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Magnesium in PDB 1yq2: Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)

Enzymatic activity of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)

All present enzymatic activity of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1):
3.2.1.23;

Protein crystallography data

The structure of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1), PDB code: 1yq2 was solved by T.Skalova, J.Dohnalek, V.Spiwok, P.Lipovova, E.Vondrackova, H.Petrokova, H.Strnad, B.Kralova, J.Hasek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 140.091, 205.698, 140.458, 90.00, 102.34, 90.00
R / Rfree (%) 15.7 / 19.5

Other elements in 1yq2:

The structure of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) (pdb code 1yq2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1), PDB code: 1yq2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1yq2

Go back to Magnesium Binding Sites List in 1yq2
Magnesium binding site 1 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7001

b:17.6
occ:1.00
 O A:HOH9635 2.1 26.2 1.0
O A:GLY529 2.2 10.8 1.0
O A:GLY527 2.3 10.3 1.0
O A:ALA525 2.5 13.1 1.0
O A:HOH9069 2.6 13.3 1.0
C A:GLY529 3.3 10.9 1.0
C A:GLY527 3.5 11.3 1.0
N A:GLY529 3.5 11.3 1.0
C A:ALA525 3.7 12.1 1.0
CA A:GLY529 4.0 11.1 1.0
C A:ASN528 4.2 11.0 1.0
N A:PRO530 4.3 10.8 1.0
OG1 A:THR598 4.3 9.7 1.0
O A:HOH9120 4.3 16.2 1.0
N A:GLY527 4.3 11.4 1.0
CA A:ASN528 4.3 10.9 1.0
C A:MET526 4.4 12.0 1.0
CA A:ALA525 4.4 11.9 1.0
N A:ASN528 4.4 10.2 1.0
CE2 A:TYR918 4.4 14.0 1.0
CB A:ALA525 4.5 11.6 1.0
O A:MET526 4.5 12.0 1.0
CA A:GLY527 4.5 11.2 1.0
O A:HOH9531 4.5 36.5 1.0
O A:GLY589 4.5 12.5 1.0
CD A:PRO530 4.6 11.0 1.0
O A:HOH9023 4.6 13.4 1.0
CB A:THR598 4.7 11.5 1.0
OH A:TYR918 4.7 13.9 1.0
N A:MET526 4.7 11.9 1.0
CA A:GLY600 4.8 10.0 1.0
CG2 A:THR598 5.0 11.4 1.0
CZ A:TYR918 5.0 13.4 1.0
N A:GLY600 5.0 10.6 1.0
CA A:MET526 5.0 12.2 1.0

Magnesium binding site 2 out of 6 in 1yq2

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Magnesium binding site 2 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7002

b:18.3
occ:1.00
 O B:HOH9630 2.0 21.7 1.0
O B:GLY529 2.2 11.7 1.0
O B:GLY527 2.3 10.5 1.0
O B:HOH9124 2.7 13.0 1.0
O B:ALA525 2.7 13.5 1.0
C B:GLY529 3.3 11.1 1.0
N B:GLY529 3.5 11.7 1.0
C B:GLY527 3.5 11.9 1.0
C B:ALA525 3.7 12.2 1.0
CA B:GLY529 4.0 11.4 1.0
O B:HOH9604 4.1 13.6 1.0
C B:ASN528 4.2 11.4 1.0
OG1 B:THR598 4.2 7.8 1.0
N B:PRO530 4.2 10.8 1.0
CA B:ASN528 4.3 11.4 1.0
CA B:ALA525 4.3 11.5 1.0
N B:GLY527 4.3 12.6 1.0
N B:ASN528 4.4 10.8 1.0
C B:MET526 4.4 12.6 1.0
CD B:PRO530 4.4 10.6 1.0
CB B:ALA525 4.5 10.9 1.0
CE2 B:TYR918 4.5 12.2 1.0
CA B:GLY527 4.5 12.4 1.0
O B:MET526 4.5 12.3 1.0
O B:HOH9008 4.6 8.6 1.0
O B:GLY589 4.6 12.8 1.0
CB B:THR598 4.7 9.8 1.0
OH B:TYR918 4.7 13.6 1.0
CA B:GLY600 4.7 6.7 1.0
N B:MET526 4.8 12.4 1.0
O B:HOH9705 4.9 26.2 1.0
N B:GLY600 4.9 7.5 1.0
CG2 B:THR598 5.0 10.9 1.0

Magnesium binding site 3 out of 6 in 1yq2

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Magnesium binding site 3 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg7003

b:19.9
occ:1.00
 O C:HOH9817 2.1 26.5 1.0
O C:GLY529 2.2 12.2 1.0
O C:GLY527 2.4 11.9 1.0
O C:ALA525 2.5 13.4 1.0
O C:HOH9929 2.7 44.0 1.0
O C:HOH9034 2.8 15.3 1.0
C C:GLY529 3.3 12.0 1.0
N C:GLY529 3.5 12.1 1.0
C C:GLY527 3.6 12.4 1.0
C C:ALA525 3.6 12.4 1.0
CA C:GLY529 4.1 11.9 1.0
CA C:ALA525 4.3 11.6 1.0
OG1 C:THR598 4.3 11.8 1.0
C C:ASN528 4.3 11.6 1.0
N C:GLY527 4.3 12.1 1.0
C C:MET526 4.3 11.7 1.0
N C:PRO530 4.3 12.2 1.0
CB C:ALA525 4.3 11.4 1.0
O C:MET526 4.3 11.4 1.0
CA C:ASN528 4.4 11.5 1.0
N C:ASN528 4.4 11.6 1.0
O C:HOH9272 4.4 18.3 1.0
CE2 C:TYR918 4.4 14.4 1.0
O C:GLY589 4.5 11.7 1.0
CD C:PRO530 4.5 12.1 1.0
CA C:GLY527 4.5 12.0 1.0
O C:HOH9490 4.6 27.3 1.0
O C:HOH9436 4.6 9.5 1.0
N C:MET526 4.7 12.0 1.0
CB C:THR598 4.7 12.2 1.0
OH C:TYR918 4.7 15.1 1.0
CA C:GLY600 4.9 9.1 1.0
CA C:MET526 4.9 12.2 1.0
CG2 C:THR598 5.0 15.3 1.0

Magnesium binding site 4 out of 6 in 1yq2

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Magnesium binding site 4 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg7004

b:20.5
occ:1.00
 O D:HOH9826 2.0 28.5 1.0
O D:GLY529 2.2 10.9 1.0
O D:GLY527 2.3 11.8 1.0
O D:ALA525 2.5 13.2 1.0
O D:HOH9445 2.6 12.2 1.0
C D:GLY529 3.3 11.2 1.0
N D:GLY529 3.5 10.4 1.0
C D:GLY527 3.5 11.7 1.0
C D:ALA525 3.7 11.1 1.0
CA D:GLY529 4.0 11.5 1.0
OG1 D:THR598 4.2 10.2 1.0
C D:ASN528 4.2 10.7 1.0
O D:HOH9084 4.2 13.8 1.0
CA D:ASN528 4.3 10.2 1.0
N D:PRO530 4.3 11.2 1.0
N D:ASN528 4.3 11.0 1.0
N D:GLY527 4.3 12.2 1.0
CA D:ALA525 4.4 10.3 1.0
C D:MET526 4.4 12.3 1.0
CE2 D:TYR918 4.4 12.7 1.0
CA D:GLY527 4.5 11.4 1.0
O D:MET526 4.5 11.9 1.0
O D:GLY589 4.5 14.2 1.0
CB D:ALA525 4.5 10.1 1.0
CD D:PRO530 4.5 10.6 1.0
O D:HOH9052 4.5 7.8 1.0
CB D:THR598 4.7 11.6 1.0
N D:MET526 4.7 11.4 1.0
OH D:TYR918 4.7 14.5 1.0
O D:HOH9522 4.7 21.0 1.0
CA D:GLY600 4.8 8.6 1.0
CG2 D:THR598 4.9 10.9 1.0
N D:GLY600 5.0 8.7 1.0
CA D:MET526 5.0 12.1 1.0
CZ D:TYR918 5.0 13.6 1.0

Magnesium binding site 5 out of 6 in 1yq2

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Magnesium binding site 5 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg7005

b:15.7
occ:1.00
 O E:HOH9801 2.2 26.4 1.0
O E:GLY527 2.2 9.3 1.0
O E:GLY529 2.3 9.4 1.0
O E:ALA525 2.4 12.8 1.0
O E:HOH9034 2.9 9.1 1.0
C E:GLY529 3.3 9.5 1.0
C E:GLY527 3.5 10.5 1.0
C E:ALA525 3.5 11.6 1.0
N E:GLY529 3.5 9.8 1.0
CA E:GLY529 4.0 9.4 1.0
CA E:ALA525 4.2 10.8 1.0
C E:MET526 4.2 10.2 1.0
N E:GLY527 4.3 10.8 1.0
C E:ASN528 4.3 10.1 1.0
O E:MET526 4.3 9.3 1.0
N E:PRO530 4.3 9.2 1.0
OG1 E:THR598 4.3 9.5 1.0
N E:ASN528 4.3 9.8 1.0
CB E:ALA525 4.4 10.6 1.0
CA E:ASN528 4.4 9.7 1.0
O E:HOH9040 4.4 16.3 1.0
CA E:GLY527 4.4 10.5 1.0
CE2 E:TYR918 4.4 12.1 1.0
O E:HOH9112 4.5 6.5 1.0
O E:GLY589 4.5 12.0 1.0
CD E:PRO530 4.5 9.0 1.0
N E:MET526 4.5 11.0 1.0
O E:HOH9610 4.6 21.8 1.0
CB E:THR598 4.8 10.8 1.0
OH E:TYR918 4.8 14.0 1.0
CA E:MET526 4.8 10.9 1.0
CA E:GLY600 5.0 8.8 1.0

Magnesium binding site 6 out of 6 in 1yq2

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Magnesium binding site 6 out of 6 in the Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Beta-Galactosidase From Arthrobacter Sp. C2-2 (Isoenzyme C2- 2-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg7006

b:17.9
occ:1.00
 O F:HOH9255 2.1 27.0 1.0
O F:GLY529 2.2 10.1 1.0
O F:GLY527 2.3 8.8 1.0
O F:ALA525 2.4 11.1 1.0
O F:HOH9016 2.7 15.8 1.0
C F:GLY529 3.3 10.5 1.0
C F:GLY527 3.5 10.1 1.0
C F:ALA525 3.6 10.7 1.0
N F:GLY529 3.6 10.7 1.0
CA F:GLY529 4.1 10.2 1.0
C F:ASN528 4.2 9.6 1.0
CA F:ALA525 4.2 10.3 1.0
OG1 F:THR598 4.3 9.3 1.0
N F:GLY527 4.3 11.1 1.0
N F:PRO530 4.3 10.7 1.0
C F:MET526 4.3 11.1 1.0
O F:HOH9567 4.3 12.8 1.0
CB F:ALA525 4.3 9.8 1.0
N F:ASN528 4.4 9.7 1.0
CA F:ASN528 4.4 9.9 1.0
CE2 F:TYR918 4.4 11.6 1.0
O F:MET526 4.4 10.2 1.0
O F:GLY589 4.5 11.8 1.0
CA F:GLY527 4.5 10.3 1.0
O F:HOH9630 4.5 11.6 1.0
CD F:PRO530 4.5 11.3 1.0
N F:MET526 4.6 10.3 1.0
CB F:THR598 4.7 9.2 1.0
O F:HOH9386 4.7 29.5 1.0
OH F:TYR918 4.8 9.2 1.0
CA F:MET526 4.9 11.1 1.0
CG2 F:THR598 4.9 9.6 1.0
CA F:GLY600 4.9 7.8 1.0
CZ F:TYR918 5.0 11.2 1.0

Reference:

T.Skalova, J.Dohnalek, V.Spiwok, P.Lipovova, E.Vondrackova, H.Petrokova, J.Duskova, H.Strnad, B.Kralova, J.Hasek. Cold-Active Beta-Galactosidase From Arthrobacter Sp. C2-2 Forms Compact 660KDA Hexamers: Crystal Structure at 1.9A Resolution J.Mol.Biol. V. 353 282 2005.
ISSN: ISSN 0022-2836
PubMed: 16171818
DOI: 10.1016/J.JMB.2005.08.028
Page generated: Tue Aug 13 19:40:57 2024

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