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Zinc in PDB 3tty: Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose

Enzymatic activity of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose

All present enzymatic activity of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose, PDB code: 3tty was solved by M.Maksimainen, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 228.200, 228.200, 246.800, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose (pdb code 3tty). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose, PDB code: 3tty:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3tty

Go back to Zinc Binding Sites List in 3tty
Zinc binding site 1 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn676

b:17.9
occ:1.00
 SG A:CYS160 2.3 16.9 1.0
SG A:CYS155 2.4 16.7 1.0
SG A:CYS115 2.4 16.1 1.0
SG A:CYS157 2.5 17.2 1.0
CB A:CYS155 3.3 15.1 1.0
CB A:CYS160 3.3 11.8 1.0
CB A:CYS115 3.4 18.1 1.0
CB A:CYS157 3.6 17.7 1.0
N A:CYS160 3.8 15.7 1.0
N A:CYS157 4.0 12.4 1.0
CA A:CYS160 4.1 13.4 1.0
CA A:CYS115 4.2 15.8 1.0
CA A:CYS157 4.3 15.3 1.0
CD A:PRO116 4.3 16.3 1.0
C A:CYS155 4.5 16.0 1.0
CA A:CYS155 4.5 13.2 1.0
O A:HOH1003 4.5 16.7 1.0
N A:TYR156 4.7 17.3 1.0
CB A:ASN117 4.7 18.2 1.0
C A:CYS115 4.8 17.1 1.0
N A:ASN117 4.8 16.3 1.0
C A:CYS157 4.8 18.1 1.0
O A:CYS157 4.8 16.4 1.0
O A:CYS155 4.8 14.8 1.0
N A:PRO116 4.8 17.7 1.0
C A:ASN159 4.9 17.6 1.0
CB A:ASN159 5.0 16.0 1.0

Zinc binding site 2 out of 6 in 3tty

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Zinc binding site 2 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn676

b:18.9
occ:1.00
 SG B:CYS155 2.3 14.4 1.0
SG B:CYS160 2.4 15.2 1.0
SG B:CYS115 2.4 16.8 1.0
SG B:CYS157 2.6 15.4 1.0
CB B:CYS160 3.2 13.8 1.0
CB B:CYS155 3.2 14.0 1.0
CB B:CYS115 3.4 13.7 1.0
CB B:CYS157 3.7 17.5 1.0
N B:CYS160 3.8 13.5 1.0
N B:CYS157 3.9 12.2 1.0
CA B:CYS160 4.1 14.7 1.0
CA B:CYS115 4.2 16.4 1.0
CA B:CYS157 4.3 12.2 1.0
CD B:PRO116 4.4 16.6 1.0
O B:HOH744 4.4 18.6 1.0
C B:CYS155 4.4 15.0 1.0
CA B:CYS155 4.5 15.9 1.0
N B:TYR156 4.6 14.1 1.0
O B:CYS157 4.7 14.6 1.0
C B:CYS157 4.7 16.4 1.0
O B:CYS155 4.7 13.6 1.0
C B:CYS115 4.8 16.2 1.0
N B:ASN117 4.8 13.1 1.0
N B:PRO116 4.9 18.7 1.0
CB B:ASN117 4.9 16.3 1.0
C B:ASN159 4.9 13.5 1.0

Zinc binding site 3 out of 6 in 3tty

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Zinc binding site 3 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn676

b:19.6
occ:1.00
 SG C:CYS155 2.3 16.8 1.0
SG C:CYS160 2.3 14.9 1.0
SG C:CYS115 2.4 15.9 1.0
SG C:CYS157 2.7 22.0 1.0
CB C:CYS155 3.2 16.3 1.0
CB C:CYS160 3.3 12.8 1.0
CB C:CYS115 3.4 17.3 1.0
CB C:CYS157 3.7 16.5 1.0
N C:CYS160 3.9 16.3 1.0
N C:CYS157 4.0 15.6 1.0
CA C:CYS160 4.1 16.6 1.0
CA C:CYS115 4.1 17.3 1.0
CD C:PRO116 4.3 15.9 1.0
CA C:CYS157 4.4 17.7 1.0
CA C:CYS155 4.5 14.5 1.0
C C:CYS155 4.5 17.9 1.0
O C:HOH700 4.6 15.8 1.0
O C:CYS157 4.6 17.1 1.0
N C:TYR156 4.7 16.8 1.0
C C:CYS115 4.7 14.8 1.0
C C:CYS157 4.7 16.8 1.0
N C:ASN117 4.8 14.8 1.0
N C:PRO116 4.8 16.8 1.0
O C:CYS155 4.8 14.0 1.0
CB C:ASN117 4.9 14.7 1.0
C C:ASN159 4.9 17.5 1.0
CB C:ASN159 5.0 22.3 1.0

Zinc binding site 4 out of 6 in 3tty

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Zinc binding site 4 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn676

b:18.1
occ:1.00
 SG D:CYS160 2.3 15.9 1.0
SG D:CYS155 2.3 17.3 1.0
SG D:CYS115 2.4 16.8 1.0
SG D:CYS157 2.7 19.5 1.0
CB D:CYS160 3.2 12.3 1.0
CB D:CYS155 3.3 15.0 1.0
CB D:CYS115 3.4 16.6 1.0
CB D:CYS157 3.7 15.3 1.0
N D:CYS160 3.8 13.6 1.0
N D:CYS157 3.9 15.2 1.0
CA D:CYS160 4.0 13.7 1.0
CA D:CYS115 4.2 17.1 1.0
CD D:PRO116 4.3 16.6 1.0
CA D:CYS157 4.3 15.2 1.0
O D:HOH716 4.3 17.7 1.0
C D:CYS155 4.4 18.6 1.0
CA D:CYS155 4.5 14.7 1.0
N D:TYR156 4.6 15.6 1.0
O D:CYS155 4.7 16.0 1.0
C D:CYS115 4.7 15.9 1.0
N D:PRO116 4.7 17.6 1.0
N D:ASN117 4.7 16.8 1.0
C D:CYS157 4.8 19.1 1.0
O D:CYS157 4.8 18.2 1.0
C D:ASN159 4.9 17.1 1.0
CB D:ASN117 4.9 16.5 1.0

Zinc binding site 5 out of 6 in 3tty

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Zinc binding site 5 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn676

b:19.0
occ:1.00
 SG E:CYS155 2.3 15.5 1.0
SG E:CYS160 2.4 16.5 1.0
SG E:CYS115 2.5 18.2 1.0
SG E:CYS157 2.6 20.1 1.0
CB E:CYS155 3.2 13.7 1.0
CB E:CYS160 3.2 14.3 1.0
CB E:CYS115 3.5 16.4 1.0
CB E:CYS157 3.6 18.3 1.0
N E:CYS160 3.8 15.4 1.0
N E:CYS157 4.0 15.4 1.0
CA E:CYS160 4.0 19.7 1.0
CA E:CYS115 4.2 17.2 1.0
CA E:CYS157 4.3 15.9 1.0
C E:CYS155 4.4 17.0 1.0
CD E:PRO116 4.4 16.2 1.0
CA E:CYS155 4.4 12.8 1.0
O E:HOH731 4.5 22.7 1.0
N E:TYR156 4.6 14.8 1.0
O E:CYS155 4.7 15.6 1.0
C E:CYS157 4.7 15.9 1.0
O E:CYS157 4.7 22.1 1.0
C E:CYS115 4.8 14.5 1.0
N E:ASN117 4.8 18.4 1.0
N E:PRO116 4.9 16.9 1.0
C E:ASN159 4.9 17.9 1.0
CB E:ASN159 5.0 21.1 1.0
CB E:ASN117 5.0 20.7 1.0

Zinc binding site 6 out of 6 in 3tty

Go back to Zinc Binding Sites List in 3tty
Zinc binding site 6 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn676

b:20.1
occ:1.00
 SG F:CYS155 2.3 16.3 1.0
SG F:CYS160 2.3 16.4 1.0
SG F:CYS115 2.4 16.6 1.0
SG F:CYS157 2.7 17.1 1.0
CB F:CYS160 3.2 13.8 1.0
CB F:CYS155 3.3 17.2 1.0
CB F:CYS115 3.5 17.2 1.0
CB F:CYS157 3.8 18.6 1.0
N F:CYS160 3.8 17.8 1.0
N F:CYS157 4.0 19.7 1.0
CA F:CYS160 4.1 15.9 1.0
CA F:CYS115 4.2 19.0 1.0
CD F:PRO116 4.3 13.4 1.0
CA F:CYS157 4.4 16.4 1.0
C F:CYS155 4.5 17.9 1.0
CA F:CYS155 4.5 17.1 1.0
O F:HOH706 4.7 20.2 1.0
N F:TYR156 4.7 17.8 1.0
O F:CYS155 4.7 17.3 1.0
N F:ASN117 4.8 17.9 1.0
C F:CYS115 4.8 15.1 1.0
C F:CYS157 4.8 17.7 1.0
CB F:ASN117 4.8 17.5 1.0
O F:CYS157 4.8 20.3 1.0
N F:PRO116 4.8 17.2 1.0
C F:ASN159 4.9 17.9 1.0

Reference:

M.Maksimainen, S.Paavilainen, N.Hakulinen, J.Rouvinen. Structural Analysis, Enzymatic Characterization, and Catalytic Mechanisms of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus. Febs J. V. 279 1788 2012.
ISSN: ISSN 1742-464X
PubMed: 22385475
DOI: 10.1111/J.1742-4658.2012.08555.X
Page generated: Sat Oct 26 16:48:10 2024

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