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Sodium in PDB 3t0b: E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex, PDB code: 3t0b 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) 67.79 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.970, 163.140, 204.020, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 23.3

Other elements in 3t0b:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex 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 (S796T) Iptg Complex (pdb code 3t0b). 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 (S796T) Iptg Complex, PDB code: 3t0b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 3t0b

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Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:16.9
occ:1.00
 O A:PHE601 2.4 17.9 1.0
O6 A:IPT2001 2.4 16.8 0.9
OD1 A:ASN604 2.4 13.8 1.0
OD2 A:ASP201 2.4 24.0 1.0
O A:HOH4252 2.4 22.1 1.0
CG A:ASP201 3.3 20.8 1.0
C6 A:IPT2001 3.3 13.2 0.9
CG A:ASN604 3.3 16.7 1.0
C A:PHE601 3.5 18.3 1.0
ND2 A:ASN604 3.6 18.7 1.0
OD1 A:ASP201 3.6 19.9 1.0
OH A:TYR100 3.7 17.9 1.0
NE1 A:TRP568 4.0 15.0 1.0
O4 A:IPT2001 4.1 14.4 0.9
CA A:CYS602 4.2 18.2 1.0
N A:CYS602 4.3 18.9 1.0
O A:HOH4048 4.3 13.6 1.0
C4 A:IPT2001 4.4 21.0 0.9
C5 A:IPT2001 4.4 14.5 0.9
CA A:PHE601 4.5 17.6 1.0
CB A:PHE601 4.5 13.4 1.0
CB A:ASP201 4.5 15.5 1.0
O A:ASP201 4.6 16.0 1.0
C A:CYS602 4.6 17.4 1.0
NE2 A:HIS540 4.7 11.9 1.0
CB A:ASN604 4.7 16.0 1.0
CZ A:TYR100 4.8 21.7 1.0
CE2 A:TRP568 4.8 15.0 1.0
CZ2 A:TRP568 4.9 17.3 1.0

Sodium binding site 2 out of 14 in 3t0b

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Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:14.6
occ:1.00
 O A:PHE556 2.4 10.6 1.0
O A:LEU562 2.4 11.2 1.0
O A:TYR559 2.5 17.6 1.0
O A:HOH4505 2.6 19.1 1.0
O A:HOH4358 2.8 29.4 1.0
O A:PRO560 3.2 8.1 1.0
C A:LEU562 3.4 10.8 1.0
C A:PHE556 3.5 11.1 1.0
C A:TYR559 3.5 13.5 1.0
C A:PRO560 3.7 11.2 1.0
CA A:PRO560 3.9 13.4 1.0
O A:HOH4258 3.9 17.1 1.0
N A:PRO560 4.1 13.1 1.0
N A:LEU562 4.2 8.2 1.0
CA A:GLN563 4.3 12.5 1.0
CA A:PHE556 4.3 10.3 1.0
N A:GLN563 4.3 10.3 1.0
CA A:LEU562 4.3 9.7 1.0
N A:ARG557 4.6 8.5 1.0
CB A:LEU562 4.6 10.3 1.0
CD1 A:LEU350 4.6 4.0 1.0
CG A:GLN563 4.6 11.0 1.0
N A:ARG561 4.7 9.8 1.0
CA A:TYR559 4.7 12.6 1.0
O A:HOH4582 4.7 32.0 1.0
N A:TYR559 4.7 12.0 1.0
CA A:ARG557 4.7 12.5 1.0
CB A:PHE556 4.8 11.2 1.0
C A:ARG557 4.9 12.3 1.0
C A:ARG561 5.0 11.1 1.0

Sodium binding site 3 out of 14 in 3t0b

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Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:31.9
occ:1.00
 O A:LEU967 2.6 23.0 1.0
O A:THR970 2.6 27.9 1.0
O A:PRO932 2.8 16.6 1.0
O A:HOH4187 3.0 21.1 1.0
O A:HOH4550 3.0 39.2 1.0
O A:HOH4452 3.2 17.2 1.0
CZ A:PHE931 3.4 22.3 1.0
C A:THR970 3.6 24.7 1.0
O A:MET968 3.7 24.0 1.0
CE1 A:PHE931 3.7 17.7 1.0
C A:LEU967 3.8 21.7 1.0
CE2 A:PHE931 3.8 16.2 1.0
CA A:MET968 3.8 25.5 1.0
C A:MET968 3.8 24.9 1.0
C A:PRO932 3.8 17.8 1.0
N A:THR970 4.1 22.9 1.0
CD A:PRO932 4.1 15.4 1.0
CB A:PRO932 4.3 17.2 1.0
N A:MET968 4.3 23.4 1.0
N A:PRO932 4.3 18.4 1.0
CA A:PRO932 4.4 17.6 1.0
CD1 A:PHE931 4.4 18.2 1.0
CA A:SER971 4.4 23.9 1.0
N A:SER971 4.4 24.4 1.0
CD2 A:PHE931 4.4 18.5 1.0
CA A:THR970 4.5 23.4 1.0
N A:GLU969 4.6 25.6 1.0
CG A:PRO932 4.6 17.1 1.0
CG A:PHE931 4.7 19.6 1.0
N A:SER933 4.9 14.5 1.0
C A:GLU969 4.9 25.9 1.0

Sodium binding site 4 out of 14 in 3t0b

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Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:15.2
occ:1.00
 O6 B:IPT2001 2.3 17.3 1.0
O B:HOH4271 2.3 13.5 1.0
O B:PHE601 2.4 12.2 1.0
OD1 B:ASN604 2.4 9.6 1.0
OD2 B:ASP201 2.4 19.5 1.0
CG B:ASP201 3.2 13.2 1.0
CG B:ASN604 3.3 10.5 1.0
C6 B:IPT2001 3.4 15.6 1.0
OD1 B:ASP201 3.5 17.7 1.0
C B:PHE601 3.5 12.7 1.0
OH B:TYR100 3.6 12.1 1.0
ND2 B:ASN604 3.6 2.0 1.0
NE1 B:TRP568 4.1 5.6 1.0
O4 B:IPT2001 4.1 15.3 1.0
CA B:CYS602 4.2 10.4 1.0
N B:CYS602 4.3 11.3 1.0
O B:HOH4058 4.3 17.8 1.0
C4 B:IPT2001 4.5 16.1 1.0
C5 B:IPT2001 4.5 13.7 1.0
CB B:ASP201 4.5 12.5 1.0
O B:ASP201 4.5 12.7 1.0
CA B:PHE601 4.6 12.0 1.0
C B:CYS602 4.6 8.6 1.0
CB B:PHE601 4.6 10.2 1.0
CZ B:TYR100 4.7 12.3 1.0
CB B:ASN604 4.7 9.2 1.0
NE2 B:HIS540 4.8 9.1 1.0
CE2 B:TRP568 4.8 6.6 1.0
CZ2 B:TRP568 4.9 4.5 1.0

Sodium binding site 5 out of 14 in 3t0b

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Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:16.1
occ:1.00
 O B:HOH4537 2.2 19.1 1.0
O B:LEU562 2.4 14.2 1.0
O B:PHE556 2.4 11.7 1.0
O B:TYR559 2.4 15.9 1.0
O B:HOH4382 2.8 36.0 1.0
O B:PRO560 3.2 13.4 1.0
C B:LEU562 3.4 9.8 1.0
C B:TYR559 3.4 13.6 1.0
C B:PHE556 3.5 11.9 1.0
C B:PRO560 3.6 12.0 1.0
CA B:PRO560 3.8 12.0 1.0
O B:HOH4278 4.0 16.3 1.0
O B:HOH4639 4.0 39.3 1.0
N B:PRO560 4.0 11.2 1.0
N B:LEU562 4.1 8.9 1.0
O B:HOH4656 4.2 32.5 1.0
CA B:LEU562 4.2 9.3 1.0
CA B:PHE556 4.2 11.1 1.0
N B:GLN563 4.3 11.2 1.0
CA B:GLN563 4.3 9.4 1.0
CB B:LEU562 4.5 9.5 1.0
N B:ARG557 4.5 10.7 1.0
CA B:TYR559 4.5 13.2 1.0
N B:ARG561 4.6 9.0 1.0
N B:TYR559 4.6 12.3 1.0
CG B:GLN563 4.7 8.8 1.0
CD1 B:LEU350 4.7 8.3 1.0
CA B:ARG557 4.7 9.8 1.0
C B:ARG557 4.8 9.5 1.0
CB B:PHE556 4.8 10.2 1.0
O B:ARG557 4.9 10.1 1.0
C B:ARG561 4.9 10.0 1.0

Sodium binding site 6 out of 14 in 3t0b

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Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:28.1
occ:1.00
 O B:PRO932 2.5 14.6 1.0
O B:LEU967 2.6 17.5 1.0
O B:THR970 2.8 21.7 1.0
O B:HOH4208 2.9 9.2 1.0
O B:HOH4499 3.4 16.7 1.0
O B:HOH4596 3.4 38.5 1.0
CZ B:PHE931 3.4 11.8 1.0
C B:PRO932 3.6 15.6 1.0
O B:MET968 3.7 16.2 1.0
C B:LEU967 3.7 15.6 1.0
CE1 B:PHE931 3.7 9.0 1.0
C B:THR970 3.7 16.8 1.0
CE2 B:PHE931 3.8 11.0 1.0
C B:MET968 3.9 19.2 1.0
CA B:MET968 3.9 19.5 1.0
CD B:PRO932 4.1 12.8 1.0
N B:PRO932 4.2 14.2 1.0
N B:THR970 4.2 21.7 1.0
CA B:PRO932 4.2 14.8 1.0
CB B:PRO932 4.2 14.7 1.0
N B:MET968 4.3 16.4 1.0
CD1 B:PHE931 4.4 15.3 1.0
CD2 B:PHE931 4.4 14.1 1.0
N B:SER971 4.6 16.5 1.0
CA B:THR970 4.6 19.3 1.0
CA B:SER971 4.6 19.2 1.0
CG B:PRO932 4.6 13.1 1.0
CG B:PHE931 4.7 11.6 1.0
N B:GLU969 4.7 19.9 1.0
N B:SER933 4.7 15.4 1.0
C B:PHE931 4.9 15.0 1.0
CA B:LEU967 5.0 14.2 1.0
CA B:SER933 5.0 13.8 1.0

Sodium binding site 7 out of 14 in 3t0b

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Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:36.4
occ:1.00
 O B:SER647 2.7 18.1 1.0
O B:LEU670 2.7 20.3 1.0
O B:GLU650 2.7 20.3 1.0
O B:HOH4605 2.8 34.9 1.0
O B:HOH4982 3.0 38.9 1.0
N B:GLU650 3.5 11.4 1.0
C B:GLU650 3.7 17.8 1.0
C B:LEU670 3.8 24.7 1.0
C B:SER647 3.9 18.0 1.0
C B:ASP648 3.9 17.4 1.0
N B:LEU670 4.0 27.5 1.0
N B:ASN649 4.0 15.9 1.0
CA B:GLU650 4.0 16.9 1.0
CA B:ASP648 4.1 19.7 1.0
O B:ASP648 4.2 20.9 1.0
CB B:GLU650 4.3 13.2 1.0
CA B:LEU670 4.3 25.5 1.0
N B:ASP648 4.5 17.6 1.0
C B:ASN649 4.5 12.4 1.0
CA B:ASN649 4.5 14.0 1.0
OG B:SER647 4.6 15.3 1.0
CB B:LEU670 4.6 26.4 1.0
C B:PRO669 4.8 29.8 1.0
CB B:PRO669 4.9 31.9 1.0
N B:LEU651 4.9 20.7 1.0
OE2 B:GLU650 4.9 16.7 1.0
N B:ASP671 5.0 22.8 1.0
CB B:SER647 5.0 18.2 1.0

Sodium binding site 8 out of 14 in 3t0b

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Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:13.1
occ:1.00
 O C:HOH4992 2.2 15.5 1.0
O6 C:IPT2001 2.3 14.8 1.0
O C:PHE601 2.4 9.9 1.0
OD1 C:ASN604 2.4 6.7 1.0
OD2 C:ASP201 2.4 13.2 1.0
CG C:ASP201 3.2 15.4 1.0
CG C:ASN604 3.4 7.0 1.0
C6 C:IPT2001 3.4 10.9 1.0
OD1 C:ASP201 3.5 13.1 1.0
C C:PHE601 3.5 11.3 1.0
OH C:TYR100 3.5 12.7 1.0
ND2 C:ASN604 3.7 2.2 1.0
CA C:CYS602 4.1 10.6 1.0
O4 C:IPT2001 4.1 9.4 1.0
N C:CYS602 4.2 9.7 1.0
NE1 C:TRP568 4.2 7.3 1.0
O C:HOH4076 4.3 8.5 1.0
CB C:ASP201 4.4 12.7 1.0
C4 C:IPT2001 4.5 14.4 1.0
C5 C:IPT2001 4.5 12.1 1.0
O C:ASP201 4.5 7.8 1.0
CA C:PHE601 4.6 9.8 1.0
CB C:PHE601 4.6 6.8 1.0
C C:CYS602 4.6 10.9 1.0
CZ C:TYR100 4.6 12.1 1.0
CB C:ASN604 4.7 8.0 1.0
NE2 C:HIS540 4.8 12.5 1.0
CZ2 C:TRP568 4.8 10.7 1.0
CE2 C:TRP568 4.8 12.3 1.0

Sodium binding site 9 out of 14 in 3t0b

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Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:15.9
occ:1.00
 O C:HOH4578 2.3 24.2 1.0
O C:PHE556 2.4 13.5 1.0
O C:LEU562 2.4 11.3 1.0
O C:TYR559 2.5 14.9 1.0
O C:HOH4406 2.7 26.5 1.0
O C:PRO560 3.2 12.2 1.0
C C:LEU562 3.4 9.6 1.0
C C:PHE556 3.5 12.8 1.0
C C:TYR559 3.5 12.0 1.0
C C:PRO560 3.7 13.2 1.0
CA C:PRO560 3.8 10.9 1.0
O C:HOH4300 3.8 18.8 1.0
N C:PRO560 4.1 10.6 1.0
N C:LEU562 4.2 7.7 1.0
CA C:PHE556 4.2 11.3 1.0
CA C:GLN563 4.2 10.3 1.0
N C:GLN563 4.2 10.7 1.0
CA C:LEU562 4.3 8.2 1.0
N C:ARG557 4.6 12.9 1.0
CD1 C:LEU350 4.6 8.3 1.0
N C:ARG561 4.6 10.1 1.0
CB C:LEU562 4.6 8.0 1.0
CA C:TYR559 4.7 12.3 1.0
CG C:GLN563 4.7 11.3 1.0
N C:TYR559 4.7 11.1 1.0
CA C:ARG557 4.8 14.4 1.0
CB C:PHE556 4.8 7.9 1.0
C C:ARG557 4.9 13.1 1.0
C C:ARG561 5.0 10.0 1.0
O C:ARG557 5.0 16.6 1.0

Sodium binding site 10 out of 14 in 3t0b

Go back to Sodium Binding Sites List in 3t0b
Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3103

b:26.6
occ:1.00
 O C:THR970 2.4 22.1 1.0
O C:LEU967 2.5 12.7 1.0
O C:HOH4641 2.6 33.3 1.0
O C:PRO932 2.8 15.2 1.0
O C:HOH4226 3.3 9.2 1.0
C C:THR970 3.4 21.0 1.0
CZ C:PHE931 3.6 15.5 1.0
C C:LEU967 3.7 14.6 1.0
C C:PRO932 3.7 13.4 1.0
O C:HOH4515 3.7 19.1 1.0
CE1 C:PHE931 3.8 13.5 1.0
O C:MET968 3.9 20.1 1.0
C C:MET968 3.9 18.7 1.0
CB C:PRO932 4.0 9.2 1.0
CD C:PRO932 4.0 12.1 1.0
CA C:MET968 4.1 20.3 1.0
N C:THR970 4.1 20.7 1.0
CE2 C:PHE931 4.1 6.5 1.0
N C:PRO932 4.2 13.5 1.0
CA C:PRO932 4.2 11.4 1.0
N C:SER971 4.3 16.4 1.0
CA C:SER971 4.3 17.7 1.0
N C:MET968 4.3 17.7 1.0
CA C:THR970 4.3 20.1 1.0
CD1 C:PHE931 4.4 13.5 1.0
CG C:PRO932 4.4 11.2 1.0
N C:GLU969 4.5 16.6 1.0
CD2 C:PHE931 4.6 10.5 1.0
CG C:PHE931 4.8 9.9 1.0
C C:GLU969 4.8 20.7 1.0
N C:SER933 4.8 13.3 1.0
CA C:LEU967 4.9 13.2 1.0
C C:PHE931 5.0 12.9 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Er-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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