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Sodium in PDB 3ob8: Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose

Enzymatic activity of Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose

All present enzymatic activity of Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose, PDB code: 3ob8 was solved by R.Fernandez-Leiro, A.Pereira-Rodriguez, M.Becerra, I.Gonzalez-Siso, M.E.Cerdan, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 140.381, 153.454, 217.166, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.6

Other elements in 3ob8:

The structure of Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Manganese (Mn) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose (pdb code 3ob8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose, PDB code: 3ob8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 3ob8

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Sodium binding site 1 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3002

b:2.3
occ:1.00
 O A:GLN186 2.5 31.9 1.0
O A:THR87 2.6 31.6 1.0
OD1 A:ASP185 2.6 32.5 1.0
O A:ASN88 2.9 31.6 1.0
OG1 A:THR87 3.1 30.8 1.0
C A:GLN186 3.4 31.8 1.0
C A:THR87 3.4 31.5 1.0
O A:ASP185 3.6 31.5 1.0
CG A:ASP185 3.6 31.1 1.0
C A:ASP185 3.6 31.3 1.0
C A:ASN88 3.8 31.4 1.0
NE1 A:TRP190 3.8 30.7 1.0
CZ2 A:TRP190 3.9 30.4 1.0
N A:GLN186 4.0 31.4 1.0
CE2 A:TRP190 4.1 30.8 1.0
CA A:ASP185 4.1 31.1 1.0
CB A:THR87 4.1 31.3 1.0
N A:ASP187 4.2 32.2 1.0
N A:ASN88 4.2 31.5 1.0
CA A:ASN88 4.2 31.4 1.0
CA A:ASP187 4.2 32.3 1.0
CA A:THR87 4.3 31.4 1.0
OD2 A:ASP185 4.3 30.4 1.0
CA A:GLN186 4.3 31.4 1.0
N A:GLN188 4.4 32.3 1.0
O A:GLN188 4.4 31.8 1.0
CB A:ASP185 4.5 31.0 1.0
O A:GLN90 4.7 31.1 1.0
N A:THR87 4.7 31.2 1.0
O A:VAL89 4.8 30.9 1.0
N A:VAL89 4.8 31.1 1.0
CD1 A:TRP190 4.8 30.8 1.0
C A:ASP187 4.9 32.3 1.0
CH2 A:TRP190 4.9 30.0 1.0

Sodium binding site 2 out of 16 in 3ob8

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Sodium binding site 2 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3003

b:19.2
occ:1.00
 O A:TYR576 2.3 32.6 1.0
O A:PHE570 2.5 34.5 1.0
O A:GLU573 2.6 35.7 1.0
C A:TYR576 3.6 32.6 1.0
C A:GLU573 3.6 35.5 1.0
C A:PHE570 3.7 34.8 1.0
CA A:LYS574 4.0 35.3 1.0
N A:LYS574 4.2 35.4 1.0
O A:LYS574 4.2 35.4 1.0
C A:LYS574 4.2 35.1 1.0
CA A:TYR576 4.4 32.8 1.0
N A:TYR576 4.5 33.2 1.0
N A:GLN577 4.5 32.3 1.0
CA A:GLN577 4.5 32.2 1.0
CB A:TYR576 4.6 32.5 1.0
CA A:PHE570 4.6 34.8 1.0
N A:TYR571 4.6 34.9 1.0
CA A:TYR571 4.7 35.0 1.0
N A:GLU573 4.7 35.5 1.0
CA A:GLU573 4.8 35.5 1.0
O A:TYR571 4.8 35.2 1.0
C A:TYR571 4.8 35.2 1.0
CD1 A:LEU348 4.9 31.5 1.0

Sodium binding site 3 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 3 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3004

b:2.0
occ:1.00
 O A:VAL970 2.7 32.6 1.0
O A:ALA973 2.7 31.7 1.0
O A:PRO929 2.7 31.1 1.0
O A:ASP971 2.9 33.0 1.0
OH A:TYR928 3.2 34.0 1.0
CZ A:TYR928 3.2 33.5 1.0
CE2 A:TYR928 3.5 32.9 1.0
C A:ASP971 3.6 33.4 1.0
C A:ALA973 3.8 32.1 1.0
CE1 A:TYR928 3.8 32.9 1.0
C A:PRO929 3.8 30.8 1.0
C A:VAL970 3.8 32.6 1.0
N A:ALA973 4.1 32.8 1.0
CA A:ASP971 4.1 33.3 1.0
CB A:PRO929 4.2 30.9 1.0
CD2 A:TYR928 4.3 32.7 1.0
CA A:ALA973 4.4 32.4 1.0
CA A:PRO929 4.4 30.9 1.0
N A:ASP971 4.4 33.0 1.0
N A:GLU972 4.4 33.5 1.0
C A:GLU972 4.5 33.5 1.0
CD1 A:TYR928 4.5 32.3 1.0
CD A:PRO929 4.5 30.9 1.0
N A:PRO929 4.5 30.9 1.0
CG A:TYR928 4.8 31.8 1.0
CG A:PRO929 4.8 30.7 1.0
CB A:ALA973 4.8 32.4 1.0
N A:ALA974 4.8 31.8 1.0
N A:GLN930 4.9 30.7 1.0
CA A:GLU972 4.9 34.1 1.0

Sodium binding site 4 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 4 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3006

b:22.8
occ:1.00
 O A:PHE620 2.1 33.1 1.0
OD2 A:ASP623 2.4 32.6 1.0
OD2 A:ASP187 2.6 35.1 1.0
O6 A:GAL2001 2.7 39.5 1.0
C A:PHE620 3.3 33.2 1.0
CG A:ASP623 3.4 31.9 1.0
CG A:ASP187 3.5 33.7 1.0
C6 A:GAL2001 3.6 40.3 1.0
CD1 A:PHE620 3.7 36.9 1.0
OD1 A:ASP187 3.9 34.7 1.0
OH A:TYR86 4.0 31.0 1.0
OD1 A:ASP623 4.0 31.5 1.0
NE1 A:TRP582 4.0 32.6 1.0
CB A:PHE620 4.1 33.9 1.0
CA A:PHE620 4.2 33.5 1.0
N A:ILE621 4.2 33.0 1.0
CG A:PHE620 4.3 35.5 1.0
CA A:ILE621 4.4 32.6 1.0
CB A:ASP623 4.4 31.8 1.0
NE2 A:HIS554 4.4 31.5 1.0
C4 A:GAL2001 4.5 42.0 1.0
C5 A:GAL2001 4.5 40.6 1.0
CE1 A:PHE620 4.7 38.1 1.0
CB A:ASP187 4.7 32.6 1.0
O4 A:GAL2001 4.8 42.5 1.0
CE1 A:HIS554 4.8 31.5 1.0
OE2 A:GLU583 4.9 34.3 1.0
CE2 A:TRP582 4.9 32.7 1.0
CD1 A:TRP582 4.9 33.0 1.0
C A:ILE621 4.9 32.5 1.0

Sodium binding site 5 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 5 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3002

b:2.0
occ:1.00
 O B:GLN186 2.4 31.8 1.0
O B:THR87 2.5 31.5 1.0
OD1 B:ASP185 2.7 32.5 1.0
O B:ASN88 2.9 31.5 1.0
OG1 B:THR87 3.0 30.8 1.0
C B:THR87 3.4 31.5 1.0
C B:GLN186 3.4 31.7 1.0
CG B:ASP185 3.7 31.1 1.0
O B:ASP185 3.7 31.6 1.0
C B:ASN88 3.7 31.4 1.0
C B:ASP185 3.8 31.3 1.0
NE1 B:TRP190 3.8 30.7 1.0
CZ2 B:TRP190 3.9 30.3 1.0
CE2 B:TRP190 4.0 30.6 1.0
CB B:THR87 4.1 31.3 1.0
N B:ASN88 4.1 31.5 1.0
N B:GLN186 4.1 31.4 1.0
N B:ASP187 4.2 32.1 1.0
CA B:ASN88 4.2 31.4 1.0
CA B:ASP187 4.2 32.3 1.0
CA B:THR87 4.2 31.4 1.0
CA B:ASP185 4.2 31.1 1.0
O B:GLN188 4.2 31.8 1.0
N B:GLN188 4.3 32.2 1.0
CA B:GLN186 4.4 31.4 1.0
OD2 B:ASP185 4.4 30.5 1.0
CB B:ASP185 4.6 31.0 1.0
N B:THR87 4.7 31.3 1.0
O B:GLN90 4.7 31.1 1.0
N B:VAL89 4.8 31.2 1.0
O B:VAL89 4.8 30.9 1.0
CD1 B:TRP190 4.8 30.8 1.0
C B:ASP187 4.8 32.3 1.0
CH2 B:TRP190 4.9 30.1 1.0

Sodium binding site 6 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 6 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3003

b:13.0
occ:1.00
 O B:TYR576 2.2 32.7 1.0
O B:PHE570 2.5 34.5 1.0
O B:GLU573 2.6 35.4 1.0
O B:HOH1292 3.1 28.2 1.0
C B:TYR576 3.4 32.7 1.0
C B:GLU573 3.7 35.4 1.0
C B:PHE570 3.7 34.8 1.0
CA B:LYS574 4.1 35.3 1.0
O B:LYS574 4.3 35.4 1.0
N B:LYS574 4.3 35.4 1.0
C B:LYS574 4.3 35.0 1.0
CA B:TYR576 4.3 32.7 1.0
N B:GLN577 4.4 32.4 1.0
CA B:GLN577 4.4 32.2 1.0
N B:TYR576 4.4 33.1 1.0
CB B:TYR576 4.5 32.7 1.0
CA B:PHE570 4.6 34.8 1.0
N B:TYR571 4.6 34.8 1.0
CA B:TYR571 4.7 35.0 1.0
CD1 B:LEU348 4.8 31.6 1.0
N B:GLU573 4.8 35.4 1.0
CA B:GLU573 4.8 35.6 1.0
C B:TYR571 4.8 35.2 1.0
O B:TYR571 4.9 35.3 1.0

Sodium binding site 7 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 7 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3004

b:5.7
occ:1.00
 O B:ALA973 2.5 31.7 1.0
O B:VAL970 2.6 32.5 1.0
O B:PRO929 2.7 31.0 1.0
O B:ASP971 2.9 33.0 1.0
OH B:TYR928 3.3 33.9 1.0
CZ B:TYR928 3.3 33.5 1.0
CE2 B:TYR928 3.6 32.9 1.0
C B:ASP971 3.6 33.3 1.0
C B:ALA973 3.7 32.1 1.0
C B:PRO929 3.7 30.8 1.0
C B:VAL970 3.8 32.6 1.0
CE1 B:TYR928 3.8 33.0 1.0
CB B:PRO929 4.0 30.9 1.0
N B:ALA973 4.1 32.7 1.0
CA B:ASP971 4.1 33.2 1.0
CD2 B:TYR928 4.3 32.6 1.0
CA B:PRO929 4.3 30.8 1.0
CA B:ALA973 4.3 32.3 1.0
N B:ASP971 4.4 32.9 1.0
CD B:PRO929 4.4 30.9 1.0
N B:PRO929 4.4 30.9 1.0
N B:GLU972 4.4 33.6 1.0
C B:GLU972 4.5 33.5 1.0
CD1 B:TYR928 4.5 32.3 1.0
CG B:PRO929 4.6 30.6 1.0
CB B:ALA973 4.6 32.5 1.0
CG B:TYR928 4.7 31.7 1.0
N B:ALA974 4.8 31.8 1.0
N B:GLN930 4.8 30.6 1.0
CA B:GLU972 4.9 34.1 1.0
CA B:VAL970 5.0 32.2 1.0

Sodium binding site 8 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 8 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3006

b:20.0
occ:1.00
 OD2 B:ASP623 2.1 32.6 1.0
O B:PHE620 2.2 33.2 1.0
O6 B:GAL2001 2.7 35.6 1.0
OD2 B:ASP187 2.7 35.0 1.0
CG B:ASP623 3.2 31.9 1.0
C B:PHE620 3.4 33.3 1.0
C6 B:GAL2001 3.5 37.9 1.0
CG B:ASP187 3.6 33.6 1.0
OD1 B:ASP623 3.8 31.5 1.0
NE1 B:TRP582 3.8 32.6 1.0
CD1 B:PHE620 3.9 36.9 1.0
OD1 B:ASP187 4.1 34.7 1.0
OH B:TYR86 4.1 30.8 1.0
CB B:ASP623 4.2 31.8 1.0
CB B:PHE620 4.3 33.9 1.0
C4 B:GAL2001 4.3 38.7 1.0
N B:ILE621 4.3 32.9 1.0
CA B:PHE620 4.3 33.6 1.0
NE2 B:HIS554 4.4 31.6 1.0
C5 B:GAL2001 4.4 38.0 1.0
CA B:ILE621 4.4 32.6 1.0
O4 B:GAL2001 4.5 38.5 1.0
CG B:PHE620 4.5 35.4 1.0
OE2 B:GLU583 4.7 34.3 1.0
CD1 B:TRP582 4.7 33.1 1.0
CE2 B:TRP582 4.7 32.6 1.0
CB B:ASP187 4.8 32.6 1.0
CE1 B:PHE620 4.8 38.1 1.0
CE1 B:HIS554 4.8 31.5 1.0
CZ2 B:TRP582 4.9 32.9 1.0
C B:ILE621 4.9 32.4 1.0

Sodium binding site 9 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 9 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3002

b:9.6
occ:1.00
 O D:GLN186 2.5 31.9 1.0
O D:THR87 2.7 31.5 1.0
OD1 D:ASP185 2.7 32.6 1.0
O D:ASN88 3.0 31.5 1.0
OG1 D:THR87 3.0 31.0 1.0
C D:THR87 3.4 31.5 1.0
C D:GLN186 3.5 31.7 1.0
CG D:ASP185 3.7 31.0 1.0
NE1 D:TRP190 3.7 30.7 1.0
C D:ASP185 3.7 31.2 1.0
O D:ASP185 3.8 31.4 1.0
CZ2 D:TRP190 3.8 30.3 1.0
C D:ASN88 3.8 31.5 1.0
CE2 D:TRP190 4.0 30.6 1.0
N D:GLN186 4.1 31.4 1.0
CB D:THR87 4.1 31.5 1.0
CA D:ASP185 4.2 31.0 1.0
N D:ASN88 4.2 31.5 1.0
N D:ASP187 4.2 32.0 1.0
CA D:ASP187 4.2 32.4 1.0
CA D:THR87 4.3 31.5 1.0
CA D:ASN88 4.3 31.5 1.0
O D:GLN188 4.3 31.9 1.0
N D:GLN188 4.3 32.1 1.0
CA D:GLN186 4.4 31.4 1.0
OD2 D:ASP185 4.4 30.4 1.0
CB D:ASP185 4.5 30.9 1.0
N D:THR87 4.7 31.4 1.0
CD1 D:TRP190 4.7 30.9 1.0
O D:GLN90 4.7 31.0 1.0
O D:HOH1265 4.7 22.1 1.0
CH2 D:TRP190 4.8 30.0 1.0
N D:VAL89 4.9 31.2 1.0
C D:ASP187 4.9 32.3 1.0
O D:VAL89 4.9 30.8 1.0

Sodium binding site 10 out of 16 in 3ob8

Go back to Sodium Binding Sites List in 3ob8
Sodium binding site 10 out of 16 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis 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 Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3003

b:20.5
occ:1.00
 O D:PHE570 2.4 34.6 1.0
O D:TYR576 2.5 32.7 1.0
O D:GLU573 2.6 35.5 1.0
C D:PHE570 3.6 34.8 1.0
C D:GLU573 3.6 35.5 1.0
C D:TYR576 3.8 32.6 1.0
CA D:LYS574 4.1 35.5 1.0
N D:LYS574 4.2 35.5 1.0
O D:LYS574 4.4 35.4 1.0
C D:LYS574 4.4 35.1 1.0
CA D:TYR571 4.5 35.0 1.0
N D:TYR571 4.5 34.8 1.0
CA D:PHE570 4.6 34.8 1.0
C D:TYR571 4.6 35.3 1.0
O D:TYR571 4.6 35.3 1.0
CA D:TYR576 4.6 32.8 1.0
N D:GLN577 4.7 32.3 1.0
N D:TYR576 4.7 33.2 1.0
CA D:GLN577 4.7 32.1 1.0
N D:GLU573 4.7 35.5 1.0
CA D:GLU573 4.7 35.7 1.0
CB D:TYR576 4.8 32.6 1.0
CD1 D:LEU348 4.8 31.6 1.0

Reference:

A.Pereira-Rodriguez, R.Fernandez-Leiro, M.I.Gonzalez-Siso, M.E.Cerdan, M.Becerra, J.Sanz-Aparicio. Structural Basis of Specificity in Tetrameric Kluyveromyces Lactis Beta-Galactosidase. J.Struct.Biol. V. 177 392 2012.
ISSN: ISSN 1047-8477
PubMed: 22193516
DOI: 10.1016/J.JSB.2011.11.031
Page generated: Tue Dec 15 06:19:49 2020

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