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Magnesium 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:

Manganese (Mn) 4 atoms
Sodium (Na) 16 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 3ob8

Go back to Magnesium Binding Sites List in 3ob8
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg3001

b:22.3
occ:1.00
 OE2 A:GLU414 2.1 34.6 1.0
OE1 A:GLU482 2.4 38.9 1.0
ND1 A:HIS416 2.4 34.5 1.0
CE1 A:HIS416 3.1 34.9 1.0
O4 A:GAL2001 3.2 42.5 1.0
CD A:GLU414 3.3 34.0 1.0
CD A:GLU482 3.5 38.4 1.0
OD1 A:ASN88 3.6 31.6 1.0
CG A:HIS416 3.6 34.0 1.0
OE1 A:GLU414 3.7 34.9 1.0
CB A:ASP187 3.9 32.6 1.0
CB A:HIS416 4.1 33.4 1.0
OE2 A:GLU482 4.1 38.5 1.0
O3 A:GAL2001 4.1 42.9 1.0
N A:ASP187 4.1 32.2 1.0
C2 A:GAL2001 4.2 42.5 1.0
O A:ASN88 4.4 31.6 1.0
C4 A:GAL2001 4.4 42.0 1.0
NE2 A:HIS416 4.4 34.5 1.0
C3 A:GAL2001 4.4 42.7 1.0
ND2 A:ASN481 4.5 35.7 1.0
CA A:ASP187 4.5 32.3 1.0
CG A:GLU414 4.5 33.0 1.0
O A:ASP185 4.5 31.5 1.0
CD2 A:HIS416 4.6 34.3 1.0
CG A:GLU482 4.7 36.9 1.0
CG2 A:VAL89 4.8 30.3 1.0
CB A:GLU482 4.8 36.4 1.0
CG A:ASN88 4.8 31.8 1.0
O2 A:GAL2001 4.9 42.4 1.0
C A:ASN88 4.9 31.4 1.0
C A:GLN186 4.9 31.8 1.0
CG A:ASP187 4.9 33.7 1.0

Magnesium binding site 2 out of 4 in 3ob8

Go back to Magnesium Binding Sites List in 3ob8
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg3001

b:30.6
occ:1.00
 OE2 B:GLU414 2.1 34.5 1.0
OE1 B:GLU482 2.5 38.8 1.0
ND1 B:HIS416 2.5 34.7 1.0
CD B:GLU414 3.2 34.0 1.0
CE1 B:HIS416 3.2 35.0 1.0
O4 B:GAL2001 3.5 38.5 1.0
OD1 B:ASN88 3.6 31.6 1.0
CD B:GLU482 3.6 38.4 1.0
CG B:HIS416 3.6 33.9 1.0
OE1 B:GLU414 3.7 34.9 1.0
O3 B:GAL2001 3.9 39.7 1.0
CB B:ASP187 3.9 32.6 1.0
N B:ASP187 4.0 32.1 1.0
CB B:HIS416 4.1 33.5 1.0
C2 B:GAL2001 4.2 40.0 1.0
OE2 B:GLU482 4.2 38.2 1.0
O B:ASN88 4.3 31.5 1.0
O B:ASP185 4.4 31.6 1.0
C3 B:GAL2001 4.4 39.6 1.0
CA B:ASP187 4.4 32.3 1.0
NE2 B:HIS416 4.5 34.5 1.0
CG B:GLU414 4.5 33.0 1.0
ND2 B:ASN481 4.5 35.7 1.0
C4 B:GAL2001 4.6 38.7 1.0
CD2 B:HIS416 4.7 34.3 1.0
C B:GLN186 4.7 31.7 1.0
O2 B:GAL2001 4.8 38.9 1.0
CG B:GLU482 4.8 37.1 1.0
C B:ASN88 4.8 31.4 1.0
CB B:GLU482 4.8 36.5 1.0
CG B:ASN88 4.8 31.9 1.0
CG2 B:VAL89 4.9 30.3 1.0
CG B:ASP187 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 3ob8

Go back to Magnesium Binding Sites List in 3ob8
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg3001

b:23.6
occ:1.00
 OE1 D:GLU482 2.0 38.9 1.0
ND1 D:HIS416 2.1 34.6 1.0
OE2 D:GLU414 2.3 34.4 1.0
O D:HOH1120 2.5 23.4 1.0
O D:HOH1265 2.5 22.1 1.0
CE1 D:HIS416 2.7 34.9 1.0
CD D:GLU482 3.1 38.4 1.0
CG D:HIS416 3.4 33.9 1.0
O4 D:GAL2001 3.4 43.6 1.0
CD D:GLU414 3.4 34.0 1.0
OE2 D:GLU482 3.6 38.4 1.0
OD1 D:ASN88 3.8 31.7 1.0
C2 D:GAL2001 3.9 45.1 1.0
OE1 D:GLU414 3.9 35.1 1.0
CB D:HIS416 4.0 33.3 1.0
NE2 D:HIS416 4.0 34.4 1.0
O3 D:GAL2001 4.2 44.4 1.0
CG D:GLU482 4.3 36.9 1.0
CD2 D:HIS416 4.3 34.3 1.0
ND2 D:ASN481 4.3 35.6 1.0
CB D:ASP187 4.3 32.6 1.0
C3 D:GAL2001 4.4 45.0 1.0
CB D:GLU482 4.4 36.4 1.0
O2 D:GAL2001 4.4 45.2 1.0
C4 D:GAL2001 4.5 44.3 1.0
N D:ASP187 4.6 32.0 1.0
CG D:GLU414 4.7 33.0 1.0
O D:HOH1186 4.7 21.9 1.0
O D:ASN88 4.8 31.5 1.0
CG2 D:VAL89 4.8 30.3 1.0
O D:ASP185 4.9 31.4 1.0
C1 D:GAL2001 4.9 44.6 1.0
O1 D:GAL2001 4.9 45.7 1.0
CG D:ASN88 5.0 31.9 1.0

Magnesium binding site 4 out of 4 in 3ob8

Go back to Magnesium Binding Sites List in 3ob8
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg3001

b:38.3
occ:1.00
 ND1 C:HIS416 2.1 34.6 1.0
OE2 C:GLU414 2.2 34.5 1.0
OE1 C:GLU482 2.5 38.8 1.0
O C:HOH1141 2.7 37.5 1.0
CE1 C:HIS416 2.9 34.9 1.0
CG C:HIS416 3.3 34.0 1.0
CD C:GLU414 3.4 34.0 1.0
OD1 C:ASN88 3.5 31.7 1.0
CD C:GLU482 3.5 38.4 1.0
O4 C:GAL2001 3.6 45.5 1.0
CB C:HIS416 3.8 33.4 1.0
OE1 C:GLU414 3.9 35.0 1.0
OE2 C:GLU482 4.1 38.5 1.0
NE2 C:HIS416 4.1 34.5 1.0
CB C:ASP187 4.1 32.5 1.0
O C:ASN88 4.2 31.6 1.0
CD2 C:HIS416 4.3 34.2 1.0
N C:ASP187 4.3 32.0 1.0
C2 C:GAL2001 4.4 45.6 1.0
O C:ASP185 4.5 31.6 1.0
CG2 C:VAL89 4.6 30.3 1.0
CG C:GLU414 4.6 33.0 1.0
O3 C:GAL2001 4.6 46.2 1.0
ND2 C:ASN481 4.7 35.8 1.0
CG C:GLU482 4.7 36.9 1.0
CB C:GLU482 4.7 36.4 1.0
CA C:ASP187 4.7 32.3 1.0
C C:ASN88 4.7 31.5 1.0
CG C:ASN88 4.8 31.9 1.0
C4 C:GAL2001 4.8 45.2 1.0
C3 C:GAL2001 4.8 45.8 1.0
O2 C:GAL2001 5.0 44.0 1.0
CA C:VAL89 5.0 31.0 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: Thu Aug 15 08:14:09 2024

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