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Manganese 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
Sodium (Na) 16 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose, PDB code: 3ob8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3ob8

Go back to Manganese Binding Sites List in 3ob8
Manganese binding site 1 out of 4 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn3005

b:24.2
occ:1.00
 OD2 A:ASP978 1.8 35.3 1.0
OD2 A:ASP593 1.9 35.4 1.0
ND1 A:HIS975 2.1 31.4 1.0
CG A:ASP978 2.7 34.2 1.0
CG A:ASP593 2.7 35.4 1.0
OD1 A:ASP978 2.9 35.2 1.0
CE1 A:HIS975 3.0 31.1 1.0
OD1 A:ASP593 3.0 36.2 1.0
CG A:HIS975 3.2 31.2 1.0
CB A:HIS975 3.5 31.6 1.0
N A:HIS975 3.8 31.5 1.0
CB A:ALA974 3.8 31.2 1.0
O A:HOH1109 4.0 36.7 1.0
CB A:ASP593 4.1 34.6 1.0
CB A:ASP978 4.1 33.3 1.0
NE2 A:HIS975 4.1 30.5 1.0
O A:VAL594 4.1 34.3 1.0
CD2 A:HIS975 4.2 30.5 1.0
CA A:HIS975 4.3 31.6 1.0
C A:ALA974 4.4 31.5 1.0
SG A:CYS977 4.4 34.5 1.0
CA A:ALA974 4.5 31.5 1.0
N A:ALA974 4.6 31.8 1.0

Manganese binding site 2 out of 4 in 3ob8

Go back to Manganese Binding Sites List in 3ob8
Manganese binding site 2 out of 4 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
B:Mn3005

b:30.1
occ:1.00
 OD2 B:ASP593 1.8 35.5 1.0
OD2 B:ASP978 1.8 35.1 1.0
ND1 B:HIS975 2.1 31.4 1.0
CG B:ASP978 2.7 34.2 1.0
CG B:ASP593 2.7 35.4 1.0
OD1 B:ASP978 2.9 35.2 1.0
CE1 B:HIS975 3.0 31.1 1.0
OD1 B:ASP593 3.0 36.2 1.0
CG B:HIS975 3.1 31.2 1.0
O B:HOH1191 3.2 42.2 1.0
CB B:HIS975 3.5 31.5 1.0
N B:HIS975 3.8 31.6 1.0
CB B:ALA974 3.9 31.1 1.0
CB B:ASP593 4.0 34.6 1.0
O B:VAL594 4.1 34.2 1.0
CB B:ASP978 4.1 33.3 1.0
NE2 B:HIS975 4.1 30.8 1.0
CD2 B:HIS975 4.2 30.6 1.0
CA B:HIS975 4.2 31.6 1.0
SG B:CYS977 4.4 34.0 1.0
C B:ALA974 4.4 31.6 1.0
CA B:ALA974 4.6 31.5 1.0
N B:ALA974 4.7 31.8 1.0
O B:HOH1143 4.7 29.7 1.0
O B:HIS975 5.0 31.8 1.0
C B:HIS975 5.0 31.8 1.0

Manganese binding site 3 out of 4 in 3ob8

Go back to Manganese Binding Sites List in 3ob8
Manganese binding site 3 out of 4 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
D:Mn3005

b:25.5
occ:1.00
 OD2 D:ASP593 1.8 35.3 1.0
OD2 D:ASP978 2.0 35.3 1.0
ND1 D:HIS975 2.1 31.6 1.0
CG D:ASP593 2.6 35.4 1.0
CG D:ASP978 2.8 34.2 1.0
OD1 D:ASP593 2.9 36.4 1.0
CE1 D:HIS975 2.9 31.2 1.0
OD1 D:ASP978 3.0 35.2 1.0
CG D:HIS975 3.2 31.4 1.0
CB D:HIS975 3.6 31.6 1.0
N D:HIS975 3.8 31.6 1.0
CB D:ALA974 3.9 31.3 1.0
CB D:ASP593 4.0 34.7 1.0
NE2 D:HIS975 4.1 30.7 1.0
O D:VAL594 4.1 34.3 1.0
CB D:ASP978 4.2 33.3 1.0
CD2 D:HIS975 4.2 30.5 1.0
CA D:HIS975 4.3 31.7 1.0
C D:ALA974 4.4 31.6 1.0
SG D:CYS977 4.5 34.5 1.0
CA D:ALA974 4.5 31.6 1.0
N D:ALA974 4.7 31.8 1.0

Manganese binding site 4 out of 4 in 3ob8

Go back to Manganese Binding Sites List in 3ob8
Manganese binding site 4 out of 4 in the Structure of the Beta-Galactosidase From Kluyveromyces Lactis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
C:Mn3005

b:30.6
occ:1.00
 OD2 C:ASP978 1.8 35.4 1.0
OD2 C:ASP593 1.9 35.6 1.0
ND1 C:HIS975 2.1 31.4 1.0
O C:HOH1171 2.2 25.8 1.0
CG C:ASP978 2.7 34.2 1.0
CG C:ASP593 2.7 35.5 1.0
OD1 C:ASP978 2.9 35.3 1.0
CE1 C:HIS975 3.0 31.1 1.0
OD1 C:ASP593 3.0 36.2 1.0
CG C:HIS975 3.2 31.3 1.0
CB C:HIS975 3.6 31.6 1.0
N C:HIS975 3.8 31.6 1.0
CB C:ALA974 3.8 31.3 1.0
O C:VAL594 4.1 34.4 1.0
CB C:ASP978 4.1 33.3 1.0
CB C:ASP593 4.1 34.7 1.0
NE2 C:HIS975 4.1 30.7 1.0
CD2 C:HIS975 4.3 30.6 1.0
CA C:HIS975 4.3 31.6 1.0
C C:ALA974 4.3 31.6 1.0
CA C:ALA974 4.5 31.5 1.0
SG C:CYS977 4.5 34.4 1.0
N C:ALA974 4.6 31.7 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: Sat Oct 5 17:23:01 2024

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