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Sodium in PDB 1jz5: E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on, PDB code: 1jz5 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) 17.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.690, 168.020, 201.040, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 23.1

Other elements in 1jz5:

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on also contains other interesting chemical elements:

Magnesium (Mg) 11 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 D-Galctopyranosyl-1- on (pdb code 1jz5). 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 D-Galctopyranosyl-1- on, PDB code: 1jz5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 1jz5

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


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:23.0
occ:1.00
O A:HOH8869 2.4 20.3 1.0
OD1 A:ASN604 2.4 20.9 1.0
O A:PHE601 2.4 20.1 1.0
OD2 A:ASP201 2.5 19.1 1.0
O6 A:1492001 2.5 21.3 1.0
CD2 A:PHE601 3.2 24.7 1.0
CE2 A:PHE601 3.2 29.5 1.0
CG A:ASP201 3.3 25.7 1.0
CG A:ASN604 3.4 21.9 1.0
C A:PHE601 3.6 28.1 1.0
ND2 A:ASN604 3.6 16.7 1.0
OD1 A:ASP201 3.7 22.7 1.0
C6 A:1492001 3.7 19.6 1.0
OH A:TYR100 3.9 23.6 1.0
CG A:PHE601 3.9 25.1 1.0
CZ A:PHE601 4.0 27.1 1.0
O4 A:1492001 4.1 16.4 1.0
C4 A:1492001 4.1 17.3 1.0
NE1 A:TRP568 4.2 20.9 1.0
CA A:CYS602 4.3 19.8 1.0
N A:CYS602 4.4 19.6 1.0
C5 A:1492001 4.5 17.6 1.0
NE2 A:HIS540 4.5 24.1 1.0
O A:HOH8652 4.5 23.9 1.0
CB A:ASP201 4.5 22.2 1.0
CD1 A:PHE601 4.6 22.1 1.0
CA A:PHE601 4.6 19.9 1.0
CE1 A:PHE601 4.6 23.9 1.0
CB A:PHE601 4.7 20.1 1.0
CB A:ASN604 4.8 14.1 1.0
C A:CYS602 4.8 24.8 1.0
O A:ASP201 4.8 16.6 1.0
CE2 A:TRP568 4.9 22.6 1.0

Sodium binding site 2 out of 16 in 1jz5

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Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:17.1
occ:1.00
O A:TYR559 2.3 18.8 1.0
O A:PHE556 2.4 19.3 1.0
O A:LEU562 2.4 17.3 1.0
O A:HOH8992 2.5 25.4 1.0
O A:HOH9188 2.6 24.3 1.0
O A:PRO560 3.1 17.1 1.0
C A:TYR559 3.3 20.8 1.0
C A:LEU562 3.5 17.9 1.0
C A:PHE556 3.5 21.2 1.0
C A:PRO560 3.6 14.8 1.0
CA A:PRO560 3.6 11.0 1.0
N A:PRO560 3.9 18.2 1.0
N A:LEU562 3.9 14.2 1.0
O A:HOH9334 4.0 62.2 1.0
O A:HOH8876 4.0 23.0 1.0
CA A:PHE556 4.2 11.2 1.0
CA A:LEU562 4.2 15.3 1.0
N A:GLN563 4.4 15.2 1.0
CB A:LEU562 4.4 12.6 1.0
CA A:GLN563 4.4 15.1 1.0
N A:TYR559 4.4 12.6 1.0
CA A:TYR559 4.4 12.9 1.0
N A:ARG561 4.5 13.3 1.0
N A:ARG557 4.5 16.6 1.0
CG A:GLN563 4.6 14.2 1.0
CA A:ARG557 4.7 9.1 1.0
C A:ARG557 4.7 13.7 1.0
O A:ARG557 4.8 18.0 1.0
CB A:PHE556 4.8 11.5 1.0
C A:ARG561 4.9 16.4 1.0
O A:ALA555 4.9 16.2 1.0
CD1 A:LEU350 4.9 14.3 1.0

Sodium binding site 3 out of 16 in 1jz5

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Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:34.7
occ:1.00
O A:HOH9273 2.2 38.9 1.0
O A:LEU967 2.6 24.6 1.0
O A:PRO932 2.6 25.8 1.0
O A:THR970 2.7 34.4 1.0
O A:HOH8803 3.0 24.8 1.0
O A:HOH9113 3.4 38.5 1.0
CZ A:PHE931 3.5 35.3 1.0
C A:PRO932 3.6 28.7 1.0
C A:LEU967 3.7 23.6 1.0
O A:MET968 3.8 27.6 1.0
CE1 A:PHE931 3.8 33.1 1.0
C A:THR970 3.9 44.0 1.0
C A:MET968 3.9 37.7 1.0
CE2 A:PHE931 3.9 32.6 1.0
CB A:PRO932 4.0 26.3 1.0
CA A:MET968 4.0 22.3 1.0
CD A:PRO932 4.2 19.4 1.0
CA A:PRO932 4.2 25.4 1.0
N A:PRO932 4.3 24.8 1.0
N A:THR970 4.3 20.5 1.0
N A:MET968 4.3 22.6 1.0
CD1 A:PHE931 4.5 26.3 1.0
CG A:PRO932 4.5 32.9 1.0
CD2 A:PHE931 4.5 24.8 1.0
N A:SER933 4.7 17.3 1.0
CA A:THR970 4.7 23.4 1.0
N A:SER971 4.7 34.4 1.0
N A:GLU969 4.7 24.0 1.0
CA A:SER971 4.8 35.4 1.0
CG A:PHE931 4.8 20.7 1.0
CA A:LEU967 4.9 18.4 1.0
C A:GLU969 4.9 31.1 1.0
C A:PHE931 4.9 29.4 1.0
CA A:SER933 5.0 17.4 1.0

Sodium binding site 4 out of 16 in 1jz5

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Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:30.6
occ:1.00
O A:DMS8425 2.2 43.7 1.0
O A:LEU670 2.4 21.8 1.0
O A:SER647 2.4 19.9 1.0
O A:GLU650 2.5 24.2 1.0
O A:HOH9284 2.6 48.0 1.0
S A:DMS8425 3.1 49.1 1.0
N A:GLU650 3.4 18.7 1.0
C A:GLU650 3.5 26.1 1.0
C A:LEU670 3.6 28.3 1.0
C A:SER647 3.6 23.6 1.0
C2 A:DMS8425 3.9 89.5 1.0
CA A:GLU650 3.9 20.3 1.0
N A:LEU670 4.0 23.6 1.0
N A:ASN649 4.0 23.1 1.0
C A:ASP648 4.1 27.7 1.0
CA A:ASP648 4.1 22.3 1.0
CB A:GLU650 4.1 20.4 1.0
CA A:LEU670 4.2 28.8 1.0
OG A:SER647 4.3 21.4 1.0
CB A:LEU670 4.3 30.0 1.0
N A:ASP648 4.4 21.9 1.0
OD1 A:ASP671 4.4 0.0 1.0
C A:ASN649 4.5 26.1 1.0
CA A:ASN649 4.6 22.2 1.0
O A:ASP648 4.6 22.1 1.0
CB A:SER647 4.6 19.0 1.0
N A:ASP671 4.7 23.8 1.0
N A:LEU651 4.7 23.7 1.0
C1 A:DMS8425 4.8 35.0 1.0
CA A:SER647 4.8 19.8 1.0
OE1 A:GLU650 4.8 20.6 1.0
CA A:ASP671 4.9 29.6 1.0
C A:PRO669 5.0 23.7 1.0

Sodium binding site 5 out of 16 in 1jz5

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Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:21.7
occ:1.00
O B:HOH8887 2.2 19.2 1.0
O B:PHE601 2.4 17.3 1.0
OD2 B:ASP201 2.4 18.8 1.0
O6 B:1492001 2.5 21.1 1.0
OD1 B:ASN604 2.5 17.5 1.0
CD2 B:PHE601 3.1 29.5 1.0
CE2 B:PHE601 3.2 21.6 1.0
CG B:ASP201 3.3 25.5 1.0
CG B:ASN604 3.4 24.0 1.0
C B:PHE601 3.5 23.3 1.0
C6 B:1492001 3.6 24.7 1.0
OD1 B:ASP201 3.6 20.6 1.0
ND2 B:ASN604 3.7 19.3 1.0
OH B:TYR100 3.8 19.0 1.0
CG B:PHE601 3.9 26.1 1.0
CZ B:PHE601 4.0 32.5 1.0
O4 B:1492001 4.1 18.6 1.0
C4 B:1492001 4.2 33.1 1.0
CA B:CYS602 4.2 19.8 1.0
N B:CYS602 4.3 17.4 1.0
NE1 B:TRP568 4.3 16.0 1.0
C5 B:1492001 4.4 20.2 1.0
NE2 B:HIS540 4.5 15.8 1.0
CB B:ASP201 4.5 17.0 1.0
CA B:PHE601 4.5 20.7 1.0
O B:HOH8665 4.5 17.7 1.0
CD1 B:PHE601 4.6 24.9 1.0
CB B:PHE601 4.7 23.6 1.0
CE1 B:PHE601 4.7 26.9 1.0
O B:ASP201 4.7 19.4 1.0
C B:CYS602 4.9 23.2 1.0
CB B:ASN604 4.9 15.3 1.0
CZ B:TYR100 4.9 24.7 1.0

Sodium binding site 6 out of 16 in 1jz5

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Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:20.4
occ:1.00
O B:PHE556 2.2 12.6 1.0
O B:LEU562 2.2 16.9 1.0
O B:TYR559 2.3 19.1 1.0
O B:HOH9007 2.6 28.1 1.0
O B:HOH9201 2.7 29.8 1.0
O B:PRO560 3.2 16.4 1.0
C B:TYR559 3.3 15.0 1.0
C B:LEU562 3.3 24.7 1.0
C B:PHE556 3.4 17.6 1.0
C B:PRO560 3.6 19.8 1.0
CA B:PRO560 3.7 14.1 1.0
N B:PRO560 3.9 17.9 1.0
N B:LEU562 4.0 13.0 1.0
CA B:PHE556 4.0 15.3 1.0
O B:HOH8894 4.0 23.1 1.0
CA B:LEU562 4.1 13.5 1.0
CB B:LEU562 4.2 10.6 1.0
N B:GLN563 4.3 16.7 1.0
CA B:TYR559 4.3 15.2 1.0
N B:TYR559 4.3 15.8 1.0
CA B:GLN563 4.4 13.7 1.0
N B:ARG557 4.5 15.6 1.0
N B:ARG561 4.5 11.6 1.0
CA B:ARG557 4.7 17.3 1.0
CB B:PHE556 4.7 14.5 1.0
CG B:GLN563 4.7 13.3 1.0
C B:ARG557 4.7 19.4 1.0
O B:ARG557 4.8 19.2 1.0
O B:ALA555 4.8 16.6 1.0
CD1 B:LEU350 4.8 13.8 1.0
CB B:TYR559 4.9 14.0 1.0
C B:ARG561 4.9 14.1 1.0

Sodium binding site 7 out of 16 in 1jz5

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Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:29.9
occ:1.00
O B:PRO932 2.4 28.1 1.0
O B:HOH9283 2.4 42.6 1.0
O B:LEU967 2.4 25.0 1.0
O B:THR970 2.7 42.1 1.0
O B:HOH8817 2.7 24.9 1.0
C B:PRO932 3.4 23.9 1.0
CZ B:PHE931 3.4 31.0 1.0
C B:LEU967 3.6 20.6 1.0
O B:HOH9130 3.7 32.7 1.0
CE2 B:PHE931 3.7 28.4 1.0
C B:THR970 3.8 39.3 1.0
CE1 B:PHE931 3.8 19.6 1.0
CA B:MET968 3.8 21.5 1.0
O B:MET968 4.0 26.7 1.0
C B:MET968 4.0 35.2 1.0
CB B:PRO932 4.1 19.4 1.0
CA B:PRO932 4.1 17.3 1.0
N B:PRO932 4.2 25.4 1.0
N B:MET968 4.2 17.6 1.0
N B:THR970 4.3 21.1 1.0
CD B:PRO932 4.3 28.9 1.0
CD2 B:PHE931 4.4 20.9 1.0
N B:SER933 4.4 17.4 1.0
CD1 B:PHE931 4.4 20.9 1.0
CA B:THR970 4.6 26.0 1.0
CG B:PRO932 4.6 23.5 1.0
CA B:SER933 4.7 16.4 1.0
CG B:PHE931 4.7 25.3 1.0
N B:SER971 4.7 34.2 1.0
CA B:LEU967 4.7 21.3 1.0
CA B:SER971 4.8 30.4 1.0
N B:GLU969 4.8 24.2 1.0
C B:PHE931 4.9 26.2 1.0
O B:HOH9304 4.9 44.1 1.0
CB B:MET968 4.9 25.8 1.0

Sodium binding site 8 out of 16 in 1jz5

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Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:33.5
occ:1.00
O B:DMS8425 2.0 31.5 1.0
O B:HOH9407 2.5 43.9 1.0
O B:SER647 2.5 21.9 1.0
O B:LEU670 2.5 26.7 1.0
O B:GLU650 2.6 26.1 1.0
O B:HOH9293 2.8 32.2 1.0
S B:DMS8425 3.2 49.7 1.0
N B:GLU650 3.5 24.0 1.0
C B:GLU650 3.6 30.6 1.0
C B:LEU670 3.6 28.3 1.0
C B:SER647 3.7 22.8 1.0
C2 B:DMS8425 3.7 43.0 1.0
N B:LEU670 3.8 28.8 1.0
CA B:GLU650 4.0 16.9 1.0
CB B:LEU670 4.0 27.8 1.0
CA B:LEU670 4.1 26.9 1.0
CA B:ASP648 4.2 28.3 1.0
OG B:SER647 4.2 19.4 1.0
N B:ASN649 4.2 20.9 1.0
C B:ASP648 4.3 32.3 1.0
CB B:GLU650 4.3 16.2 1.0
N B:ASP648 4.4 17.1 1.0
C1 B:DMS8425 4.6 24.3 1.0
CB B:SER647 4.7 25.9 1.0
C B:ASN649 4.7 26.9 1.0
N B:ASP671 4.7 20.8 1.0
CA B:ASP671 4.7 20.0 1.0
C B:PRO669 4.8 22.1 1.0
CA B:SER647 4.8 21.2 1.0
N B:LEU651 4.8 22.5 1.0
O B:HOH9391 4.8 38.4 1.0
CA B:ASN649 4.9 18.4 1.0
O B:ASP648 4.9 24.1 1.0
OE1 B:GLU650 5.0 23.8 1.0

Sodium binding site 9 out of 16 in 1jz5

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Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:19.7
occ:1.00
O6 C:1492001 2.3 17.5 1.0
OD2 C:ASP201 2.4 16.8 1.0
O C:PHE601 2.5 18.4 1.0
O C:HOH8897 2.5 26.3 1.0
OD1 C:ASN604 2.5 16.4 1.0
CD2 C:PHE601 3.1 33.8 1.0
CE2 C:PHE601 3.1 28.5 1.0
CG C:ASP201 3.3 24.1 1.0
C6 C:1492001 3.4 22.2 1.0
CG C:ASN604 3.5 22.1 1.0
C C:PHE601 3.6 21.5 1.0
OD1 C:ASP201 3.7 18.2 1.0
ND2 C:ASN604 3.7 26.4 1.0
OH C:TYR100 3.8 20.9 1.0
CG C:PHE601 3.9 27.2 1.0
CZ C:PHE601 4.0 19.6 1.0
C4 C:1492001 4.1 26.1 1.0
O4 C:1492001 4.1 21.1 1.0
NE1 C:TRP568 4.3 18.8 1.0
C5 C:1492001 4.3 26.0 1.0
CA C:CYS602 4.3 22.4 1.0
N C:CYS602 4.4 21.0 1.0
CB C:ASP201 4.5 21.6 1.0
NE2 C:HIS540 4.5 17.6 1.0
CD1 C:PHE601 4.6 22.3 1.0
CA C:PHE601 4.6 19.1 1.0
CB C:PHE601 4.6 21.5 1.0
O C:HOH8676 4.6 17.4 1.0
CE1 C:PHE601 4.6 23.6 1.0
O C:ASP201 4.8 15.2 1.0
C C:CYS602 4.9 30.1 1.0
CB C:ASN604 4.9 12.4 1.0
CZ C:TYR100 4.9 29.8 1.0
CE2 C:TRP568 5.0 17.9 1.0
CE1 C:HIS540 5.0 21.9 1.0

Sodium binding site 10 out of 16 in 1jz5

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Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:19.5
occ:1.00
O C:PHE556 2.2 15.7 1.0
O C:TYR559 2.3 17.3 1.0
O C:LEU562 2.4 16.3 1.0
O C:HOH9016 2.5 28.3 1.0
O C:HOH9210 2.6 37.1 1.0
O C:PRO560 3.2 16.6 1.0
C C:TYR559 3.3 16.1 1.0
C C:PHE556 3.4 17.7 1.0
C C:LEU562 3.5 20.9 1.0
C C:PRO560 3.6 18.7 1.0
CA C:PRO560 3.7 18.6 1.0
N C:PRO560 3.9 16.6 1.0
N C:LEU562 4.0 13.4 1.0
O C:HOH8904 4.0 22.7 1.0
CA C:PHE556 4.1 15.5 1.0
CA C:LEU562 4.2 12.0 1.0
CB C:LEU562 4.3 11.1 1.0
N C:ARG557 4.4 15.4 1.0
N C:TYR559 4.4 17.2 1.0
CA C:TYR559 4.4 14.2 1.0
N C:GLN563 4.4 14.7 1.0
N C:ARG561 4.5 13.8 1.0
CA C:GLN563 4.5 12.8 1.0
CA C:ARG557 4.6 15.2 1.0
C C:ARG557 4.7 23.9 1.0
CB C:PHE556 4.7 17.8 1.0
O C:ARG557 4.7 19.2 1.0
O C:ALA555 4.8 19.0 1.0
CG C:GLN563 4.8 15.7 1.0
CB C:TYR559 4.9 15.9 1.0
C C:ARG561 4.9 15.1 1.0
CD1 C:LEU350 5.0 13.9 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 05:26:49 2020

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Zn in 7M4O
Zn in 7M4N
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