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

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose, PDB code: 1jyn 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 (°) 149.550, 168.630, 200.880, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 21.9

Other elements in 1jyn:

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

Magnesium (Mg) 14 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose (pdb code 1jyn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose, PDB code: 1jyn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 1jyn

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Sodium binding site 1 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:10.2
occ:1.00
O A:HOH8781 2.2 12.6 1.0
O6 A:LAT2001 2.2 9.2 0.9
OD2 A:ASP201 2.3 9.4 1.0
OD1 A:ASN604 2.4 11.4 1.0
O A:PHE601 2.4 10.3 1.0
C6 A:LAT2001 3.1 9.7 0.9
CG A:ASP201 3.2 10.4 1.0
CG A:ASN604 3.3 12.4 1.0
OD1 A:ASP201 3.6 11.1 1.0
C A:PHE601 3.6 13.0 1.0
ND2 A:ASN604 3.6 10.5 1.0
OH A:TYR100 3.6 10.9 1.0
NE1 A:TRP568 4.2 7.8 1.0
O4 A:LAT2001 4.2 9.8 0.9
CA A:CYS602 4.3 7.7 1.0
C5 A:LAT2001 4.3 13.7 0.9
C4 A:LAT2001 4.3 13.7 0.9
N A:CYS602 4.4 7.5 1.0
CB A:ASP201 4.4 10.5 1.0
O A:HOH8559 4.5 8.9 1.0
CB A:PHE601 4.5 8.1 1.0
CA A:PHE601 4.6 10.9 1.0
NE2 A:HIS540 4.6 10.3 1.0
O A:ASP201 4.6 6.8 1.0
C A:CYS602 4.7 9.8 1.0
CB A:ASN604 4.7 3.8 1.0
CZ2 A:TRP568 4.8 11.0 1.0
CZ A:TYR100 4.8 16.2 1.0
CE2 A:TRP568 4.8 5.5 1.0

Sodium binding site 2 out of 15 in 1jyn

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Sodium binding site 2 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:12.3
occ:1.00
O A:HOH9129 2.3 21.4 1.0
O A:PHE556 2.3 11.4 1.0
O A:TYR559 2.3 10.9 1.0
O A:LEU562 2.3 7.6 1.0
O A:HOH8908 2.5 20.9 1.0
O A:PRO560 3.1 10.5 1.0
C A:TYR559 3.4 12.9 1.0
C A:LEU562 3.4 9.5 1.0
C A:PHE556 3.5 10.8 1.0
C A:PRO560 3.5 8.0 1.0
CA A:PRO560 3.6 5.7 1.0
N A:LEU562 3.9 5.6 1.0
N A:PRO560 3.9 10.6 1.0
O A:HOH8788 4.1 12.1 1.0
CA A:PHE556 4.1 9.7 1.0
CA A:LEU562 4.1 6.8 1.0
O A:HOH9305 4.2 33.4 1.0
CB A:LEU562 4.3 4.0 1.0
O A:HOH9513 4.3 30.2 1.0
N A:GLN563 4.3 6.8 1.0
N A:TYR559 4.4 6.3 1.0
CA A:GLN563 4.5 5.7 1.0
N A:ARG561 4.5 7.8 1.0
CA A:TYR559 4.5 4.1 1.0
N A:ARG557 4.5 5.3 1.0
O A:HOH9319 4.5 33.0 1.0
CA A:ARG557 4.6 1.7 1.0
O A:ARG557 4.7 7.5 1.0
C A:ARG557 4.7 9.4 1.0
CG A:GLN563 4.7 8.0 1.0
CB A:PHE556 4.7 7.1 1.0
C A:ARG561 4.8 8.4 1.0
O A:ALA555 4.8 9.3 1.0
CD1 A:LEU350 4.9 6.1 1.0

Sodium binding site 3 out of 15 in 1jyn

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Sodium binding site 3 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:21.8
occ:1.00
O A:HOH9229 2.4 38.8 1.0
O A:LEU967 2.5 14.6 1.0
O A:PRO932 2.5 11.3 1.0
O A:HOH8711 2.6 12.6 1.0
O A:THR970 2.9 21.3 1.0
CZ A:PHE931 3.4 18.3 1.0
C A:PRO932 3.6 10.8 1.0
O A:HOH9048 3.6 26.5 1.0
C A:LEU967 3.6 11.8 1.0
CE2 A:PHE931 3.7 12.8 1.0
CE1 A:PHE931 3.8 22.8 1.0
O A:MET968 3.9 19.1 1.0
CA A:MET968 3.9 12.4 1.0
C A:MET968 3.9 18.4 1.0
C A:THR970 4.0 19.1 1.0
CB A:PRO932 4.1 17.1 1.0
CA A:PRO932 4.2 13.9 1.0
N A:MET968 4.2 10.1 1.0
CD A:PRO932 4.2 13.1 1.0
N A:PRO932 4.3 12.6 1.0
N A:THR970 4.3 10.8 1.0
CD2 A:PHE931 4.4 12.5 1.0
CD1 A:PHE931 4.4 11.9 1.0
N A:SER933 4.6 6.7 1.0
CG A:PRO932 4.6 30.0 1.0
N A:GLU969 4.7 8.7 1.0
CG A:PHE931 4.7 10.2 1.0
CA A:THR970 4.7 13.5 1.0
CA A:SER933 4.8 11.3 1.0
CA A:LEU967 4.8 10.7 1.0
N A:SER971 4.9 17.2 1.0
CA A:SER971 4.9 19.3 1.0
C A:PHE931 5.0 17.7 1.0

Sodium binding site 4 out of 15 in 1jyn

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Sodium binding site 4 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:26.4
occ:1.00
O A:DMS8425 2.1 35.6 1.0
O A:LEU670 2.3 13.1 1.0
O A:HOH9404 2.5 44.4 1.0
O A:SER647 2.5 11.4 1.0
O A:HOH9243 2.6 37.8 1.0
O A:GLU650 2.6 14.2 1.0
S A:DMS8425 3.2 40.7 1.0
C A:LEU670 3.5 16.5 1.0
N A:GLU650 3.5 7.8 1.0
C A:GLU650 3.6 15.7 1.0
C2 A:DMS8425 3.6 37.0 1.0
C A:SER647 3.7 16.2 1.0
N A:LEU670 3.8 18.8 1.0
O A:HOH9553 3.9 51.2 1.0
CA A:GLU650 4.0 10.4 1.0
CA A:LEU670 4.1 15.6 1.0
N A:ASN649 4.1 13.1 1.0
CB A:GLU650 4.1 8.1 1.0
C A:ASP648 4.2 19.3 1.0
CA A:ASP648 4.2 14.8 1.0
CB A:LEU670 4.2 16.0 1.0
OG A:SER647 4.3 13.8 1.0
N A:ASP648 4.4 13.6 1.0
N A:ASP671 4.6 16.2 1.0
C A:ASN649 4.6 13.8 1.0
CB A:SER647 4.6 15.7 1.0
C1 A:DMS8425 4.7 26.1 1.0
CA A:ASN649 4.7 12.2 1.0
CA A:ASP671 4.8 15.9 1.0
O A:ASP648 4.8 13.7 1.0
C A:PRO669 4.8 11.4 1.0
CA A:SER647 4.8 8.1 1.0
N A:LEU651 4.8 12.8 1.0
OE1 A:GLU650 4.9 12.5 1.0

Sodium binding site 5 out of 15 in 1jyn

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Sodium binding site 5 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:11.7
occ:1.00
O B:HOH8893 2.2 11.1 1.0
O6 B:LAT2001 2.3 10.1 0.9
OD2 B:ASP201 2.3 10.5 1.0
OD1 B:ASN604 2.4 7.6 1.0
O B:PHE601 2.4 9.7 1.0
C6 B:LAT2001 3.2 4.7 0.9
CG B:ASP201 3.3 17.2 1.0
CG B:ASN604 3.4 16.5 1.0
C B:PHE601 3.5 12.9 1.0
OD1 B:ASP201 3.6 8.9 1.0
OH B:TYR100 3.7 10.9 1.0
ND2 B:ASN604 3.7 11.1 1.0
NE1 B:TRP568 4.1 7.6 1.0
O4 B:LAT2001 4.2 5.7 0.9
CA B:CYS602 4.2 9.8 1.0
N B:CYS602 4.3 9.3 1.0
C5 B:LAT2001 4.3 10.5 0.9
O B:HOH8673 4.4 11.5 1.0
C4 B:LAT2001 4.4 5.7 0.9
CB B:ASP201 4.5 4.6 1.0
CB B:PHE601 4.5 9.9 1.0
CA B:PHE601 4.5 8.1 1.0
NE2 B:HIS540 4.6 6.3 1.0
O B:ASP201 4.7 9.2 1.0
C B:CYS602 4.7 9.7 1.0
CB B:ASN604 4.8 5.9 1.0
CZ B:TYR100 4.8 14.2 1.0
CZ2 B:TRP568 4.8 9.2 1.0
CE2 B:TRP568 4.8 6.9 1.0

Sodium binding site 6 out of 15 in 1jyn

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Sodium binding site 6 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:10.9
occ:1.00
O B:LEU562 2.2 6.2 1.0
O B:PHE556 2.3 8.5 1.0
O B:TYR559 2.3 9.8 1.0
O B:HOH9246 2.3 19.3 1.0
O B:HOH9017 2.6 19.9 1.0
O B:PRO560 3.2 9.3 1.0
C B:TYR559 3.3 8.7 1.0
C B:LEU562 3.3 9.1 1.0
C B:PHE556 3.4 8.1 1.0
C B:PRO560 3.6 12.0 1.0
CA B:PRO560 3.6 6.3 1.0
N B:PRO560 3.9 10.2 1.0
N B:LEU562 3.9 3.8 1.0
CA B:PHE556 4.0 5.4 1.0
CA B:LEU562 4.1 4.4 1.0
CB B:LEU562 4.2 2.4 1.0
O B:HOH8900 4.2 10.8 1.0
N B:GLN563 4.2 5.8 1.0
O B:HOH9472 4.3 23.5 1.0
N B:TYR559 4.4 7.4 1.0
CA B:TYR559 4.4 8.1 1.0
CA B:GLN563 4.4 4.6 1.0
N B:ARG557 4.5 5.0 1.0
O B:HOH9427 4.5 32.1 1.0
N B:ARG561 4.5 8.7 1.0
CA B:ARG557 4.6 7.4 1.0
CB B:PHE556 4.7 3.4 1.0
C B:ARG557 4.7 12.1 1.0
O B:ARG557 4.7 13.6 1.0
CG B:GLN563 4.7 8.3 1.0
C B:ARG561 4.8 7.4 1.0
CD1 B:LEU350 4.8 8.7 1.0
O B:ALA555 4.9 9.1 1.0
CB B:TYR559 4.9 5.8 1.0

Sodium binding site 7 out of 15 in 1jyn

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Sodium binding site 7 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:19.7
occ:1.00
O B:PRO932 2.4 9.8 1.0
O B:LEU967 2.5 15.5 1.0
O B:HOH9339 2.6 37.0 1.0
O B:THR970 2.7 24.2 1.0
O B:HOH8824 2.7 12.5 1.0
CZ B:PHE931 3.4 15.0 1.0
C B:PRO932 3.5 10.6 1.0
C B:LEU967 3.7 21.3 1.0
CE1 B:PHE931 3.7 13.5 1.0
O B:HOH9161 3.7 24.1 1.0
CE2 B:PHE931 3.8 12.8 1.0
C B:THR970 3.8 19.0 1.0
O B:MET968 3.9 21.1 1.0
CA B:MET968 3.9 9.4 1.0
C B:MET968 4.0 24.2 1.0
CA B:PRO932 4.1 12.3 1.0
CB B:PRO932 4.1 12.6 1.0
CD B:PRO932 4.2 15.8 1.0
N B:PRO932 4.2 15.8 1.0
N B:THR970 4.2 12.4 1.0
N B:MET968 4.3 9.1 1.0
CD1 B:PHE931 4.3 12.3 1.0
CD2 B:PHE931 4.4 10.8 1.0
N B:SER933 4.5 10.8 1.0
CG B:PRO932 4.6 9.3 1.0
CA B:THR970 4.6 14.8 1.0
CA B:SER971 4.7 15.3 1.0
CA B:SER933 4.7 5.3 1.0
CG B:PHE931 4.7 10.8 1.0
N B:SER971 4.7 16.2 1.0
N B:GLU969 4.8 13.8 1.0
CA B:LEU967 4.8 11.2 1.0
C B:PHE931 4.9 14.2 1.0
O B:HOH9368 5.0 27.4 1.0

Sodium binding site 8 out of 15 in 1jyn

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Sodium binding site 8 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:27.2
occ:1.00
O B:DMS8425 1.9 38.0 1.0
O B:SER647 2.5 14.2 1.0
O B:GLU650 2.6 15.0 1.0
O B:LEU670 2.7 17.0 1.0
O B:HOH9509 2.8 39.0 1.0
O B:HOH9355 2.8 31.8 1.0
S B:DMS8425 3.0 42.7 1.0
N B:GLU650 3.2 12.1 1.0
C B:GLU650 3.5 20.6 1.0
C2 B:DMS8425 3.5 26.4 1.0
C B:SER647 3.6 26.0 1.0
N B:ASN649 3.7 13.8 1.0
C B:ASP648 3.8 20.4 1.0
C B:LEU670 3.8 16.9 1.0
CA B:ASP648 3.8 14.8 1.0
CA B:GLU650 3.8 12.0 1.0
N B:LEU670 4.0 17.6 1.0
CB B:GLU650 4.1 11.2 1.0
N B:ASP648 4.2 10.2 1.0
C B:ASN649 4.3 24.4 1.0
CB B:LEU670 4.3 19.1 1.0
CA B:LEU670 4.3 14.1 1.0
O B:ASP648 4.4 13.7 1.0
OG B:SER647 4.4 11.8 1.0
CA B:ASN649 4.4 5.8 1.0
C1 B:DMS8425 4.5 21.9 1.0
OE1 B:GLU650 4.6 10.7 1.0
N B:LEU651 4.8 13.1 1.0
CB B:SER647 4.8 12.4 1.0
CA B:SER647 4.8 12.8 1.0
N B:ASP671 4.9 11.0 1.0
C B:PRO669 4.9 24.1 1.0

Sodium binding site 9 out of 15 in 1jyn

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Sodium binding site 9 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:9.6
occ:1.00
O C:HOH8905 2.3 14.8 1.0
O6 C:LAT2001 2.3 7.6 0.9
OD2 C:ASP201 2.3 8.6 1.0
O C:PHE601 2.4 11.2 1.0
OD1 C:ASN604 2.4 9.7 1.0
C6 C:LAT2001 3.2 5.4 0.9
CG C:ASP201 3.3 11.4 1.0
CG C:ASN604 3.4 12.9 1.0
C C:PHE601 3.5 12.3 1.0
OD1 C:ASP201 3.6 10.0 1.0
OH C:TYR100 3.6 8.4 1.0
ND2 C:ASN604 3.6 10.7 1.0
CA C:CYS602 4.2 11.3 1.0
O4 C:LAT2001 4.2 7.6 0.9
NE1 C:TRP568 4.2 9.8 1.0
N C:CYS602 4.3 8.8 1.0
C5 C:LAT2001 4.4 6.0 0.9
C4 C:LAT2001 4.4 4.0 0.9
O C:HOH8682 4.4 10.0 1.0
CB C:PHE601 4.5 7.1 1.0
CB C:ASP201 4.5 5.5 1.0
CA C:PHE601 4.5 9.4 1.0
O C:ASP201 4.6 8.7 1.0
C C:CYS602 4.7 17.9 1.0
CZ C:TYR100 4.7 9.7 1.0
NE2 C:HIS540 4.7 7.4 1.0
CB C:ASN604 4.8 5.1 1.0
CZ2 C:TRP568 4.8 10.3 1.0
CE2 C:TRP568 4.9 7.3 1.0

Sodium binding site 10 out of 15 in 1jyn

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Sodium binding site 10 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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

b:11.6
occ:1.00
O C:HOH9253 2.3 20.2 1.0
O C:LEU562 2.3 7.7 1.0
O C:PHE556 2.3 7.1 1.0
O C:TYR559 2.4 10.4 1.0
O C:HOH9030 2.5 20.7 1.0
O C:PRO560 3.1 10.7 1.0
C C:TYR559 3.3 7.1 1.0
C C:LEU562 3.4 4.9 1.0
C C:PHE556 3.5 11.5 1.0
C C:PRO560 3.5 13.0 1.0
CA C:PRO560 3.7 7.3 1.0
N C:LEU562 3.9 9.0 1.0
N C:PRO560 3.9 4.8 1.0
O C:HOH8912 4.1 10.3 1.0
CA C:PHE556 4.2 5.1 1.0
CA C:LEU562 4.2 5.2 1.0
O C:HOH9619 4.2 29.2 1.0
N C:GLN563 4.3 6.8 1.0
CB C:LEU562 4.3 5.0 1.0
O C:HOH9696 4.4 29.3 1.0
CA C:GLN563 4.4 8.8 1.0
CA C:TYR559 4.4 8.5 1.0
N C:TYR559 4.5 12.8 1.0
O C:HOH9463 4.5 36.0 1.0
N C:ARG557 4.5 9.6 1.0
N C:ARG561 4.5 6.6 1.0
CA C:ARG557 4.6 5.2 1.0
CG C:GLN563 4.7 7.8 1.0
C C:ARG557 4.7 13.0 1.0
O C:ARG557 4.8 13.6 1.0
CB C:PHE556 4.8 6.8 1.0
C C:ARG561 4.8 9.4 1.0
CD1 C:LEU350 4.8 3.1 1.0
O C:ALA555 4.9 9.4 1.0
CB C:TYR559 4.9 6.7 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 05:26:31 2020

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