 4.6 11.1 1.0
N A:TYR559 4.6 12.5 1.0
N A:ARG557 4.6 9.6 1.0
CG A:GLN563 4.6 10.7 1.0
CD1 A:LEU350 4.7 10.0 1.0
CA A:ARG557 4.8 12.8 1.0
CB A:PHE556 4.8 11.8 1.0
C A:ARG557 4.8 13.3 1.0
O A:ARG557 4.9 12.8 1.0
C A:ARG561 4.9 10.4 1.0

Sodium binding site 3 out of 16 in 3t0d

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Sodium binding site 3 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:39.9
occ:1.00
 O A:LEU967 2.6 20.9 1.0
O A:HOH4647 2.7 36.4 1.0
O A:PRO932 2.8 15.9 1.0
O A:THR970 2.8 26.5 1.0
O A:HOH4200 3.0 23.0 1.0
O A:HOH4500 3.3 26.5 1.0
CZ A:PHE931 3.5 24.7 1.0
O A:MET968 3.6 25.7 1.0
C A:PRO932 3.8 16.8 1.0
C A:LEU967 3.8 21.2 1.0
C A:THR970 3.8 28.3 1.0
CE1 A:PHE931 3.8 24.9 1.0
C A:MET968 3.9 26.8 1.0
CE2 A:PHE931 3.9 21.0 1.0
CA A:MET968 4.1 25.7 1.0
CB A:PRO932 4.2 20.9 1.0
CD A:PRO932 4.3 18.6 1.0
N A:THR970 4.3 24.7 1.0
CA A:PRO932 4.3 17.2 1.0
N A:PRO932 4.3 20.4 1.0
N A:MET968 4.4 22.9 1.0
CD1 A:PHE931 4.4 26.5 1.0
CD2 A:PHE931 4.5 24.1 1.0
CA A:SER971 4.6 25.7 1.0
N A:SER971 4.6 27.4 1.0
CA A:THR970 4.7 26.2 1.0
N A:GLU969 4.7 26.2 1.0
CG A:PRO932 4.7 19.9 1.0
CG A:PHE931 4.8 21.8 1.0
N A:SER933 4.8 17.6 1.0
CA A:LEU967 5.0 22.3 1.0

Sodium binding site 4 out of 16 in 3t0d

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Sodium binding site 4 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:37.4
occ:1.00
 O A:HOH4657 2.4 42.7 1.0
O A:GLU650 2.8 18.3 1.0
O A:HOH4655 2.9 47.0 1.0
O A:SER647 3.0 20.1 1.0
O A:LEU670 3.1 25.8 1.0
O A:HOH4656 3.1 37.2 1.0
N A:GLU650 3.2 17.5 1.0
C A:ASP648 3.7 25.8 1.0
C A:GLU650 3.7 19.4 1.0
N A:ASN649 3.8 21.4 1.0
CA A:GLU650 4.0 19.5 1.0
CA A:ASP648 4.0 27.4 1.0
O A:ASP648 4.0 25.0 1.0
C A:SER647 4.0 21.5 1.0
CA A:ASN649 4.2 20.6 1.0
C A:ASN649 4.2 20.0 1.0
C A:LEU670 4.2 22.6 1.0
N A:LEU670 4.3 21.9 1.0
CB A:GLU650 4.4 18.0 1.0
N A:ASP648 4.5 24.8 1.0
CA A:LEU670 4.7 23.5 1.0
CB A:PRO669 4.8 31.1 1.0
N A:LEU651 4.9 20.3 1.0
OG A:SER647 4.9 19.7 1.0
OE1 A:GLU650 5.0 18.7 1.0

Sodium binding site 5 out of 16 in 3t0d

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Sodium binding site 5 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:13.6
occ:1.00
 O B:HOH4311 2.3 15.8 1.0
OD1 B:ASN604 2.4 11.9 1.0
O B:PHE601 2.4 10.5 1.0
O6 B:1492001 2.4 16.6 1.0
OD2 B:ASP201 2.4 11.6 1.0
CG B:ASP201 3.3 11.9 1.0
CG B:ASN604 3.4 13.2 1.0
CD2 B:PHE601 3.5 21.5 1.0
C6 B:1492001 3.6 11.5 1.0
C B:PHE601 3.6 13.2 1.0
CE2 B:PHE601 3.7 22.3 1.0
OD1 B:ASP201 3.7 15.3 1.0
OH B:TYR100 3.8 12.0 1.0
ND2 B:ASN604 3.8 10.6 1.0
CG B:PHE601 4.1 20.1 1.0
O4 B:1492001 4.1 10.6 1.0
C4 B:1492001 4.1 8.4 1.0
NE1 B:TRP568 4.2 10.2 1.0
C5 B:1492001 4.3 12.3 1.0
CA B:CYS602 4.3 11.9 1.0
N B:CYS602 4.4 13.6 1.0
CZ B:PHE601 4.4 17.2 1.0
O B:HOH4090 4.4 15.9 1.0
CB B:ASP201 4.5 10.6 1.0
NE2 B:HIS540 4.5 9.0 1.0
CA B:PHE601 4.6 13.6 1.0
CB B:PHE601 4.7 15.3 1.0
O B:ASP201 4.7 10.8 1.0
CD1 B:PHE601 4.7 12.8 1.0
CB B:ASN604 4.8 8.8 1.0
C B:CYS602 4.8 11.3 1.0
CE1 B:PHE601 4.9 21.6 1.0
CZ B:TYR100 4.9 11.0 1.0
CE2 B:TRP568 4.9 11.1 1.0

Sodium binding site 6 out of 16 in 3t0d

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Sodium binding site 6 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:15.1
occ:1.00
 O B:HOH4971 2.2 29.0 1.0
O B:TYR559 2.4 14.0 1.0
O B:LEU562 2.4 13.2 1.0
O B:PHE556 2.4 10.0 1.0
O B:HOH4436 2.5 27.8 1.0
O B:PRO560 3.2 14.0 1.0
C B:TYR559 3.3 13.7 1.0
C B:LEU562 3.4 12.5 1.0
C B:PHE556 3.5 9.5 1.0
C B:PRO560 3.6 13.3 1.0
CA B:PRO560 3.7 12.4 1.0
N B:PRO560 3.9 13.0 1.0
O B:HOH4318 4.0 18.4 1.0
N B:LEU562 4.1 10.9 1.0
O B:HOH4970 4.1 31.2 1.0
CA B:LEU562 4.2 10.8 1.0
O B:HOH4642 4.2 28.7 1.0
CA B:PHE556 4.2 11.4 1.0
N B:GLN563 4.3 9.8 1.0
CA B:GLN563 4.4 8.9 1.0
CB B:LEU562 4.5 9.3 1.0
CA B:TYR559 4.5 12.9 1.0
N B:TYR559 4.5 14.0 1.0
N B:ARG561 4.5 11.2 1.0
N B:ARG557 4.6 8.7 1.0
CG B:GLN563 4.7 10.9 1.0
CA B:ARG557 4.7 10.2 1.0
C B:ARG557 4.8 10.7 1.0
CB B:PHE556 4.8 10.2 1.0
O B:ARG557 4.8 12.0 1.0
CD1 B:LEU350 4.9 12.6 1.0
C B:ARG561 4.9 12.2 1.0

Sodium binding site 7 out of 16 in 3t0d

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Sodium binding site 7 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:30.6
occ:1.00
 O B:LEU967 2.7 19.2 1.0
O B:PRO932 2.7 15.9 1.0
O B:THR970 2.8 20.0 1.0
O B:HOH4732 3.0 35.8 1.0
O B:HOH4242 3.1 14.8 1.0
O B:HOH4568 3.3 30.7 1.0
CZ B:PHE931 3.5 18.2 1.0
O B:MET968 3.7 19.5 1.0
C B:PRO932 3.7 12.2 1.0
C B:THR970 3.8 18.3 1.0
C B:LEU967 3.8 16.6 1.0
CE2 B:PHE931 3.8 17.1 1.0
CE1 B:PHE931 3.9 21.3 1.0
C B:MET968 3.9 21.0 1.0
CD B:PRO932 4.1 14.4 1.0
CA B:MET968 4.1 19.5 1.0
CB B:PRO932 4.2 13.8 1.0
N B:PRO932 4.2 12.2 1.0
N B:THR970 4.2 18.3 1.0
CA B:PRO932 4.3 13.4 1.0
CD2 B:PHE931 4.4 15.8 1.0
N B:MET968 4.4 17.1 1.0
CD1 B:PHE931 4.4 16.7 1.0
CA B:SER971 4.5 19.8 1.0
N B:SER971 4.5 17.5 1.0
CG B:PRO932 4.6 14.3 1.0
CA B:THR970 4.6 17.7 1.0
CG B:PHE931 4.7 14.3 1.0
N B:GLU969 4.7 17.2 1.0
N B:SER933 4.8 13.4 1.0
C B:PHE931 4.9 13.1 1.0

Sodium binding site 8 out of 16 in 3t0d

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Sodium binding site 8 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:43.0
occ:1.00
 O B:GLU650 2.7 15.9 1.0
O B:SER647 2.7 19.8 1.0
O B:HOH5086 2.8 37.0 1.0
O B:LEU670 2.8 21.4 1.0
O B:HOH4742 2.9 35.4 1.0
N B:GLU650 3.3 16.5 1.0
C B:GLU650 3.6 17.3 1.0
C B:ASP648 3.8 16.6 1.0
C B:SER647 3.9 19.5 1.0
N B:ASN649 3.9 15.4 1.0
CA B:GLU650 3.9 16.5 1.0
C B:LEU670 3.9 23.3 1.0
CA B:ASP648 4.0 20.7 1.0
N B:LEU670 4.1 25.2 1.0
O B:ASP648 4.2 18.2 1.0
CB B:GLU650 4.3 14.3 1.0
C B:ASN649 4.3 15.4 1.0
N B:ASP648 4.4 20.0 1.0
CA B:ASN649 4.4 15.6 1.0
CA B:LEU670 4.5 24.9 1.0
OG B:SER647 4.7 18.3 1.0
CB B:LEU670 4.8 25.0 1.0
N B:LEU651 4.8 19.5 1.0
OE1 B:GLU650 4.9 15.6 1.0
C B:PRO669 4.9 28.3 1.0
CB B:PRO669 5.0 30.3 1.0

Sodium binding site 9 out of 16 in 3t0d

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Sodium binding site 9 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:10.9
occ:1.00
 O C:HOH4327 2.3 13.0 1.0
OD1 C:ASN604 2.4 9.9 1.0
O C:PHE601 2.4 11.0 1.0
O6 C:1492001 2.4 15.9 1.0
OD2 C:ASP201 2.4 10.7 1.0
CG C:ASP201 3.3 14.5 1.0
CG C:ASN604 3.4 9.8 1.0
C6 C:1492001 3.5 12.6 1.0
CD2 C:PHE601 3.5 21.4 1.0
C C:PHE601 3.6 12.5 1.0
OD1 C:ASP201 3.7 12.4 1.0
CE2 C:PHE601 3.7 17.4 1.0
ND2 C:ASN604 3.7 8.7 1.0
OH C:TYR100 3.8 11.8 1.0
C4 C:1492001 4.1 12.8 1.0
O4 C:1492001 4.1 13.0 1.0
CG C:PHE601 4.1 16.2 1.0
NE1 C:TRP568 4.2 9.3 1.0
CA C:CYS602 4.3 12.9 1.0
C5 C:1492001 4.3 14.8 1.0
N C:CYS602 4.3 11.5 1.0
CZ C:PHE601 4.4 18.4 1.0
O C:HOH4107 4.4 10.3 1.0
CB C:ASP201 4.5 9.3 1.0
NE2 C:HIS540 4.6 7.5 1.0
CA C:PHE601 4.6 11.8 1.0
O C:ASP201 4.7 10.8 1.0
CB C:PHE601 4.7 11.8 1.0
CB C:ASN604 4.7 8.4 1.0
CD1 C:PHE601 4.8 16.6 1.0
C C:CYS602 4.8 12.4 1.0
CE1 C:PHE601 4.9 19.3 1.0
CE2 C:TRP568 4.9 10.6 1.0
CZ C:TYR100 4.9 10.5 1.0

Sodium binding site 10 out of 16 in 3t0d

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Sodium binding site 10 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:16.6
occ:1.00
 O C:HOH4652 2.3 26.8 1.0
O C:PHE556 2.4 11.3 1.0
O C:LEU562 2.4 13.4 1.0
O C:TYR559 2.4 12.9 1.0
O C:HOH4450 2.5 26.2 1.0
O C:PRO560 3.2 10.7 1.0
C C:LEU562 3.4 10.2 1.0
C C:TYR559 3.4 11.2 1.0
C C:PHE556 3.5 13.2 1.0
C C:PRO560 3.6 11.8 1.0
CA C:PRO560 3.7 10.4 1.0
N C:PRO560 4.0 12.6 1.0
O C:HOH4334 4.0 19.6 1.0
N C:LEU562 4.1 9.8 1.0
CA C:PHE556 4.2 12.1 1.0
CA C:LEU562 4.2 12.2 1.0
N C:GLN563 4.2 9.4 1.0
CA C:GLN563 4.3 9.7 1.0
CB C:LEU562 4.5 9.5 1.0
CA C:TYR559 4.5 12.1 1.0
N C:ARG561 4.5 10.3 1.0
N C:TYR559 4.6 11.8 1.0
N C:ARG557 4.6 10.5 1.0
CG C:GLN563 4.7 11.2 1.0
CD1 C:LEU350 4.7 12.7 1.0
CA C:ARG557 4.8 12.2 1.0
CB C:PHE556 4.8 8.8 1.0
C C:ARG557 4.8 14.3 1.0
O C:ARG557 4.9 12.8 1.0
C C:ARG561 4.9 13.3 1.0
O C:HOH4917 4.9 43.5 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Mon Oct 7 13:07:30 2024

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