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

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg, PDB code: 1jyx 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) 27.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.770, 161.190, 202.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 24.4

Other elements in 1jyx:

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

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

Sodium binding site 1 out of 14 in 1jyx

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Sodium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:18.7
occ:1.00
OD1 A:ASN604 2.3 19.0 1.0
O A:PHE601 2.3 20.9 1.0
O A:HOH8876 2.4 27.4 1.0
O6 A:IPT2001 2.4 18.6 0.9
OD2 A:ASP201 2.4 21.7 1.0
C6 A:IPT2001 3.1 16.3 0.9
CG A:ASN604 3.2 18.6 1.0
CG A:ASP201 3.4 22.0 1.0
ND2 A:ASN604 3.5 21.1 1.0
C A:PHE601 3.5 24.7 1.0
OD1 A:ASP201 3.6 20.7 1.0
OH A:TYR100 3.8 17.7 1.0
NE1 A:TRP568 4.0 18.0 1.0
O4 A:IPT2001 4.2 17.1 0.9
CA A:CYS602 4.2 14.7 1.0
N A:CYS602 4.2 17.1 1.0
C5 A:IPT2001 4.3 18.3 0.9
C4 A:IPT2001 4.5 19.1 0.9
NE2 A:HIS540 4.5 17.6 1.0
O A:HOH8654 4.5 16.8 1.0
CA A:PHE601 4.5 18.3 1.0
CB A:PHE601 4.5 15.4 1.0
CB A:ASP201 4.6 16.0 1.0
CB A:ASN604 4.6 17.9 1.0
C A:CYS602 4.7 13.2 1.0
O A:ASP201 4.7 19.2 1.0
CE2 A:TRP568 4.8 15.7 1.0
CZ2 A:TRP568 4.9 17.5 1.0
CZ A:TYR100 4.9 27.5 1.0

Sodium binding site 2 out of 14 in 1jyx

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Sodium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:16.1
occ:1.00
O A:LEU562 2.3 14.6 1.0
O A:TYR559 2.3 18.2 1.0
O A:PHE556 2.3 13.3 1.0
O A:HOH8995 2.4 21.6 1.0
O A:HOH9181 2.5 21.4 1.0
O A:PRO560 3.2 15.5 1.0
C A:TYR559 3.3 12.8 1.0
C A:LEU562 3.4 18.1 1.0
C A:PHE556 3.4 13.5 1.0
C A:PRO560 3.6 16.0 1.0
CA A:PRO560 3.7 17.8 1.0
O A:HOH8882 3.9 22.6 1.0
O A:HOH9296 3.9 47.5 1.0
N A:PRO560 3.9 20.7 1.0
N A:LEU562 4.0 12.9 1.0
CA A:PHE556 4.2 12.3 1.0
CA A:LEU562 4.2 12.1 1.0
N A:GLN563 4.3 14.4 1.0
CA A:GLN563 4.4 12.7 1.0
CA A:TYR559 4.5 10.1 1.0
N A:ARG557 4.5 11.6 1.0
CB A:LEU562 4.5 12.0 1.0
N A:TYR559 4.6 10.4 1.0
N A:ARG561 4.6 12.2 1.0
CA A:ARG557 4.6 15.4 1.0
CG A:GLN563 4.7 14.6 1.0
C A:ARG557 4.7 17.6 1.0
CD1 A:LEU350 4.8 12.6 1.0
O A:ARG557 4.8 14.3 1.0
CB A:PHE556 4.8 13.9 1.0
C A:ARG561 4.9 17.8 1.0
O A:ALA555 5.0 17.3 1.0

Sodium binding site 3 out of 14 in 1jyx

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Sodium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:29.5
occ:1.00
O A:HOH9246 2.3 34.0 1.0
O A:PRO932 2.4 20.2 1.0
O A:HOH8807 2.6 23.9 1.0
O A:LEU967 2.6 22.1 1.0
O A:THR970 2.8 30.4 1.0
O A:HOH9116 3.4 39.1 1.0
CZ A:PHE931 3.4 33.8 1.0
C A:PRO932 3.5 14.3 1.0
CE1 A:PHE931 3.7 22.6 1.0
C A:LEU967 3.7 17.9 1.0
O A:MET968 3.9 31.9 1.0
CE2 A:PHE931 3.9 20.4 1.0
CA A:MET968 3.9 23.9 1.0
C A:MET968 4.0 43.6 1.0
C A:THR970 4.0 31.4 1.0
CA A:PRO932 4.2 20.8 1.0
N A:PRO932 4.2 24.8 1.0
CB A:PRO932 4.3 27.8 1.0
CD1 A:PHE931 4.3 23.6 1.0
CD A:PRO932 4.3 21.6 1.0
N A:MET968 4.3 17.4 1.0
N A:THR970 4.4 22.3 1.0
O A:HOH9404 4.5 50.7 1.0
N A:SER933 4.5 17.1 1.0
CD2 A:PHE931 4.5 19.8 1.0
CG A:PRO932 4.7 20.7 1.0
N A:GLU969 4.7 20.5 1.0
CG A:PHE931 4.7 18.8 1.0
CA A:SER933 4.7 17.4 1.0
CA A:THR970 4.8 17.7 1.0
CA A:SER971 4.8 23.7 1.0
N A:SER971 4.9 32.7 1.0
CA A:LEU967 4.9 26.6 1.0
C A:PHE931 5.0 27.7 1.0

Sodium binding site 4 out of 14 in 1jyx

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Sodium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:17.2
occ:1.00
O B:HOH8786 2.3 16.1 1.0
OD2 B:ASP201 2.3 16.5 1.0
OD1 B:ASN604 2.4 15.7 1.0
O6 B:IPT2001 2.4 16.0 1.0
O B:PHE601 2.5 17.7 1.0
CG B:ASP201 3.2 17.5 1.0
C6 B:IPT2001 3.3 10.7 1.0
CG B:ASN604 3.4 16.1 1.0
OD1 B:ASP201 3.5 15.5 1.0
C B:PHE601 3.6 30.1 1.0
OH B:TYR100 3.7 16.9 1.0
ND2 B:ASN604 3.7 11.6 1.0
NE1 B:TRP568 4.0 15.2 1.0
O4 B:IPT2001 4.1 16.1 1.0
CA B:CYS602 4.2 15.8 1.0
O B:HOH8567 4.2 23.2 1.0
C5 B:IPT2001 4.3 15.9 1.0
N B:CYS602 4.3 23.3 1.0
C4 B:IPT2001 4.4 19.6 1.0
CB B:ASP201 4.4 18.1 1.0
O B:ASP201 4.5 14.0 1.0
CA B:PHE601 4.7 16.5 1.0
CB B:PHE601 4.7 13.3 1.0
C B:CYS602 4.7 16.1 1.0
NE2 B:HIS540 4.7 16.6 1.0
CB B:ASN604 4.7 14.3 1.0
CE2 B:TRP568 4.8 13.2 1.0
CZ B:TYR100 4.8 15.4 1.0
CZ2 B:TRP568 4.9 13.4 1.0

Sodium binding site 5 out of 14 in 1jyx

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Sodium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:17.0
occ:1.00
O B:LEU562 2.2 14.7 1.0
O B:PHE556 2.3 13.6 1.0
O B:TYR559 2.3 13.2 1.0
O B:HOH9095 2.4 30.3 1.0
O B:HOH8908 2.5 33.6 1.0
O B:PRO560 3.3 16.1 1.0
C B:LEU562 3.3 20.1 1.0
C B:TYR559 3.3 23.8 1.0
C B:PHE556 3.5 14.3 1.0
C B:PRO560 3.6 16.2 1.0
CA B:PRO560 3.6 14.4 1.0
N B:PRO560 3.9 17.5 1.0
N B:LEU562 3.9 12.6 1.0
O B:HOH8793 4.0 19.2 1.0
CA B:LEU562 4.2 13.1 1.0
CA B:PHE556 4.2 10.1 1.0
N B:GLN563 4.2 12.4 1.0
CA B:GLN563 4.4 13.5 1.0
CB B:LEU562 4.4 9.1 1.0
N B:ARG561 4.5 13.9 1.0
CA B:TYR559 4.5 13.2 1.0
O B:HOH9255 4.5 43.0 1.0
O B:HOH9226 4.5 42.6 1.0
N B:TYR559 4.5 11.9 1.0
N B:ARG557 4.6 13.9 1.0
CD1 B:LEU350 4.6 20.4 1.0
CG B:GLN563 4.7 12.0 1.0
O B:ARG557 4.7 15.1 1.0
CA B:ARG557 4.7 12.7 1.0
CB B:PHE556 4.7 15.8 1.0
C B:ARG557 4.7 20.6 1.0
C B:ARG561 4.8 15.2 1.0
CB B:TYR559 4.9 12.4 1.0
O B:ALA555 5.0 15.0 1.0

Sodium binding site 6 out of 14 in 1jyx

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Sodium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:35.2
occ:1.00
O B:PRO932 2.3 20.0 1.0
O B:LEU967 2.5 22.9 1.0
O B:HOH8719 2.7 23.4 1.0
O B:THR970 2.8 34.2 1.0
CZ B:PHE931 3.3 23.7 1.0
C B:PRO932 3.3 14.2 1.0
CE1 B:PHE931 3.6 23.5 1.0
C B:LEU967 3.6 23.4 1.0
CE2 B:PHE931 3.7 19.2 1.0
O B:HOH9166 3.8 48.3 1.0
C B:THR970 3.9 34.1 1.0
O B:HOH9034 3.9 37.7 1.0
CA B:MET968 3.9 19.6 1.0
O B:MET968 4.0 26.7 1.0
CA B:PRO932 4.1 17.7 1.0
C B:MET968 4.1 21.7 1.0
N B:PRO932 4.2 22.2 1.0
CB B:PRO932 4.2 36.1 1.0
CD B:PRO932 4.2 27.7 1.0
N B:SER933 4.3 21.9 1.0
N B:MET968 4.3 21.9 1.0
CD1 B:PHE931 4.4 17.7 1.0
N B:THR970 4.4 18.3 1.0
CD2 B:PHE931 4.4 17.7 1.0
CG B:PRO932 4.5 35.9 1.0
CA B:SER933 4.5 23.0 1.0
CG B:PHE931 4.7 19.3 1.0
CA B:THR970 4.7 17.9 1.0
N B:SER971 4.8 27.1 1.0
CA B:LEU967 4.8 21.7 1.0
CA B:SER971 4.8 31.4 1.0
C B:PHE931 4.8 23.5 1.0
N B:GLU969 4.9 24.7 1.0

Sodium binding site 7 out of 14 in 1jyx

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Sodium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:28.2
occ:1.00
O B:DMS8425 2.2 64.8 1.0
O B:SER647 2.4 19.9 1.0
O B:GLU650 2.4 22.5 1.0
O B:LEU670 2.7 24.8 1.0
O B:HOH9280 2.8 39.4 1.0
O B:HOH9175 3.2 46.4 1.0
S B:DMS8425 3.3 54.8 1.0
N B:GLU650 3.3 17.7 1.0
C B:GLU650 3.4 23.8 1.0
C B:SER647 3.6 25.0 1.0
CA B:GLU650 3.7 22.8 1.0
C B:LEU670 3.8 25.8 1.0
N B:ASN649 3.9 17.5 1.0
CA B:ASP648 3.9 21.8 1.0
CB B:GLU650 3.9 16.1 1.0
C B:ASP648 3.9 20.8 1.0
N B:LEU670 4.0 28.0 1.0
C2 B:DMS8425 4.1 43.0 1.0
OG B:SER647 4.1 20.3 1.0
N B:ASP648 4.2 21.4 1.0
CA B:LEU670 4.3 23.2 1.0
C B:ASN649 4.4 19.0 1.0
CB B:LEU670 4.4 24.0 1.0
CB B:SER647 4.5 26.1 1.0
CA B:ASN649 4.6 19.2 1.0
N B:LEU651 4.6 19.3 1.0
O B:ASP648 4.6 21.2 1.0
OE2 B:GLU650 4.7 15.3 1.0
C1 B:DMS8425 4.7 0.0 1.0
CA B:SER647 4.8 17.1 1.0
N B:ASP671 4.9 21.8 1.0

Sodium binding site 8 out of 14 in 1jyx

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Sodium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:17.4
occ:1.00
O6 C:IPT2001 2.2 18.1 1.0
OD1 C:ASN604 2.3 17.0 1.0
O C:HOH8799 2.3 20.7 1.0
OD2 C:ASP201 2.4 17.1 1.0
O C:PHE601 2.4 16.4 1.0
C6 C:IPT2001 3.2 20.3 1.0
CG C:ASN604 3.3 15.3 1.0
CG C:ASP201 3.3 28.1 1.0
ND2 C:ASN604 3.6 16.2 1.0
OD1 C:ASP201 3.6 19.5 1.0
C C:PHE601 3.6 19.1 1.0
OH C:TYR100 3.8 13.8 1.0
NE1 C:TRP568 4.0 16.6 1.0
O4 C:IPT2001 4.1 17.5 1.0
CA C:CYS602 4.2 19.1 1.0
C5 C:IPT2001 4.3 19.1 1.0
C4 C:IPT2001 4.3 16.1 1.0
O C:HOH8578 4.4 16.6 1.0
N C:CYS602 4.4 13.5 1.0
CB C:ASP201 4.5 10.6 1.0
CB C:PHE601 4.5 10.6 1.0
CA C:PHE601 4.6 11.9 1.0
NE2 C:HIS540 4.6 17.2 1.0
CB C:ASN604 4.7 13.6 1.0
O C:ASP201 4.7 18.7 1.0
C C:CYS602 4.7 21.9 1.0
CE2 C:TRP568 4.7 13.7 1.0
CZ2 C:TRP568 4.8 14.4 1.0
CZ C:TYR100 4.9 23.7 1.0
CD1 C:TRP568 5.0 14.3 1.0

Sodium binding site 9 out of 14 in 1jyx

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Sodium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:16.7
occ:1.00
O C:LEU562 2.2 14.1 1.0
O C:TYR559 2.3 15.2 1.0
O C:PHE556 2.4 14.1 1.0
O C:HOH9123 2.5 34.2 1.0
O C:HOH8924 2.6 26.9 1.0
O C:PRO560 3.2 14.3 1.0
C C:LEU562 3.3 16.8 1.0
C C:TYR559 3.4 16.5 1.0
C C:PHE556 3.5 16.3 1.0
C C:PRO560 3.6 15.3 1.0
CA C:PRO560 3.7 16.6 1.0
N C:LEU562 3.9 11.2 1.0
N C:PRO560 4.0 16.4 1.0
CA C:LEU562 4.1 12.8 1.0
O C:HOH8806 4.1 17.1 1.0
CA C:PHE556 4.2 10.7 1.0
N C:GLN563 4.2 12.6 1.0
CB C:LEU562 4.3 9.2 1.0
CA C:GLN563 4.3 14.1 1.0
CA C:TYR559 4.5 10.2 1.0
N C:TYR559 4.5 14.1 1.0
N C:ARG561 4.5 9.6 1.0
O C:HOH9370 4.5 60.1 1.0
N C:ARG557 4.6 13.8 1.0
CG C:GLN563 4.7 13.7 1.0
CB C:PHE556 4.7 14.4 1.0
O C:ARG557 4.8 14.0 1.0
C C:ARG561 4.8 12.3 1.0
C C:ARG557 4.8 15.1 1.0
CA C:ARG557 4.8 18.4 1.0
CD1 C:LEU350 4.8 16.1 1.0
O C:ALA555 4.9 14.8 1.0
CB C:TYR559 4.9 12.7 1.0

Sodium binding site 10 out of 14 in 1jyx

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Sodium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg


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 Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3103

b:30.2
occ:1.00
O C:LEU967 2.5 19.7 1.0
O C:PRO932 2.5 16.9 1.0
O C:HOH8730 2.7 19.3 1.0
O C:THR970 2.8 26.7 1.0
O C:HOH9205 2.9 41.4 1.0
CZ C:PHE931 3.4 24.2 1.0
C C:PRO932 3.5 18.7 1.0
C C:LEU967 3.6 19.4 1.0
CE1 C:PHE931 3.7 22.0 1.0
O C:HOH9052 3.7 42.0 1.0
C C:THR970 3.8 24.0 1.0
CA C:MET968 3.8 18.3 1.0
CE2 C:PHE931 3.9 14.3 1.0
O C:MET968 4.0 28.1 1.0
C C:MET968 4.0 32.3 1.0
CA C:PRO932 4.1 22.4 1.0
N C:THR970 4.2 19.7 1.0
N C:MET968 4.2 14.9 1.0
CB C:PRO932 4.2 22.5 1.0
N C:PRO932 4.2 20.1 1.0
CD C:PRO932 4.3 22.1 1.0
CD1 C:PHE931 4.3 18.4 1.0
N C:SER933 4.5 19.5 1.0
CD2 C:PHE931 4.6 17.8 1.0
CA C:THR970 4.6 13.3 1.0
N C:SER971 4.7 23.0 1.0
CA C:SER971 4.7 32.7 1.0
CG C:PHE931 4.7 18.7 1.0
N C:GLU969 4.8 18.5 1.0
CA C:SER933 4.8 19.4 1.0
CA C:LEU967 4.8 17.6 1.0
CG C:PRO932 4.8 17.4 1.0
C C:PHE931 5.0 22.6 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 05:26:41 2020

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