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Sodium in PDB 3i3d: E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg, PDB code: 3i3d was solved by M.L.Dugdale, D.Dymianiw, B.Minhas, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.97 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.540, 162.390, 203.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.2

Other elements in 3i3d:

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg also contains other interesting chemical elements:

Magnesium (Mg) 13 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg (pdb code 3i3d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (M542A) in Complex with Iptg, PDB code: 3i3d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 3i3d

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Sodium binding site 1 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:27.4
occ:1.00
O6 A:IPT2001 2.3 21.6 0.9
O A:HOH4266 2.4 28.0 1.0
O A:PHE601 2.5 27.1 1.0
OD2 A:ASP201 2.5 19.2 1.0
OD1 A:ASN604 2.6 23.0 1.0
C6 A:IPT2001 3.1 20.8 0.9
ND2 A:ASN604 3.2 20.6 1.0
CG A:ASN604 3.2 20.3 1.0
CG A:ASP201 3.5 17.5 1.0
C A:PHE601 3.7 27.3 1.0
NE1 A:TRP568 3.8 13.4 1.0
OD1 A:ASP201 3.9 18.9 1.0
OH A:TYR100 4.0 25.8 1.0
O A:HOH4050 4.2 16.5 1.0
O4 A:IPT2001 4.2 19.9 0.9
CA A:CYS602 4.2 22.8 1.0
C5 A:IPT2001 4.3 22.3 0.9
C4 A:IPT2001 4.4 23.3 0.9
N A:CYS602 4.4 25.0 1.0
NE2 A:HIS540 4.4 10.1 1.0
C A:CYS602 4.6 21.6 1.0
CE2 A:TRP568 4.6 14.5 1.0
CB A:ASN604 4.7 20.0 1.0
CZ2 A:TRP568 4.7 15.1 1.0
CB A:ASP201 4.7 18.0 1.0
CA A:PHE601 4.7 28.7 1.0
O A:ASP201 4.8 17.7 1.0
CD1 A:TRP568 4.8 14.0 1.0
CE1 A:HIS540 4.9 11.2 1.0
CB A:PHE601 4.9 31.4 1.0
O A:CYS602 4.9 21.9 1.0
N A:MET603 5.0 20.2 1.0

Sodium binding site 2 out of 17 in 3i3d

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Sodium binding site 2 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:9.4
occ:1.00
O A:TYR559 2.2 12.3 1.0
O A:PHE556 2.3 10.0 1.0
O A:LEU562 2.3 8.4 1.0
O A:HOH4561 2.5 14.3 1.0
O A:HOH4384 2.5 24.2 1.0
O A:PRO560 3.3 7.2 1.0
C A:TYR559 3.3 9.4 1.0
C A:LEU562 3.4 9.1 1.0
C A:PHE556 3.5 9.5 1.0
C A:PRO560 3.7 7.9 1.0
CA A:PRO560 3.8 8.3 1.0
O A:HOH4273 4.0 15.2 1.0
N A:PRO560 4.0 8.9 1.0
N A:LEU562 4.0 8.3 1.0
CA A:PHE556 4.2 8.4 1.0
CA A:LEU562 4.2 9.3 1.0
N A:GLN563 4.2 8.7 1.0
CA A:GLN563 4.3 9.3 1.0
CA A:TYR559 4.5 9.0 1.0
CB A:LEU562 4.5 8.2 1.0
N A:ARG557 4.5 8.8 1.0
CG A:GLN563 4.6 7.6 1.0
N A:TYR559 4.6 8.5 1.0
N A:ARG561 4.6 6.5 1.0
CD1 A:LEU350 4.7 9.3 1.0
CA A:ARG557 4.7 9.9 1.0
CB A:PHE556 4.8 8.9 1.0
C A:ARG557 4.8 9.8 1.0
O A:ARG557 4.9 10.1 1.0
C A:ARG561 4.9 9.2 1.0
CB A:TYR559 5.0 8.0 1.0

Sodium binding site 3 out of 17 in 3i3d

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Sodium binding site 3 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:31.8
occ:1.00
O A:THR970 2.8 29.6 1.0
O A:LEU967 2.8 23.9 1.0
O A:PRO932 2.8 12.9 1.0
O A:HOH4200 2.9 23.6 1.0
O A:HOH4492 3.0 38.0 1.0
CZ A:PHE931 3.4 30.5 1.0
CE1 A:PHE931 3.5 29.5 1.0
O A:MET968 3.6 28.2 1.0
O A:HOH4624 3.7 28.9 1.0
C A:PRO932 3.8 16.8 1.0
C A:MET968 3.9 28.4 1.0
C A:THR970 3.9 27.5 1.0
C A:LEU967 3.9 23.2 1.0
CA A:MET968 4.0 27.7 1.0
CE2 A:PHE931 4.1 29.6 1.0
CB A:PRO932 4.2 18.8 1.0
CD1 A:PHE931 4.2 29.1 1.0
CA A:PRO932 4.4 17.7 1.0
N A:THR970 4.4 29.0 1.0
N A:MET968 4.5 25.2 1.0
CD A:PRO932 4.5 18.9 1.0
N A:PRO932 4.5 19.3 1.0
N A:GLU969 4.6 28.8 1.0
CA A:THR970 4.8 27.9 1.0
CD2 A:PHE931 4.8 28.4 1.0
N A:SER971 4.8 26.0 1.0
CA A:SER971 4.8 23.8 1.0
CG A:PHE931 4.8 26.7 1.0
N A:SER933 4.8 16.6 1.0
CG A:PRO932 4.9 18.6 1.0
C A:GLU969 4.9 29.0 1.0

Sodium binding site 4 out of 17 in 3i3d

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Sodium binding site 4 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:29.2
occ:1.00
O A:SER647 2.7 17.8 1.0
O A:GLU650 2.8 17.4 1.0
N A:GLU650 2.9 18.2 1.0
O A:LEU670 3.3 19.7 1.0
C A:ASP648 3.3 22.1 1.0
N A:ASN649 3.3 20.1 1.0
S A:DMS9032 3.5 87.5 1.0
C A:GLU650 3.6 17.8 1.0
O A:ASP648 3.7 18.7 1.0
C A:SER647 3.7 19.6 1.0
CA A:GLU650 3.7 17.4 1.0
CA A:ASP648 3.8 24.1 1.0
CA A:ASN649 3.8 18.5 1.0
C A:ASN649 3.8 18.6 1.0
O A:DMS9032 4.0 86.8 1.0
N A:ASP648 4.2 21.0 1.0
CB A:GLU650 4.3 15.2 1.0
C A:LEU670 4.4 20.9 1.0
OE1 A:GLU650 4.4 12.6 1.0
N A:LEU670 4.4 21.4 1.0
C1 A:DMS9032 4.5 86.8 1.0
C2 A:DMS9032 4.7 87.0 1.0
CA A:LEU670 4.8 21.1 1.0
N A:LEU651 4.9 18.7 1.0
CB A:LEU670 4.9 19.6 1.0
CA A:SER647 5.0 18.4 1.0
OG A:SER647 5.0 16.7 1.0
CB A:SER647 5.0 19.0 1.0

Sodium binding site 5 out of 17 in 3i3d

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Sodium binding site 5 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:15.0
occ:1.00
O6 B:IPT2001 2.3 14.6 1.0
O B:HOH4269 2.3 24.4 1.0
O B:PHE601 2.3 16.7 1.0
OD2 B:ASP201 2.4 8.6 1.0
OD1 B:ASN604 2.4 12.5 1.0
C6 B:IPT2001 3.0 14.3 1.0
CG B:ASP201 3.4 10.2 1.0
CG B:ASN604 3.4 13.1 1.0
C B:PHE601 3.6 16.8 1.0
OD1 B:ASP201 3.7 9.3 1.0
ND2 B:ASN604 3.8 14.6 1.0
OH B:TYR100 3.8 12.1 1.0
NE1 B:TRP568 4.0 9.2 1.0
O4 B:IPT2001 4.1 17.3 1.0
CA B:CYS602 4.2 14.9 1.0
C5 B:IPT2001 4.3 17.1 1.0
O B:HOH4050 4.3 22.9 1.0
N B:CYS602 4.3 15.8 1.0
C4 B:IPT2001 4.4 18.7 1.0
NE2 B:HIS540 4.6 6.5 1.0
CA B:PHE601 4.6 18.1 1.0
C B:CYS602 4.6 13.8 1.0
CB B:ASP201 4.6 7.5 1.0
CB B:PHE601 4.7 20.2 1.0
O B:ASP201 4.7 9.2 1.0
CE2 B:TRP568 4.8 10.8 1.0
CZ2 B:TRP568 4.8 9.7 1.0
CB B:ASN604 4.8 12.6 1.0
CZ B:TYR100 4.9 12.6 1.0

Sodium binding site 6 out of 17 in 3i3d

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Sodium binding site 6 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:13.8
occ:1.00
O B:TYR559 2.1 7.6 1.0
O B:LEU562 2.2 8.7 1.0
O B:PHE556 2.3 8.1 1.0
O B:HOH4587 2.6 26.8 1.0
O B:HOH4386 2.6 19.6 1.0
C B:TYR559 3.2 9.2 1.0
C B:LEU562 3.3 6.9 1.0
O B:PRO560 3.3 12.0 1.0
C B:PHE556 3.4 8.8 1.0
C B:PRO560 3.6 10.8 1.0
CA B:PRO560 3.7 9.2 1.0
N B:PRO560 3.8 9.0 1.0
N B:LEU562 3.8 7.6 1.0
O B:HOH4276 4.0 15.0 1.0
CA B:LEU562 4.1 6.7 1.0
CA B:PHE556 4.2 8.4 1.0
CB B:LEU562 4.2 5.3 1.0
N B:GLN563 4.2 6.3 1.0
CA B:TYR559 4.3 9.4 1.0
CA B:GLN563 4.3 6.8 1.0
O B:HOH4916 4.4 39.1 1.0
N B:TYR559 4.5 9.8 1.0
N B:ARG561 4.5 9.2 1.0
N B:ARG557 4.5 8.1 1.0
CG B:GLN563 4.7 7.2 1.0
CA B:ARG557 4.7 9.1 1.0
C B:ARG561 4.8 9.1 1.0
CB B:PHE556 4.8 8.7 1.0
C B:ARG557 4.8 9.0 1.0
CD1 B:LEU350 4.8 12.9 1.0
CB B:TYR559 4.9 8.9 1.0
O B:ALA555 5.0 9.5 1.0
O B:ARG557 5.0 8.5 1.0

Sodium binding site 7 out of 17 in 3i3d

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Sodium binding site 7 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:39.5
occ:1.00
O B:PRO932 2.5 13.9 1.0
O B:LEU967 2.7 17.6 1.0
O B:THR970 2.7 20.3 1.0
O B:HOH4202 2.9 14.4 1.0
CE1 B:PHE931 3.3 22.9 1.0
CZ B:PHE931 3.4 23.7 1.0
C B:PRO932 3.5 14.4 1.0
C B:THR970 3.8 20.1 1.0
O B:MET968 3.8 21.9 1.0
C B:LEU967 3.9 17.4 1.0
O B:HOH4671 3.9 42.3 1.0
CD1 B:PHE931 4.0 22.7 1.0
CE2 B:PHE931 4.1 22.6 1.0
C B:MET968 4.1 21.9 1.0
CB B:PRO932 4.1 15.2 1.0
CA B:PRO932 4.1 14.9 1.0
CD B:PRO932 4.2 13.9 1.0
N B:PRO932 4.2 14.6 1.0
CA B:MET968 4.2 20.8 1.0
N B:THR970 4.4 21.1 1.0
N B:MET968 4.5 18.7 1.0
CG B:PHE931 4.6 19.5 1.0
N B:SER933 4.6 14.0 1.0
CD2 B:PHE931 4.6 23.0 1.0
CA B:THR970 4.7 20.5 1.0
N B:SER971 4.7 19.1 1.0
O B:HOH4513 4.7 42.2 1.0
CG B:PRO932 4.7 14.3 1.0
CA B:SER971 4.7 18.3 1.0
N B:GLU969 4.8 21.8 1.0
C B:PHE931 4.8 14.4 1.0
CA B:SER933 5.0 15.3 1.0

Sodium binding site 8 out of 17 in 3i3d

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Sodium binding site 8 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:30.1
occ:1.00
O B:SER647 2.5 17.5 1.0
O B:DMS9017 2.7 73.0 1.0
O B:GLU650 2.7 16.9 1.0
N B:GLU650 3.0 15.0 1.0
O B:HOH4680 3.0 32.4 1.0
O B:LEU670 3.0 23.3 1.0
C1 B:DMS9017 3.1 73.9 1.0
S B:DMS9017 3.2 74.3 1.0
N B:ASN649 3.5 15.5 1.0
C B:ASP648 3.5 17.1 1.0
C B:GLU650 3.5 17.5 1.0
C B:SER647 3.7 19.4 1.0
CA B:GLU650 3.7 16.7 1.0
CA B:ASP648 3.8 19.1 1.0
C B:ASN649 4.0 14.3 1.0
O B:ASP648 4.0 17.2 1.0
CA B:ASN649 4.0 15.5 1.0
CB B:GLU650 4.1 14.9 1.0
C B:LEU670 4.2 22.7 1.0
N B:ASP648 4.2 18.8 1.0
N B:LEU670 4.3 24.4 1.0
OE1 B:GLU650 4.5 16.9 1.0
OG B:SER647 4.6 16.6 1.0
CA B:LEU670 4.7 23.9 1.0
N B:LEU651 4.8 18.6 1.0
CB B:LEU670 4.8 23.8 1.0
CB B:SER647 4.9 18.0 1.0
CA B:SER647 4.9 18.6 1.0
C2 B:DMS9017 4.9 73.6 1.0

Sodium binding site 9 out of 17 in 3i3d

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Sodium binding site 9 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3105

b:42.7
occ:1.00
O B:HOH4330 2.4 16.5 1.0
O B:HOH4434 2.4 37.0 1.0
O B:HOH4950 2.6 45.5 1.0
O B:HOH4049 3.5 39.4 1.0
N B:ILE337 3.7 13.0 1.0
CA B:ARG336 3.8 13.6 1.0
CG B:PRO483 3.9 9.4 1.0
C B:ARG336 4.3 12.9 1.0
O B:HOH4156 4.4 19.8 1.0
C1 B:DMS9007 4.4 33.9 1.0
CB B:ARG336 4.4 14.9 1.0
O B:VAL335 4.4 12.3 1.0
CD B:PRO483 4.4 7.8 1.0
N B:PRO483 4.5 8.8 1.0
CG1 B:ILE337 4.5 10.3 1.0
CA B:PRO483 4.5 9.4 1.0
CB B:ILE337 4.5 11.9 1.0
CB B:PRO483 4.6 8.8 1.0
O B:PRO480 4.6 19.8 1.0
NZ B:LYS476 4.6 13.0 1.0
CA B:ILE337 4.7 12.2 1.0
N B:ARG336 4.8 12.2 1.0
C B:ARG482 4.9 11.1 1.0
C B:VAL335 5.0 11.5 1.0
O B:ILE337 5.0 10.7 1.0

Sodium binding site 10 out of 17 in 3i3d

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Sodium binding site 10 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (M542A) 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 (M542A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:18.2
occ:1.00
O6 C:IPT2001 2.3 15.4 1.0
OD2 C:ASP201 2.3 15.1 1.0
ND2 C:ASN604 2.4 11.2 1.0
O C:HOH4268 2.4 27.8 1.0
O C:PHE601 2.4 16.1 1.0
C6 C:IPT2001 3.0 16.4 1.0
CG C:ASP201 3.3 13.7 1.0
CG C:ASN604 3.4 12.4 1.0
OD1 C:ASN604 3.6 15.5 1.0
C C:PHE601 3.6 16.9 1.0
OD1 C:ASP201 3.7 12.6 1.0
OH C:TYR100 3.8 17.5 1.0
NE1 C:TRP568 4.0 10.6 1.0
O4 C:IPT2001 4.1 18.5 1.0
O C:HOH5015 4.2 9.4 1.0
CA C:CYS602 4.2 15.9 1.0
C5 C:IPT2001 4.3 18.2 1.0
C4 C:IPT2001 4.4 18.2 1.0
N C:CYS602 4.4 15.3 1.0
CB C:ASP201 4.6 11.0 1.0
CZ2 C:TRP568 4.6 12.0 1.0
NE2 C:HIS540 4.6 6.7 1.0
CE2 C:TRP568 4.7 12.6 1.0
CA C:PHE601 4.7 15.8 1.0
C C:CYS602 4.7 16.1 1.0
CB C:ASN604 4.7 12.7 1.0
CB C:PHE601 4.7 17.8 1.0
O C:ASP201 4.8 11.8 1.0
CZ C:TYR100 4.9 16.3 1.0

Reference:

M.L.Dugdale, D.L.Dymianiw, B.K.Minhas, I.D'angelo, R.E.Huber. Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009
Page generated: Tue Dec 15 06:14:04 2020

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