Atomistry » Sodium » PDB 1jb7-1k73 » 1jz8
Atomistry »
  Sodium »
    PDB 1jb7-1k73 »
      1jz8 »

Sodium in PDB 1jz8: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose, PDB code: 1jz8 was solved by D.H.Juers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.390, 168.710, 200.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.8

Other elements in 1jz8:

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose also contains other interesting chemical elements:

Magnesium (Mg) 16 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 (E537Q) in Complex with Allolactose (pdb code 1jz8). 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 (E537Q) in Complex with Allolactose, PDB code: 1jz8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:10.5
occ:1.00
O A:HOH8876 2.2 14.8 1.0
O6 A:LAK2001 2.3 12.9 1.0
OD1 A:ASN604 2.4 9.9 1.0
O A:PHE601 2.4 9.6 1.0
OD2 A:ASP201 2.4 10.2 1.0
C6 A:LAK2001 3.1 17.8 1.0
CG A:ASP201 3.3 9.5 1.0
CG A:ASN604 3.3 9.6 1.0
C A:PHE601 3.5 12.6 1.0
ND2 A:ASN604 3.6 8.9 1.0
OD1 A:ASP201 3.6 10.5 1.0
OH A:TYR100 3.7 11.0 1.0
NE1 A:TRP568 4.1 10.2 1.0
O4 A:LAK2001 4.2 15.8 1.0
C5 A:LAK2001 4.2 16.6 1.0
CA A:CYS602 4.3 9.6 1.0
C4 A:LAK2001 4.3 21.5 1.0
N A:CYS602 4.4 10.1 1.0
CB A:ASP201 4.5 8.7 1.0
O A:HOH8654 4.5 11.6 1.0
CB A:PHE601 4.5 10.4 1.0
CA A:PHE601 4.5 12.5 1.0
NE2 A:HIS540 4.6 9.6 1.0
CB A:ASN604 4.7 7.2 1.0
O A:ASP201 4.7 8.6 1.0
C A:CYS602 4.7 11.8 1.0
CZ A:TYR100 4.8 14.5 1.0
CE2 A:TRP568 4.9 10.2 1.0
CZ2 A:TRP568 4.9 12.6 1.0

Sodium binding site 2 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:9.8
occ:1.00
O A:HOH9231 2.2 24.9 1.0
O A:PHE556 2.3 10.4 1.0
O A:LEU562 2.3 8.9 1.0
O A:TYR559 2.3 9.8 1.0
O A:HOH9004 2.4 20.4 1.0
O A:PRO560 3.2 8.9 1.0
C A:TYR559 3.4 11.2 1.0
C A:LEU562 3.4 8.7 1.0
C A:PHE556 3.5 9.6 1.0
C A:PRO560 3.5 7.4 1.0
CA A:PRO560 3.6 8.0 1.0
N A:PRO560 3.9 8.0 1.0
N A:LEU562 4.0 5.9 1.0
O A:HOH8883 4.1 14.5 1.0
CA A:PHE556 4.1 7.0 1.0
CA A:LEU562 4.2 6.5 1.0
O A:HOH9632 4.2 32.0 1.0
O A:HOH9409 4.3 29.6 1.0
N A:GLN563 4.3 6.5 1.0
CB A:LEU562 4.4 7.1 1.0
N A:TYR559 4.4 7.0 1.0
CA A:GLN563 4.5 6.6 1.0
CA A:TYR559 4.5 5.9 1.0
N A:ARG561 4.5 7.0 1.0
N A:ARG557 4.5 6.7 1.0
CA A:ARG557 4.6 4.9 1.0
O A:ARG557 4.7 9.6 1.0
O A:HOH9422 4.7 39.9 1.0
C A:ARG557 4.7 8.1 1.0
CB A:PHE556 4.8 6.1 1.0
CG A:GLN563 4.8 6.3 1.0
C A:ARG561 4.9 7.4 1.0
CD1 A:LEU350 4.9 8.0 1.0
O A:ALA555 4.9 8.6 1.0

Sodium binding site 3 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:20.4
occ:1.00
O A:HOH9330 2.4 30.6 1.0
O A:PRO932 2.4 12.4 1.0
O A:LEU967 2.5 14.7 1.0
O A:THR970 2.6 20.2 1.0
O A:HOH8806 2.6 14.3 1.0
O A:HOH9146 3.4 29.3 1.0
CZ A:PHE931 3.4 18.3 1.0
C A:PRO932 3.5 12.3 1.0
C A:LEU967 3.6 15.3 1.0
C A:THR970 3.8 18.2 1.0
CE1 A:PHE931 3.8 15.7 1.0
CE2 A:PHE931 3.8 12.4 1.0
CA A:MET968 3.9 11.6 1.0
O A:MET968 3.9 20.7 1.0
CB A:PRO932 4.0 11.9 1.0
C A:MET968 4.0 18.2 1.0
CA A:PRO932 4.1 11.2 1.0
CD A:PRO932 4.2 11.1 1.0
N A:PRO932 4.2 10.6 1.0
N A:THR970 4.2 12.8 1.0
N A:MET968 4.3 12.3 1.0
CD1 A:PHE931 4.5 11.9 1.0
N A:SER933 4.5 8.9 1.0
CD2 A:PHE931 4.5 13.5 1.0
CG A:PRO932 4.6 19.8 1.0
CA A:THR970 4.6 14.6 1.0
N A:SER971 4.7 16.9 1.0
CA A:SER933 4.7 10.5 1.0
CA A:SER971 4.7 15.1 1.0
N A:GLU969 4.7 10.8 1.0
CG A:PHE931 4.8 12.3 1.0
CA A:LEU967 4.8 11.4 1.0
C A:PHE931 4.9 13.3 1.0

Sodium binding site 4 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:20.9
occ:1.00
O A:DMS8425 2.2 26.3 1.0
O A:LEU670 2.2 14.1 1.0
O A:HOH9344 2.4 32.5 1.0
O A:SER647 2.4 13.0 1.0
O A:HOH9508 2.5 34.3 1.0
O A:GLU650 2.6 14.8 1.0
S A:DMS8425 3.3 30.7 1.0
C A:LEU670 3.4 14.7 1.0
N A:GLU650 3.6 10.5 1.0
C A:GLU650 3.6 11.6 1.0
C A:SER647 3.7 14.6 1.0
C2 A:DMS8425 3.7 32.5 1.0
N A:LEU670 3.8 19.3 1.0
CA A:GLU650 4.0 11.4 1.0
CA A:LEU670 4.1 17.3 1.0
CA A:ASP648 4.1 13.2 1.0
CB A:LEU670 4.2 16.0 1.0
CB A:GLU650 4.2 9.1 1.0
N A:ASN649 4.2 14.8 1.0
C A:ASP648 4.2 15.8 1.0
OG A:SER647 4.2 14.3 1.0
N A:ASP648 4.4 12.7 1.0
N A:ASP671 4.4 14.5 1.0
CB A:SER647 4.6 14.3 1.0
C A:ASN649 4.7 12.1 1.0
CA A:ASP671 4.7 17.1 1.0
C A:PRO669 4.8 16.8 1.0
CA A:SER647 4.8 10.5 1.0
N A:LEU651 4.8 13.1 1.0
O A:ASP648 4.8 14.9 1.0
CA A:ASN649 4.9 13.2 1.0
OE1 A:GLU650 5.0 14.3 1.0
C1 A:DMS8425 5.0 23.8 1.0

Sodium binding site 5 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:10.4
occ:1.00
O6 B:LAK2001 2.2 14.5 1.0
O B:HOH9004 2.3 13.5 1.0
OD2 B:ASP201 2.3 9.9 1.0
O B:PHE601 2.3 10.3 1.0
OD1 B:ASN604 2.4 8.9 1.0
C6 B:LAK2001 3.1 19.7 1.0
CG B:ASP201 3.3 12.4 1.0
CG B:ASN604 3.4 10.2 1.0
C B:PHE601 3.5 9.2 1.0
OD1 B:ASP201 3.6 9.4 1.0
OH B:TYR100 3.7 10.2 1.0
ND2 B:ASN604 3.7 9.6 1.0
O4 B:LAK2001 4.1 15.4 1.0
NE1 B:TRP568 4.2 9.9 1.0
CA B:CYS602 4.2 8.8 1.0
N B:CYS602 4.3 9.1 1.0
C5 B:LAK2001 4.3 16.8 1.0
C4 B:LAK2001 4.4 13.8 1.0
O B:HOH8783 4.4 11.0 1.0
CB B:PHE601 4.4 8.8 1.0
CA B:PHE601 4.5 7.3 1.0
CB B:ASP201 4.5 8.4 1.0
NE2 B:HIS540 4.5 7.7 1.0
O B:ASP201 4.7 8.9 1.0
C B:CYS602 4.7 8.5 1.0
CZ B:TYR100 4.8 12.8 1.0
CB B:ASN604 4.8 6.7 1.0
CZ2 B:TRP568 4.9 11.8 1.0
CE2 B:TRP568 4.9 10.2 1.0

Sodium binding site 6 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:9.9
occ:1.00
O B:LEU562 2.2 7.3 1.0
O B:PHE556 2.3 9.3 1.0
O B:TYR559 2.3 10.4 1.0
O B:HOH9352 2.3 22.9 1.0
O B:HOH9128 2.6 17.8 1.0
O B:PRO560 3.2 9.5 1.0
C B:TYR559 3.3 9.8 1.0
C B:LEU562 3.3 9.5 1.0
C B:PHE556 3.4 8.5 1.0
C B:PRO560 3.6 7.8 1.0
CA B:PRO560 3.7 5.7 1.0
N B:PRO560 3.9 8.2 1.0
N B:LEU562 3.9 5.9 1.0
CA B:PHE556 4.0 6.3 1.0
O B:HOH9011 4.1 13.5 1.0
CA B:LEU562 4.1 6.0 1.0
CB B:LEU562 4.2 7.1 1.0
N B:GLN563 4.3 7.1 1.0
N B:TYR559 4.3 7.8 1.0
O B:HOH9575 4.3 23.2 1.0
CA B:TYR559 4.4 5.7 1.0
CA B:GLN563 4.4 5.0 1.0
O B:HOH9531 4.4 36.1 1.0
N B:ARG557 4.5 5.4 1.0
N B:ARG561 4.5 8.0 1.0
CA B:ARG557 4.6 7.8 1.0
C B:ARG557 4.7 10.1 1.0
CB B:PHE556 4.7 5.5 1.0
O B:ARG557 4.7 10.8 1.0
CG B:GLN563 4.7 8.9 1.0
CD1 B:LEU350 4.8 9.0 1.0
C B:ARG561 4.8 7.5 1.0
O B:ALA555 4.9 8.9 1.0
CB B:TYR559 4.9 7.1 1.0

Sodium binding site 7 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:18.1
occ:1.00
O B:LEU967 2.4 13.0 1.0
O B:PRO932 2.4 11.1 1.0
O B:THR970 2.6 22.3 1.0
O B:HOH9448 2.6 38.3 1.0
O B:HOH8934 2.6 14.7 1.0
CZ B:PHE931 3.4 13.6 1.0
C B:PRO932 3.5 10.4 1.0
C B:LEU967 3.6 13.7 1.0
C B:THR970 3.7 16.4 1.0
CE1 B:PHE931 3.7 11.1 1.0
O B:HOH9269 3.8 23.0 1.0
CE2 B:PHE931 3.8 12.8 1.0
O B:MET968 3.9 21.4 1.0
CA B:MET968 3.9 11.2 1.0
C B:MET968 4.0 18.4 1.0
CB B:PRO932 4.0 11.5 1.0
CA B:PRO932 4.2 10.2 1.0
N B:THR970 4.2 12.9 1.0
CD B:PRO932 4.2 10.8 1.0
N B:PRO932 4.2 11.3 1.0
N B:MET968 4.2 12.3 1.0
CD1 B:PHE931 4.4 10.9 1.0
N B:SER933 4.5 9.6 1.0
CD2 B:PHE931 4.5 10.0 1.0
CA B:THR970 4.6 13.1 1.0
CG B:PRO932 4.6 8.6 1.0
N B:SER971 4.6 15.4 1.0
CA B:SER971 4.7 15.3 1.0
CA B:SER933 4.7 8.6 1.0
CA B:LEU967 4.7 11.2 1.0
N B:GLU969 4.7 12.4 1.0
CG B:PHE931 4.7 10.9 1.0
C B:PHE931 4.9 12.8 1.0

Sodium binding site 8 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:24.3
occ:1.00
O B:DMS8425 2.1 26.6 1.0
O B:LEU670 2.3 18.5 1.0
O B:HOH9611 2.5 27.1 1.0
O B:SER647 2.5 14.5 1.0
O B:GLU650 2.6 16.0 1.0
O B:HOH9464 2.6 25.9 1.0
S B:DMS8425 3.3 32.3 1.0
C B:LEU670 3.5 16.9 1.0
N B:GLU650 3.6 13.0 1.0
C B:GLU650 3.6 16.8 1.0
C B:SER647 3.7 22.9 1.0
N B:LEU670 3.7 16.9 1.0
C2 B:DMS8425 3.8 26.6 1.0
CA B:LEU670 4.0 19.4 1.0
CA B:GLU650 4.1 11.3 1.0
CA B:ASP648 4.1 14.2 1.0
N B:ASN649 4.1 13.8 1.0
CB B:LEU670 4.2 19.2 1.0
C B:ASP648 4.2 20.4 1.0
CB B:GLU650 4.2 12.0 1.0
OG B:SER647 4.2 13.9 1.0
N B:ASP648 4.4 13.6 1.0
O B:HOH9773 4.5 41.2 1.0
N B:ASP671 4.6 13.8 1.0
O B:HOH9590 4.7 34.0 1.0
C B:ASN649 4.7 16.7 1.0
CB B:SER647 4.7 13.9 1.0
CA B:ASP671 4.8 17.7 1.0
C B:PRO669 4.8 17.3 1.0
O B:ASP648 4.8 14.8 1.0
C1 B:DMS8425 4.8 17.7 1.0
O B:HOH9759 4.8 37.1 1.0
CA B:ASN649 4.8 10.9 1.0
N B:LEU651 4.8 13.6 1.0
CA B:SER647 4.8 12.3 1.0
OE1 B:GLU650 4.9 12.0 1.0

Sodium binding site 9 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:9.7
occ:1.00
O6 C:LAK2001 2.2 10.9 1.0
O C:HOH8902 2.3 16.0 1.0
OD1 C:ASN604 2.3 8.9 1.0
O C:PHE601 2.3 11.4 1.0
OD2 C:ASP201 2.4 10.1 1.0
C6 C:LAK2001 3.1 14.3 1.0
CG C:ASP201 3.3 11.7 1.0
CG C:ASN604 3.3 11.5 1.0
C C:PHE601 3.5 12.0 1.0
ND2 C:ASN604 3.6 10.1 1.0
OH C:TYR100 3.6 10.3 1.0
OD1 C:ASP201 3.7 10.7 1.0
O4 C:LAK2001 4.1 14.7 1.0
CA C:CYS602 4.2 9.7 1.0
NE1 C:TRP568 4.2 9.8 1.0
C5 C:LAK2001 4.3 16.1 1.0
N C:CYS602 4.3 8.6 1.0
C4 C:LAK2001 4.4 20.9 1.0
O C:HOH8679 4.4 10.9 1.0
CB C:PHE601 4.4 7.4 1.0
CA C:PHE601 4.5 10.7 1.0
CB C:ASP201 4.5 9.8 1.0
NE2 C:HIS540 4.6 10.6 1.0
C C:CYS602 4.7 10.0 1.0
O C:ASP201 4.7 8.9 1.0
CB C:ASN604 4.7 7.5 1.0
CZ C:TYR100 4.8 9.7 1.0
CE2 C:TRP568 4.9 9.3 1.0
CZ2 C:TRP568 4.9 11.4 1.0

Sodium binding site 10 out of 16 in 1jz8

Go back to Sodium Binding Sites List in 1jz8
Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) 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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:10.7
occ:1.00
O C:PHE556 2.2 8.8 1.0
O C:HOH9255 2.3 25.8 1.0
O C:LEU562 2.3 8.1 1.0
O C:TYR559 2.4 10.3 1.0
O C:HOH9028 2.5 20.3 1.0
O C:PRO560 3.1 10.8 1.0
C C:TYR559 3.3 7.9 1.0
C C:LEU562 3.4 7.2 1.0
C C:PHE556 3.4 7.3 1.0
C C:PRO560 3.5 10.8 1.0
CA C:PRO560 3.7 9.4 1.0
N C:PRO560 3.9 10.0 1.0
N C:LEU562 4.0 7.2 1.0
CA C:PHE556 4.1 6.2 1.0
O C:HOH8909 4.1 13.2 1.0
CA C:LEU562 4.2 6.4 1.0
O C:HOH9618 4.3 35.5 1.0
O C:HOH9685 4.3 36.6 1.0
N C:GLN563 4.3 7.9 1.0
CB C:LEU562 4.4 7.0 1.0
N C:TYR559 4.4 8.5 1.0
CA C:GLN563 4.4 6.7 1.0
CA C:TYR559 4.4 7.8 1.0
N C:ARG557 4.5 8.1 1.0
N C:ARG561 4.5 6.7 1.0
O C:HOH9464 4.5 50.2 1.0
CA C:ARG557 4.6 5.2 1.0
CG C:GLN563 4.7 6.8 1.0
C C:ARG557 4.7 8.9 1.0
O C:ARG557 4.7 12.3 1.0
CB C:PHE556 4.7 8.2 1.0
C C:ARG561 4.8 8.1 1.0
CD1 C:LEU350 4.8 7.3 1.0
O C:ALA555 4.9 9.0 1.0
CB C:TYR559 4.9 7.9 1.0

Reference:

D.H.Juers, T.D.Heightman, A.Vasella, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews. A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Tue Dec 15 05:26:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy