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Sodium in PDB 3i3b: E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b 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) 14.18 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.600, 168.420, 201.310, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.4

Other elements in 3i3b:

The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on (pdb code 3i3b). 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 (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 3i3b

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Sodium binding site 1 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3101

b:13.8
occ:1.00
O6 A:1492001 2.3 14.0 1.0
OD1 A:ASN604 2.3 12.1 1.0
OD2 A:ASP201 2.4 18.2 1.0
O A:HOH4270 2.4 13.5 1.0
O A:PHE601 2.4 19.5 1.0
CG A:ASP201 3.4 17.5 1.0
CG A:ASN604 3.4 14.9 1.0
C6 A:1492001 3.4 13.3 1.0
CD1 A:PHE601 3.6 17.7 1.0
C A:PHE601 3.6 19.2 1.0
CE1 A:PHE601 3.7 17.2 1.0
OD1 A:ASP201 3.8 18.4 1.0
ND2 A:ASN604 3.8 15.3 1.0
CG A:PHE601 3.9 19.6 1.0
OH A:TYR100 3.9 18.2 1.0
O4 A:1492001 4.0 18.0 1.0
CZ A:PHE601 4.1 17.5 1.0
C4 A:1492001 4.1 15.2 1.0
NE1 A:TRP568 4.2 10.9 1.0
CD2 A:PHE601 4.3 17.5 1.0
C5 A:1492001 4.3 12.9 1.0
CA A:CYS602 4.4 17.2 1.0
CE2 A:PHE601 4.4 17.8 1.0
NE2 A:HIS540 4.4 11.5 1.0
N A:CYS602 4.5 18.1 1.0
O A:HOH4050 4.5 18.3 1.0
CB A:PHE601 4.6 19.2 1.0
CB A:ASP201 4.6 15.8 1.0
CA A:PHE601 4.6 20.8 1.0
CB A:ASN604 4.7 11.0 1.0
O A:ASP201 4.7 12.2 1.0
C A:CYS602 4.9 16.9 1.0
CE2 A:TRP568 4.9 13.1 1.0
CE1 A:HIS540 5.0 12.9 1.0

Sodium binding site 2 out of 16 in 3i3b

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Sodium binding site 2 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3102

b:21.8
occ:1.00
O A:PHE556 2.3 15.3 1.0
O A:LEU562 2.3 8.7 1.0
O A:TYR559 2.4 13.2 1.0
O A:HOH4387 2.7 22.9 1.0
O A:HOH4557 2.8 32.4 1.0
O A:PRO560 3.2 10.7 1.0
C A:TYR559 3.3 11.8 1.0
C A:LEU562 3.4 7.8 1.0
C A:PHE556 3.4 14.5 1.0
C A:PRO560 3.6 10.6 1.0
CA A:PRO560 3.7 9.6 1.0
O A:HOH4277 3.9 14.1 1.0
O A:HOH4672 3.9 46.6 1.0
N A:PRO560 3.9 10.2 1.0
N A:LEU562 3.9 7.3 1.0
CA A:PHE556 4.1 12.9 1.0
CA A:LEU562 4.2 8.4 1.0
CB A:LEU562 4.3 6.9 1.0
N A:GLN563 4.3 9.9 1.0
CA A:GLN563 4.4 10.8 1.0
CA A:TYR559 4.5 11.8 1.0
N A:ARG557 4.5 12.9 1.0
N A:ARG561 4.5 9.4 1.0
N A:TYR559 4.5 12.6 1.0
CG A:GLN563 4.6 10.5 1.0
CA A:ARG557 4.7 12.3 1.0
CB A:PHE556 4.7 13.4 1.0
C A:ARG561 4.8 9.0 1.0
C A:ARG557 4.8 12.3 1.0
O A:ALA555 4.9 13.0 1.0

Sodium binding site 3 out of 16 in 3i3b

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Sodium binding site 3 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3103

b:39.5
occ:1.00
O A:THR970 2.5 26.4 1.0
O A:LEU967 2.9 21.6 1.0
O A:PRO932 3.0 17.5 1.0
O A:HOH4807 3.1 39.4 1.0
CZ A:PHE931 3.2 28.1 1.0
O A:HOH4624 3.3 37.7 1.0
CE1 A:PHE931 3.4 28.8 1.0
O A:HOH4202 3.4 17.2 1.0
C A:THR970 3.6 27.0 1.0
O A:MET968 3.7 24.8 1.0
CE2 A:PHE931 3.8 27.5 1.0
C A:PRO932 3.9 17.7 1.0
CD1 A:PHE931 4.1 27.2 1.0
CD A:PRO932 4.1 18.5 1.0
C A:MET968 4.1 26.4 1.0
C A:LEU967 4.1 22.2 1.0
CB A:PRO932 4.1 19.2 1.0
N A:THR970 4.3 26.8 1.0
N A:PRO932 4.3 20.3 1.0
CA A:PRO932 4.3 19.0 1.0
CD2 A:PHE931 4.4 27.0 1.0
CA A:MET968 4.4 25.8 1.0
N A:SER971 4.4 25.4 1.0
CA A:SER971 4.4 24.7 1.0
CA A:THR970 4.5 27.7 1.0
CG A:PHE931 4.6 25.8 1.0
CG A:PRO932 4.7 18.5 1.0
N A:MET968 4.7 23.1 1.0
N A:GLU969 4.8 26.0 1.0
C A:GLU969 4.9 27.8 1.0

Sodium binding site 4 out of 16 in 3i3b

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Sodium binding site 4 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3104

b:28.4
occ:1.00
O A:DMS5018 2.4 55.2 1.0
O A:LEU670 2.6 27.9 1.0
O A:SER647 2.6 24.8 1.0
O A:GLU650 2.7 20.4 1.0
S A:DMS5018 3.5 56.3 1.0
N A:GLU650 3.6 21.7 1.0
C A:LEU670 3.6 28.2 1.0
C A:GLU650 3.7 22.6 1.0
C1 A:DMS5018 3.8 55.2 1.0
C A:SER647 3.8 23.9 1.0
N A:LEU670 3.9 29.5 1.0
C A:ASP648 4.1 24.2 1.0
N A:ASN649 4.1 23.4 1.0
CA A:LEU670 4.1 29.3 1.0
CA A:GLU650 4.2 21.7 1.0
CA A:ASP648 4.2 24.6 1.0
CB A:LEU670 4.2 29.6 1.0
OG A:SER647 4.4 20.4 1.0
N A:ASP648 4.5 23.2 1.0
O A:ASP648 4.6 23.4 1.0
CB A:GLU650 4.6 20.3 1.0
C A:ASN649 4.6 21.6 1.0
CA A:ASN649 4.7 21.6 1.0
N A:ASP671 4.7 27.5 1.0
CB A:SER647 4.8 21.7 1.0
O A:HOH4674 4.9 34.8 1.0
OE1 A:GLU650 4.9 15.3 1.0
N A:LEU651 4.9 23.6 1.0
C A:PRO669 4.9 29.6 1.0
CA A:SER647 5.0 23.1 1.0
C2 A:DMS5018 5.0 55.5 1.0

Sodium binding site 5 out of 16 in 3i3b

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Sodium binding site 5 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3101

b:15.9
occ:1.00
O6 B:1492001 2.3 12.3 1.0
OD2 B:ASP201 2.5 17.8 1.0
O B:PHE601 2.5 14.7 1.0
OD1 B:ASN604 2.5 12.6 1.0
O B:HOH4270 2.6 12.0 1.0
CD1 B:PHE601 3.3 14.4 1.0
CE1 B:PHE601 3.3 14.3 1.0
C6 B:1492001 3.3 11.1 1.0
CG B:ASP201 3.4 14.2 1.0
CG B:ASN604 3.5 12.8 1.0
C B:PHE601 3.7 15.0 1.0
ND2 B:ASN604 3.8 10.9 1.0
OD1 B:ASP201 3.8 16.3 1.0
OH B:TYR100 3.9 12.5 1.0
CG B:PHE601 3.9 16.1 1.0
O4 B:1492001 4.0 16.4 1.0
CZ B:PHE601 4.0 13.2 1.0
C4 B:1492001 4.1 13.6 1.0
NE1 B:TRP568 4.2 4.9 1.0
C5 B:1492001 4.2 12.6 1.0
NE2 B:HIS540 4.4 12.3 1.0
CA B:CYS602 4.4 16.2 1.0
CD2 B:PHE601 4.5 16.0 1.0
N B:CYS602 4.5 14.0 1.0
CE2 B:PHE601 4.5 16.1 1.0
O B:HOH4052 4.6 12.7 1.0
CB B:PHE601 4.6 15.1 1.0
CB B:ASP201 4.7 14.5 1.0
CA B:PHE601 4.7 15.9 1.0
O B:ASP201 4.7 12.8 1.0
CB B:ASN604 4.8 12.6 1.0
C B:CYS602 4.9 16.1 1.0
CE1 B:HIS540 4.9 12.0 1.0
CE2 B:TRP568 5.0 6.2 1.0

Sodium binding site 6 out of 16 in 3i3b

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Sodium binding site 6 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3102

b:16.4
occ:1.00
O B:TYR559 2.2 13.8 1.0
O B:PHE556 2.3 7.4 1.0
O B:LEU562 2.4 10.8 1.0
O B:HOH4387 2.6 32.7 1.0
O B:HOH4575 2.8 21.7 1.0
C B:TYR559 3.2 14.1 1.0
O B:PRO560 3.4 14.0 1.0
C B:LEU562 3.4 9.6 1.0
C B:PHE556 3.5 9.7 1.0
C B:PRO560 3.6 11.9 1.0
CA B:PRO560 3.6 11.9 1.0
N B:PRO560 3.8 12.4 1.0
N B:LEU562 3.9 8.9 1.0
O B:HOH4277 4.1 17.6 1.0
CA B:LEU562 4.1 10.5 1.0
CA B:PHE556 4.2 8.5 1.0
CB B:LEU562 4.3 5.7 1.0
N B:GLN563 4.3 9.8 1.0
CA B:TYR559 4.3 13.5 1.0
CA B:GLN563 4.4 9.4 1.0
N B:TYR559 4.4 13.2 1.0
N B:ARG561 4.5 10.9 1.0
N B:ARG557 4.5 9.9 1.0
CG B:GLN563 4.7 10.4 1.0
CA B:ARG557 4.7 10.1 1.0
CB B:PHE556 4.8 8.7 1.0
C B:ARG561 4.8 10.6 1.0
C B:ARG557 4.8 10.6 1.0
CB B:TYR559 4.9 12.4 1.0
CD1 B:LEU350 4.9 8.3 1.0
O B:ARG557 4.9 9.0 1.0
O B:ALA555 5.0 8.9 1.0

Sodium binding site 7 out of 16 in 3i3b

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Sodium binding site 7 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3103

b:23.9
occ:1.00
O B:LEU967 2.5 16.3 1.0
O B:PRO932 2.6 21.7 1.0
O B:THR970 2.8 24.6 1.0
O B:HOH4204 3.0 22.5 1.0
C B:PRO932 3.5 20.3 1.0
CZ B:PHE931 3.5 18.7 1.0
O B:HOH4651 3.6 35.1 1.0
C B:LEU967 3.7 17.2 1.0
CE2 B:PHE931 3.7 20.6 1.0
C B:THR970 3.8 24.2 1.0
CB B:PRO932 3.8 21.3 1.0
O B:HOH4510 3.9 23.9 1.0
O B:MET968 4.0 22.3 1.0
CA B:PRO932 4.0 20.8 1.0
CE1 B:PHE931 4.0 20.2 1.0
C B:MET968 4.1 23.3 1.0
N B:PRO932 4.1 21.6 1.0
CA B:MET968 4.1 22.4 1.0
CD B:PRO932 4.3 20.6 1.0
N B:THR970 4.3 23.8 1.0
CD2 B:PHE931 4.3 19.9 1.0
N B:MET968 4.3 18.7 1.0
N B:SER933 4.5 17.4 1.0
N B:SER971 4.5 23.7 1.0
CD1 B:PHE931 4.6 19.8 1.0
CA B:SER971 4.6 22.6 1.0
CG B:PRO932 4.6 20.2 1.0
CA B:THR970 4.7 23.3 1.0
CG B:PHE931 4.7 20.7 1.0
N B:GLU969 4.7 24.3 1.0
C B:PHE931 4.8 20.5 1.0
CA B:LEU967 4.8 17.1 1.0
CA B:SER933 4.9 16.1 1.0

Sodium binding site 8 out of 16 in 3i3b

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Sodium binding site 8 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3104

b:31.1
occ:1.00
O B:DMS5021 2.4 66.5 1.0
O B:GLU650 2.5 23.4 1.0
O B:SER647 2.6 14.9 1.0
O B:LEU670 2.8 22.4 1.0
O B:HOH4662 3.0 43.7 1.0
C1 B:DMS5021 3.1 66.6 1.0
N B:GLU650 3.1 20.0 1.0
S B:DMS5021 3.3 66.7 1.0
C B:GLU650 3.4 22.5 1.0
N B:ASN649 3.6 20.2 1.0
C B:SER647 3.7 16.1 1.0
CA B:GLU650 3.7 21.6 1.0
C B:ASP648 3.8 20.5 1.0
CA B:ASP648 3.9 20.1 1.0
C B:LEU670 3.9 23.8 1.0
N B:LEU670 4.1 25.2 1.0
C B:ASN649 4.1 19.4 1.0
CA B:ASN649 4.2 18.3 1.0
N B:ASP648 4.2 18.3 1.0
CB B:GLU650 4.2 21.4 1.0
C2 B:DMS5021 4.2 67.1 1.0
O B:ASP648 4.4 19.9 1.0
CA B:LEU670 4.4 24.2 1.0
CB B:LEU670 4.5 24.2 1.0
OE1 B:GLU650 4.6 18.4 1.0
N B:LEU651 4.7 22.5 1.0
OG B:SER647 4.7 14.2 1.0
CB B:SER647 4.8 16.6 1.0
O B:HOH4704 4.8 40.0 1.0
CA B:SER647 4.9 15.6 1.0
C B:PRO669 5.0 25.9 1.0

Sodium binding site 9 out of 16 in 3i3b

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Sodium binding site 9 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3101

b:13.8
occ:1.00
O6 C:1492001 2.3 9.3 1.0
OD2 C:ASP201 2.4 10.9 1.0
OD1 C:ASN604 2.4 12.8 1.0
O C:PHE601 2.5 14.7 1.0
O C:HOH4276 2.6 15.4 1.0
CD2 C:PHE601 3.2 12.7 1.0
CE2 C:PHE601 3.3 12.5 1.0
C6 C:1492001 3.3 9.9 1.0
CG C:ASN604 3.4 13.6 1.0
CG C:ASP201 3.5 11.3 1.0
C C:PHE601 3.6 16.3 1.0
ND2 C:ASN604 3.7 11.8 1.0
CG C:PHE601 3.8 12.6 1.0
OD1 C:ASP201 3.9 11.7 1.0
CZ C:PHE601 3.9 10.0 1.0
OH C:TYR100 3.9 15.9 1.0
O4 C:1492001 4.0 13.8 1.0
C4 C:1492001 4.1 13.0 1.0
C5 C:1492001 4.2 11.5 1.0
NE1 C:TRP568 4.3 7.9 1.0
CD1 C:PHE601 4.4 10.9 1.0
NE2 C:HIS540 4.4 9.9 1.0
CA C:CYS602 4.4 17.2 1.0
CE1 C:PHE601 4.4 11.8 1.0
N C:CYS602 4.5 16.0 1.0
CB C:PHE601 4.5 14.5 1.0
CA C:PHE601 4.6 16.5 1.0
O C:HOH4054 4.6 13.6 1.0
CB C:ASP201 4.7 9.9 1.0
CB C:ASN604 4.8 13.9 1.0
O C:ASP201 4.9 11.1 1.0
CE1 C:HIS540 4.9 10.5 1.0
C C:CYS602 4.9 16.5 1.0
CE2 C:TRP568 5.0 7.1 1.0

Sodium binding site 10 out of 16 in 3i3b

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Sodium binding site 10 out of 16 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-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 (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3102

b:14.7
occ:1.00
O C:PHE556 2.2 6.4 1.0
O C:TYR559 2.2 10.3 1.0
O C:LEU562 2.4 14.1 1.0
O C:HOH4392 2.5 20.9 1.0
O C:HOH4565 2.8 27.2 1.0
C C:TYR559 3.2 10.9 1.0
O C:PRO560 3.3 10.7 1.0
C C:PHE556 3.4 9.3 1.0
C C:LEU562 3.4 11.5 1.0
C C:PRO560 3.6 10.8 1.0
CA C:PRO560 3.6 9.9 1.0
N C:PRO560 3.8 9.3 1.0
N C:LEU562 3.9 11.0 1.0
CA C:PHE556 4.1 8.9 1.0
O C:HOH4283 4.1 14.2 1.0
CA C:LEU562 4.1 12.0 1.0
CB C:LEU562 4.3 8.2 1.0
N C:GLN563 4.4 11.5 1.0
CA C:TYR559 4.4 12.1 1.0
N C:ARG557 4.4 11.1 1.0
N C:TYR559 4.4 12.1 1.0
CA C:GLN563 4.5 12.0 1.0
N C:ARG561 4.5 10.3 1.0
CA C:ARG557 4.6 10.1 1.0
CG C:GLN563 4.7 13.8 1.0
C C:ARG557 4.7 11.9 1.0
CB C:PHE556 4.7 8.6 1.0
C C:ARG561 4.8 11.7 1.0
O C:ALA555 4.8 9.4 1.0
O C:ARG557 4.9 12.8 1.0
CB C:TYR559 5.0 12.1 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 06:14:02 2020

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