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Sodium in PDB 3e1f: E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose, PDB code: 3e1f was solved by R.E.Huber, M.L.Dugdale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.54 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.370, 152.870, 132.120, 90.00, 102.68, 90.00
R / Rfree (%) 21.8 / 24.9

Other elements in 3e1f:

The structure of E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose (pdb code 3e1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose, PDB code: 3e1f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 3e1f

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Sodium binding site 1 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3100

b:44.2
occ:1.00
 OD1 1:ASN604 2.2 48.9 1.0
OD2 1:ASP201 2.3 43.3 1.0
O 1:PHE601 2.6 51.3 1.0
O6 1:GAL2001 2.8 44.5 1.0
CG 1:ASN604 3.3 49.8 1.0
C6 1:GAL2001 3.4 42.5 1.0
CG 1:ASP201 3.5 42.8 1.0
NE1 1:TRP568 3.8 35.8 1.0
C 1:PHE601 3.8 52.0 1.0
ND2 1:ASN604 3.9 50.6 1.0
C4 1:GAL2001 4.1 41.5 1.0
OD1 1:ASP201 4.2 42.4 1.0
NE2 1:HIS540 4.2 30.1 1.0
C5 1:GAL2001 4.2 42.0 1.0
OH 1:TYR100 4.4 42.2 1.0
O4 1:GAL2001 4.5 43.8 1.0
CE2 1:TRP568 4.5 36.2 1.0
CB 1:ASN604 4.5 50.0 1.0
CZ2 1:TRP568 4.6 38.0 1.0
O 1:ASP201 4.6 42.6 1.0
CB 1:ASP201 4.6 42.7 1.0
CA 1:CYS602 4.6 51.8 1.0
N 1:CYS602 4.7 52.1 1.0
CE1 1:HIS540 4.7 31.3 1.0
CB 1:PHE601 4.8 51.8 1.0
CA 1:PHE601 4.8 52.4 1.0
CD1 1:TRP568 4.8 35.7 1.0
CD2 1:PHE601 4.9 51.0 1.0

Sodium binding site 2 out of 13 in 3e1f

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Sodium binding site 2 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3101

b:30.6
occ:1.00
 O 1:TYR559 2.3 36.4 1.0
O 1:PHE556 2.4 33.8 1.0
O 1:LEU562 2.5 33.2 1.0
O 1:PRO560 3.2 33.5 1.0
C 1:TYR559 3.3 34.6 1.0
C 1:LEU562 3.4 32.9 1.0
C 1:PRO560 3.6 33.0 1.0
C 1:PHE556 3.6 34.0 1.0
CA 1:PRO560 3.7 32.5 1.0
N 1:PRO560 3.9 33.2 1.0
N 1:LEU562 3.9 35.1 1.0
CA 1:LEU562 4.2 34.0 1.0
N 1:GLN563 4.2 30.4 1.0
CA 1:GLN563 4.3 29.1 1.0
CA 1:PHE556 4.4 34.0 1.0
CA 1:TYR559 4.4 34.0 1.0
CB 1:LEU562 4.4 33.3 1.0
N 1:ARG561 4.5 34.1 1.0
N 1:TYR559 4.5 33.2 1.0
N 1:ARG557 4.6 34.1 1.0
CG 1:GLN563 4.6 26.1 1.0
CD1 1:LEU350 4.6 34.2 1.0
CA 1:ARG557 4.7 33.2 1.0
C 1:ARG557 4.8 33.0 1.0
O 1:ARG557 4.8 32.3 1.0
C 1:ARG561 4.8 35.2 1.0

Sodium binding site 3 out of 13 in 3e1f

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Sodium binding site 3 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3103

b:43.0
occ:1.00
 O 1:GLU650 2.6 64.4 1.0
N 1:GLU650 3.1 62.4 1.0
O 1:SER647 3.4 62.8 1.0
O 1:DMS8425 3.4 0.1 1.0
C 1:GLU650 3.5 63.8 1.0
O 1:LEU670 3.7 55.3 1.0
C 1:ASP648 3.7 61.2 1.0
N 1:ASN649 3.8 61.1 1.0
CA 1:GLU650 3.9 63.6 1.0
O 1:ASP648 3.9 61.6 1.0
C 1:ASN649 4.1 61.1 1.0
CA 1:ASN649 4.1 60.9 1.0
CA 1:ASP648 4.2 61.3 1.0
C 1:SER647 4.4 61.1 1.0
N 1:LEU670 4.5 57.8 1.0
N 1:LEU651 4.6 63.2 1.0
C 1:LEU670 4.7 56.2 1.0
N 1:ASP648 4.8 60.9 1.0
CB 1:GLU650 4.8 64.6 1.0
S 1:DMS8425 4.9 0.3 1.0

Sodium binding site 4 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 4 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3100

b:36.9
occ:1.00
 OD2 2:ASP201 2.1 34.8 1.0
OD1 2:ASN604 2.6 41.1 1.0
O 2:PHE601 2.8 43.8 1.0
O6 2:GAL2001 2.9 40.0 1.0
CG 2:ASP201 3.2 33.9 1.0
C4 2:GAL2001 3.5 41.7 1.0
CG 2:ASN604 3.6 41.3 1.0
C6 2:GAL2001 3.7 41.6 1.0
O4 2:GAL2001 3.7 41.6 1.0
NE1 2:TRP568 3.8 36.6 1.0
O 2:ASP201 3.9 29.2 1.0
OD1 2:ASP201 4.0 36.9 1.0
C 2:PHE601 4.0 44.1 1.0
C5 2:GAL2001 4.1 41.8 1.0
CZ2 2:TRP568 4.2 33.9 1.0
ND2 2:ASN604 4.2 42.3 1.0
CB 2:ASP201 4.2 31.6 1.0
CA 2:CYS602 4.3 41.4 1.0
CE2 2:TRP568 4.3 35.4 1.0
OH 2:TYR100 4.4 41.7 1.0
N 2:CYS602 4.6 43.2 1.0
CB 2:ASN604 4.7 39.9 1.0
C3 2:GAL2001 4.7 41.5 1.0
C 2:CYS602 4.8 40.6 1.0
NE2 2:HIS540 4.8 31.1 1.0
C 2:ASP201 4.9 29.2 1.0
O3 2:GAL2001 4.9 41.2 1.0
CD1 2:TRP568 5.0 36.4 1.0
NE2 2:GLN573 5.0 38.5 1.0

Sodium binding site 5 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 5 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3101

b:25.4
occ:1.00
 O 2:PHE556 2.2 27.7 1.0
O 2:TYR559 2.2 28.8 1.0
O 2:LEU562 2.7 28.2 1.0
C 2:TYR559 3.0 28.9 1.0
C 2:PHE556 3.4 28.2 1.0
O 2:PRO560 3.5 26.3 1.0
CA 2:PRO560 3.6 27.0 1.0
C 2:LEU562 3.7 28.6 1.0
N 2:PRO560 3.7 27.6 1.0
C 2:PRO560 3.7 26.5 1.0
N 2:LEU562 4.0 27.7 1.0
CA 2:TYR559 4.1 29.5 1.0
N 2:TYR559 4.2 29.4 1.0
CA 2:PHE556 4.3 28.2 1.0
N 2:ARG557 4.3 27.0 1.0
CA 2:LEU562 4.3 28.0 1.0
O 2:ARG557 4.3 25.4 1.0
C 2:ARG557 4.4 26.4 1.0
CA 2:ARG557 4.4 25.8 1.0
CB 2:LEU562 4.4 28.6 1.0
N 2:ARG561 4.5 27.0 1.0
N 2:GLN563 4.5 28.5 1.0
CA 2:GLN563 4.7 27.2 1.0
CD1 2:LEU350 4.8 20.4 1.0
CB 2:TYR559 4.8 30.0 1.0
O 2:ALA555 4.9 30.6 1.0
N 2:GLN558 4.9 28.2 1.0
C 2:GLN558 4.9 28.6 1.0
C 2:ARG561 5.0 27.1 1.0
CD 2:PRO560 5.0 26.4 1.0
CB 2:PHE556 5.0 28.0 1.0

Sodium binding site 6 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 6 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3102

b:49.9
occ:1.00
 CZ 2:PHE931 3.2 38.0 1.0
O 2:LEU967 3.2 57.7 1.0
O 2:PRO932 3.2 36.7 1.0
O 2:MET968 3.3 61.6 1.0
CA 2:MET968 3.4 60.2 1.0
C 2:MET968 3.5 61.7 1.0
O 2:THR970 3.6 64.7 1.0
CE1 2:PHE931 3.6 37.7 1.0
CE2 2:PHE931 4.0 39.0 1.0
C 2:LEU967 4.1 57.7 1.0
N 2:MET968 4.2 58.6 1.0
C 2:PRO932 4.3 39.0 1.0
CB 2:MET968 4.4 58.8 1.0
N 2:GLU969 4.4 64.2 1.0
CD1 2:PHE931 4.6 38.5 1.0
C 2:THR970 4.6 64.5 1.0
O 2:PRO788 4.6 46.7 1.0
CG 2:PRO788 4.7 47.2 1.0
N 2:THR970 4.8 65.3 1.0
CD2 2:PHE931 4.9 39.9 1.0

Sodium binding site 7 out of 13 in 3e1f

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Sodium binding site 7 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3103

b:30.2
occ:1.00
 O 2:GLU650 2.7 52.6 1.0
O 2:HOH8637 2.9 6.0 1.0
O 2:SER647 3.2 47.6 1.0
O 2:LEU670 3.3 50.4 1.0
N 2:GLU650 3.5 50.6 1.0
C 2:GLU650 3.7 51.9 1.0
C 2:ASP648 3.8 49.1 1.0
N 2:ASN649 4.0 49.5 1.0
O 2:ASP648 4.1 48.9 1.0
CA 2:ASP648 4.1 48.2 1.0
CA 2:GLU650 4.2 51.2 1.0
N 2:LEU670 4.3 53.0 1.0
C 2:SER647 4.3 47.0 1.0
C 2:LEU670 4.3 51.1 1.0
CA 2:ASN649 4.5 50.1 1.0
C 2:ASN649 4.5 50.7 1.0
N 2:ASP648 4.7 47.8 1.0
CA 2:LEU670 4.8 52.0 1.0
N 2:LEU651 4.9 52.9 1.0
CB 2:PRO669 4.9 54.3 1.0

Sodium binding site 8 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 8 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Na3100

b:16.4
occ:1.00
 OD2 3:ASP201 2.1 33.2 1.0
O6 3:GAL2001 2.4 31.0 1.0
OD1 3:ASN604 2.5 26.9 1.0
O 3:PHE601 2.8 37.7 1.0
CG 3:ASP201 3.2 35.1 1.0
CG 3:ASN604 3.6 28.1 1.0
C6 3:GAL2001 3.7 31.9 1.0
NE1 3:TRP568 3.9 23.8 1.0
O 3:ASP201 3.9 37.6 1.0
OD1 3:ASP201 3.9 35.3 1.0
C 3:PHE601 3.9 39.7 1.0
C4 3:GAL2001 4.0 32.7 1.0
O4 3:GAL2001 4.1 33.2 1.0
ND2 3:ASN604 4.2 28.2 1.0
CZ2 3:TRP568 4.2 26.5 1.0
CA 3:CYS602 4.3 38.1 1.0
CB 3:ASP201 4.3 35.8 1.0
OH 3:TYR100 4.3 37.1 1.0
C5 3:GAL2001 4.4 32.4 1.0
CE2 3:TRP568 4.4 25.3 1.0
N 3:CYS602 4.6 39.0 1.0
O 3:HOH8804 4.7 23.4 1.0
CB 3:ASN604 4.7 30.1 1.0
C 3:CYS602 4.7 38.2 1.0
NE2 3:HIS540 4.9 24.1 1.0
C 3:ASP201 4.9 37.5 1.0
NE2 3:GLN573 5.0 29.5 1.0

Sodium binding site 9 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 9 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Na3101

b:38.7
occ:1.00
 O 3:PHE556 2.1 31.5 1.0
O 3:TYR559 2.2 22.9 1.0
O 3:LEU562 2.2 15.7 1.0
C 3:LEU562 3.2 17.7 1.0
C 3:TYR559 3.2 24.1 1.0
C 3:PHE556 3.3 31.2 1.0
O 3:PRO560 3.5 24.9 1.0
N 3:LEU562 3.8 19.7 1.0
C 3:PRO560 3.8 23.7 1.0
CA 3:PRO560 3.9 24.1 1.0
CA 3:LEU562 3.9 18.5 1.0
N 3:PRO560 4.0 24.2 1.0
CA 3:PHE556 4.0 31.5 1.0
CB 3:LEU562 4.1 18.5 1.0
N 3:GLN563 4.1 17.3 1.0
CA 3:GLN563 4.3 18.5 1.0
CA 3:TYR559 4.3 24.2 1.0
N 3:ARG557 4.3 29.5 1.0
N 3:TYR559 4.4 26.9 1.0
CD1 3:LEU350 4.6 19.7 1.0
CA 3:ARG557 4.6 27.9 1.0
N 3:ARG561 4.6 22.7 1.0
C 3:ARG557 4.7 27.8 1.0
CB 3:PHE556 4.7 32.4 1.0
C 3:ARG561 4.7 21.4 1.0
O 3:ARG557 4.8 27.1 1.0
CG 3:GLN563 4.8 20.0 1.0
O 3:ALA555 4.8 28.4 1.0
CB 3:TYR559 4.9 22.2 1.0

Sodium binding site 10 out of 13 in 3e1f

Go back to Sodium Binding Sites List in 3e1f
Sodium binding site 10 out of 13 in the E.Coli (Lacz) Beta-Galactosidase (H418E) in Complex with Galactose


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 (H418E) in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Na3102

b:44.5
occ:1.00
 O 3:PRO932 2.7 32.5 1.0
O 3:LEU967 2.7 36.4 1.0
O 3:THR970 3.1 47.5 1.0
CZ 3:PHE931 3.3 32.1 1.0
CA 3:MET968 3.5 39.4 1.0
CE1 3:PHE931 3.5 32.8 1.0
O 3:MET968 3.7 42.3 1.0
C 3:MET968 3.7 41.2 1.0
C 3:PRO932 3.7 34.1 1.0
C 3:LEU967 3.8 36.4 1.0
CE2 3:PHE931 4.0 32.5 1.0
N 3:MET968 4.1 37.8 1.0
C 3:THR970 4.2 47.3 1.0
CD1 3:PHE931 4.4 34.6 1.0
CB 3:PRO932 4.4 35.8 1.0
CA 3:PRO932 4.5 35.2 1.0
N 3:GLU969 4.5 43.5 1.0
N 3:THR970 4.6 46.7 1.0
N 3:SER933 4.6 33.9 1.0
CB 3:MET968 4.6 38.6 1.0
CD2 3:PHE931 4.7 33.2 1.0
N 3:PRO932 4.7 36.1 1.0
CA 3:SER933 4.8 32.9 1.0
O 3:PRO788 4.8 34.3 1.0
CG 3:PHE931 4.9 34.0 1.0
CD 3:PRO932 4.9 36.3 1.0
CA 3:THR970 5.0 47.6 1.0

Reference:

D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber. Direct and Indirect Roles of His-418 in Metal Binding and in the Activity of Beta-Galactosidase (E. Coli). Protein Sci. V. 18 1281 2009.
ISSN: ISSN 0961-8368
PubMed: 19472413
DOI: 10.1002/PRO.140
Page generated: Mon Oct 7 08:41:47 2024

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