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Sodium in PDB 1jz7: E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose, PDB code: 1jz7 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) 40.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.590, 168.530, 200.550, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.9

Other elements in 1jz7:

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

Magnesium (Mg) 15 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 in Complex with Galactose (pdb code 1jz7). 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 in Complex with Galactose, PDB code: 1jz7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 1jz7

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


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

b:13.2
occ:1.00
O A:HOH8778 2.3 17.2 1.0
O A:PHE601 2.3 11.4 1.0
OD1 A:ASN604 2.3 12.4 1.0
O6 A:GAL2001 2.3 17.4 1.0
OD2 A:ASP201 2.4 10.8 1.0
CG A:ASP201 3.3 10.6 1.0
CG A:ASN604 3.3 14.7 1.0
C A:PHE601 3.5 13.6 1.0
C6 A:GAL2001 3.5 20.9 1.0
ND2 A:ASN604 3.6 10.8 1.0
OD1 A:ASP201 3.7 11.8 1.0
OH A:TYR100 3.7 12.9 1.0
O4 A:GAL2001 4.0 15.0 1.0
C4 A:GAL2001 4.0 18.5 1.0
NE1 A:TRP568 4.1 10.3 1.0
CA A:CYS602 4.3 13.5 1.0
C5 A:GAL2001 4.3 19.1 1.0
N A:CYS602 4.3 12.4 1.0
O A:HOH8556 4.4 12.4 1.0
CB A:ASP201 4.5 8.6 1.0
CA A:PHE601 4.5 15.3 1.0
CB A:PHE601 4.5 12.2 1.0
NE2 A:HIS540 4.6 10.9 1.0
CB A:ASN604 4.7 9.1 1.0
O A:ASP201 4.8 10.7 1.0
C A:CYS602 4.8 14.3 1.0
CE2 A:TRP568 4.9 10.5 1.0
CZ A:TYR100 4.9 17.7 1.0
CD2 A:PHE601 4.9 13.9 1.0
CZ2 A:TRP568 4.9 12.2 1.0

Sodium binding site 2 out of 16 in 1jz7

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


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

b:12.0
occ:1.00
O A:PHE556 2.2 10.6 1.0
O A:LEU562 2.3 10.9 1.0
O A:TYR559 2.4 10.1 1.0
O A:HOH8904 2.4 24.5 1.0
O A:HOH9112 2.6 21.4 1.0
O A:PRO560 3.2 11.1 1.0
C A:TYR559 3.4 10.4 1.0
C A:LEU562 3.4 11.7 1.0
C A:PHE556 3.4 10.0 1.0
C A:PRO560 3.6 8.5 1.0
CA A:PRO560 3.7 9.6 1.0
N A:PRO560 4.0 10.4 1.0
N A:LEU562 4.0 8.7 1.0
O A:HOH8785 4.1 15.2 1.0
CA A:PHE556 4.1 7.4 1.0
CA A:LEU562 4.2 8.9 1.0
O A:HOH9263 4.2 33.5 1.0
N A:GLN563 4.3 7.8 1.0
CB A:LEU562 4.4 8.4 1.0
CA A:GLN563 4.4 9.0 1.0
N A:TYR559 4.5 7.6 1.0
N A:ARG557 4.5 8.0 1.0
CA A:TYR559 4.5 8.8 1.0
N A:ARG561 4.6 7.7 1.0
CA A:ARG557 4.6 5.6 1.0
CG A:GLN563 4.7 7.8 1.0
O A:ARG557 4.7 13.4 1.0
C A:ARG557 4.7 12.6 1.0
CB A:PHE556 4.8 7.8 1.0
O A:ALA555 4.9 9.8 1.0
C A:ARG561 4.9 9.3 1.0
CD1 A:LEU350 4.9 10.3 1.0

Sodium binding site 3 out of 16 in 1jz7

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


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

b:28.2
occ:1.00
O A:PRO932 2.6 13.7 1.0
O A:LEU967 2.6 16.5 1.0
O A:HOH8708 2.8 16.4 1.0
O A:THR970 3.0 21.2 1.0
O A:HOH9195 3.1 36.7 1.0
O A:HOH9034 3.2 22.2 1.0
CZ A:PHE931 3.4 15.8 1.0
C A:PRO932 3.6 12.8 1.0
CE1 A:PHE931 3.7 13.8 1.0
C A:LEU967 3.7 14.6 1.0
O A:MET968 3.8 21.4 1.0
CE2 A:PHE931 3.8 15.5 1.0
CA A:MET968 3.9 14.1 1.0
C A:MET968 3.9 20.9 1.0
C A:THR970 4.0 21.1 1.0
CB A:PRO932 4.0 13.4 1.0
CD A:PRO932 4.2 11.0 1.0
CA A:PRO932 4.2 15.2 1.0
N A:THR970 4.3 16.1 1.0
N A:PRO932 4.3 11.7 1.0
N A:MET968 4.3 12.2 1.0
CD1 A:PHE931 4.4 12.0 1.0
CD2 A:PHE931 4.5 14.3 1.0
CG A:PRO932 4.5 19.8 1.0
N A:GLU969 4.7 13.3 1.0
N A:SER933 4.7 10.7 1.0
CG A:PHE931 4.7 14.2 1.0
CA A:THR970 4.8 15.4 1.0
N A:SER971 4.8 16.9 1.0
CA A:SER971 4.8 20.2 1.0
CA A:LEU967 4.9 12.8 1.0
CA A:SER933 4.9 14.1 1.0

Sodium binding site 4 out of 16 in 1jz7

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


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

b:24.1
occ:1.00
O A:DMS8425 2.0 27.9 1.0
O A:LEU670 2.4 17.1 1.0
O A:SER647 2.5 15.8 1.0
O A:GLU650 2.5 17.6 1.0
O A:HOH9350 2.6 36.5 1.0
O A:HOH9207 2.7 42.1 1.0
S A:DMS8425 3.2 39.0 1.0
N A:GLU650 3.5 14.4 1.0
C A:GLU650 3.5 16.4 1.0
C A:LEU670 3.5 19.5 1.0
C A:SER647 3.7 15.1 1.0
C2 A:DMS8425 3.8 40.2 1.0
N A:LEU670 3.9 20.4 1.0
CA A:GLU650 4.0 13.5 1.0
N A:ASN649 4.1 18.1 1.0
CB A:GLU650 4.1 12.2 1.0
CA A:ASP648 4.1 17.1 1.0
C A:ASP648 4.1 22.8 1.0
OG A:SER647 4.2 14.9 1.0
CA A:LEU670 4.3 17.9 1.0
O A:HOH9533 4.3 48.9 1.0
CB A:LEU670 4.4 18.3 1.0
N A:ASP648 4.4 13.9 1.0
C A:ASN649 4.6 17.4 1.0
N A:ASP671 4.6 16.9 1.0
CB A:SER647 4.7 16.1 1.0
O A:ASP648 4.8 18.6 1.0
CA A:ASN649 4.8 15.2 1.0
N A:LEU651 4.8 16.7 1.0
C1 A:DMS8425 4.8 32.9 1.0
CA A:ASP671 4.8 17.0 1.0
CA A:SER647 4.9 13.3 1.0
OE1 A:GLU650 4.9 16.1 1.0
C A:PRO669 4.9 18.7 1.0

Sodium binding site 5 out of 16 in 1jz7

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


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

b:11.7
occ:1.00
O B:HOH8888 2.2 17.0 1.0
OD2 B:ASP201 2.3 13.4 1.0
O6 B:GAL2001 2.3 18.1 1.0
O B:PHE601 2.4 12.8 1.0
OD1 B:ASN604 2.4 11.2 1.0
CG B:ASP201 3.3 13.0 1.0
CG B:ASN604 3.4 11.4 1.0
C B:PHE601 3.5 12.8 1.0
C6 B:GAL2001 3.6 21.0 1.0
ND2 B:ASN604 3.7 12.6 1.0
OH B:TYR100 3.7 12.6 1.0
OD1 B:ASP201 3.7 11.2 1.0
O4 B:GAL2001 4.0 13.2 1.0
C4 B:GAL2001 4.0 31.0 1.0
NE1 B:TRP568 4.2 10.2 1.0
CA B:CYS602 4.3 12.2 1.0
N B:CYS602 4.3 10.4 1.0
C5 B:GAL2001 4.3 20.6 1.0
O B:HOH8668 4.5 12.0 1.0
CB B:ASP201 4.5 9.7 1.0
CB B:PHE601 4.5 11.8 1.0
CA B:PHE601 4.5 10.6 1.0
NE2 B:HIS540 4.6 11.4 1.0
O B:ASP201 4.7 12.5 1.0
C B:CYS602 4.7 11.6 1.0
CB B:ASN604 4.8 9.7 1.0
CZ B:TYR100 4.8 13.1 1.0
CE2 B:TRP568 4.9 15.7 1.0
CD2 B:PHE601 5.0 14.8 1.0
CZ2 B:TRP568 5.0 13.4 1.0

Sodium binding site 6 out of 16 in 1jz7

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


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

b:11.9
occ:1.00
O B:PHE556 2.2 9.5 1.0
O B:TYR559 2.3 12.1 1.0
O B:LEU562 2.3 10.1 1.0
O B:HOH9013 2.5 20.8 1.0
O B:HOH9229 2.6 25.8 1.0
O B:PRO560 3.2 10.4 1.0
C B:TYR559 3.3 11.3 1.0
C B:LEU562 3.4 9.4 1.0
C B:PHE556 3.4 8.7 1.0
C B:PRO560 3.5 11.6 1.0
CA B:PRO560 3.6 9.3 1.0
N B:PRO560 3.9 8.9 1.0
N B:LEU562 3.9 7.7 1.0
CA B:PHE556 4.1 8.4 1.0
O B:HOH8895 4.1 15.7 1.0
CA B:LEU562 4.1 7.5 1.0
CB B:LEU562 4.2 7.0 1.0
N B:GLN563 4.3 7.2 1.0
CA B:TYR559 4.3 7.3 1.0
N B:TYR559 4.4 8.9 1.0
O B:HOH9397 4.4 37.3 1.0
CA B:GLN563 4.4 7.0 1.0
O B:HOH9440 4.5 32.2 1.0
N B:ARG557 4.5 7.7 1.0
N B:ARG561 4.5 9.1 1.0
CA B:ARG557 4.6 7.7 1.0
CB B:PHE556 4.7 8.8 1.0
CG B:GLN563 4.7 7.2 1.0
C B:ARG557 4.7 11.8 1.0
O B:ARG557 4.8 13.5 1.0
CD1 B:LEU350 4.8 9.4 1.0
CB B:TYR559 4.9 8.6 1.0
C B:ARG561 4.9 7.1 1.0
O B:ALA555 4.9 10.5 1.0

Sodium binding site 7 out of 16 in 1jz7

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


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

b:24.7
occ:1.00
O B:PRO932 2.4 13.3 1.0
O B:LEU967 2.6 15.8 1.0
O B:THR970 2.8 24.3 1.0
O B:HOH8818 2.8 17.7 1.0
O B:HOH9320 3.3 35.3 1.0
CZ B:PHE931 3.4 15.7 1.0
C B:PRO932 3.4 11.4 1.0
O B:HOH9147 3.4 24.1 1.0
CE1 B:PHE931 3.7 14.8 1.0
C B:LEU967 3.7 15.2 1.0
CE2 B:PHE931 3.8 15.6 1.0
C B:THR970 3.8 18.5 1.0
O B:MET968 3.9 19.9 1.0
CA B:MET968 4.0 10.0 1.0
CB B:PRO932 4.0 12.3 1.0
C B:MET968 4.0 20.8 1.0
N B:PRO932 4.0 14.2 1.0
CD B:PRO932 4.1 14.7 1.0
CA B:PRO932 4.1 11.6 1.0
N B:THR970 4.3 16.7 1.0
CD1 B:PHE931 4.3 14.4 1.0
CD2 B:PHE931 4.4 11.7 1.0
N B:MET968 4.4 13.5 1.0
N B:SER933 4.4 11.6 1.0
CG B:PRO932 4.5 12.8 1.0
CG B:PHE931 4.6 10.7 1.0
N B:SER971 4.6 16.2 1.0
CA B:THR970 4.7 16.7 1.0
CA B:SER971 4.7 15.8 1.0
CA B:SER933 4.7 10.7 1.0
C B:PHE931 4.8 17.3 1.0
N B:GLU969 4.8 16.2 1.0
CA B:LEU967 4.8 15.8 1.0

Sodium binding site 8 out of 16 in 1jz7

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


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

b:27.3
occ:1.00
O B:DMS8425 2.1 32.6 1.0
O B:LEU670 2.4 19.7 1.0
O B:SER647 2.4 17.2 1.0
O B:HOH9473 2.5 27.5 1.0
O B:GLU650 2.6 19.4 1.0
O B:HOH9334 2.7 25.1 1.0
S B:DMS8425 3.3 40.8 1.0
N B:GLU650 3.5 16.1 1.0
C B:LEU670 3.6 16.5 1.0
C B:GLU650 3.6 19.6 1.0
C B:SER647 3.6 23.8 1.0
C2 B:DMS8425 3.7 35.4 1.0
N B:LEU670 3.9 20.8 1.0
CA B:GLU650 4.0 14.3 1.0
CA B:ASP648 4.0 17.4 1.0
C B:ASP648 4.1 21.0 1.0
CB B:LEU670 4.2 20.0 1.0
CA B:LEU670 4.2 21.4 1.0
N B:ASN649 4.2 19.1 1.0
CB B:GLU650 4.2 15.4 1.0
OG B:SER647 4.2 12.9 1.0
N B:ASP648 4.3 14.5 1.0
O B:HOH9454 4.3 32.0 1.0
C B:ASN649 4.7 20.9 1.0
N B:ASP671 4.7 18.2 1.0
O B:HOH9570 4.7 47.0 1.0
CB B:SER647 4.7 16.8 1.0
O B:ASP648 4.7 18.2 1.0
C1 B:DMS8425 4.7 27.9 1.0
CA B:SER647 4.8 17.3 1.0
N B:LEU651 4.8 17.6 1.0
CA B:ASP671 4.8 24.6 1.0
CA B:ASN649 4.8 17.0 1.0
C B:PRO669 4.9 17.7 1.0
OE1 B:GLU650 4.9 13.9 1.0

Sodium binding site 9 out of 16 in 1jz7

Go back to Sodium Binding Sites List in 1jz7
Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose


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

b:11.5
occ:1.00
O6 C:GAL2001 2.3 15.9 1.0
O C:HOH8903 2.3 17.8 1.0
OD2 C:ASP201 2.3 11.6 1.0
O C:PHE601 2.4 12.2 1.0
OD1 C:ASN604 2.4 11.5 1.0
CG C:ASP201 3.3 13.1 1.0
C6 C:GAL2001 3.4 24.0 1.0
CG C:ASN604 3.4 11.7 1.0
C C:PHE601 3.5 14.1 1.0
ND2 C:ASN604 3.7 12.7 1.0
OH C:TYR100 3.7 13.9 1.0
OD1 C:ASP201 3.7 12.2 1.0
C4 C:GAL2001 3.9 25.2 1.0
O4 C:GAL2001 4.0 14.5 1.0
NE1 C:TRP568 4.2 10.3 1.0
C5 C:GAL2001 4.2 17.7 1.0
CA C:CYS602 4.3 12.0 1.0
N C:CYS602 4.3 11.8 1.0
CB C:ASP201 4.4 12.2 1.0
O C:HOH8682 4.4 12.0 1.0
CB C:PHE601 4.5 12.5 1.0
CA C:PHE601 4.5 13.8 1.0
NE2 C:HIS540 4.6 12.1 1.0
O C:ASP201 4.7 11.0 1.0
C C:CYS602 4.8 15.9 1.0
CB C:ASN604 4.8 9.2 1.0
CZ C:TYR100 4.8 13.5 1.0
CE2 C:TRP568 4.9 11.7 1.0
CZ2 C:TRP568 5.0 12.6 1.0

Sodium binding site 10 out of 16 in 1jz7

Go back to Sodium Binding Sites List in 1jz7
Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose


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

b:12.7
occ:1.00
O C:PHE556 2.3 9.7 1.0
O C:TYR559 2.3 10.5 1.0
O C:LEU562 2.3 10.5 1.0
O C:HOH9025 2.4 23.0 1.0
O C:HOH9229 2.7 26.9 1.0
O C:PRO560 3.1 13.0 1.0
C C:TYR559 3.3 9.7 1.0
C C:LEU562 3.4 10.2 1.0
C C:PHE556 3.4 8.7 1.0
C C:PRO560 3.5 14.3 1.0
CA C:PRO560 3.7 10.5 1.0
N C:PRO560 3.9 11.9 1.0
N C:LEU562 4.0 8.1 1.0
O C:HOH8909 4.1 15.9 1.0
CA C:PHE556 4.1 8.5 1.0
CA C:LEU562 4.2 7.8 1.0
N C:GLN563 4.3 8.9 1.0
CB C:LEU562 4.4 7.3 1.0
CA C:TYR559 4.4 10.3 1.0
N C:TYR559 4.4 10.2 1.0
CA C:GLN563 4.4 8.8 1.0
N C:ARG557 4.5 9.3 1.0
O C:HOH9608 4.5 38.7 1.0
N C:ARG561 4.5 9.8 1.0
CA C:ARG557 4.6 8.1 1.0
CG C:GLN563 4.6 10.1 1.0
C C:ARG557 4.7 12.3 1.0
O C:ARG557 4.7 14.3 1.0
CB C:PHE556 4.8 10.6 1.0
C C:ARG561 4.9 10.7 1.0
CD1 C:LEU350 4.9 11.2 1.0
O C:ALA555 4.9 10.3 1.0
CB C:TYR559 4.9 9.2 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 05:26:55 2020

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