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Zinc in PDB 3tts: Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus

Enzymatic activity of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus

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

Protein crystallography data

The structure of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus, PDB code: 3tts 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) 47.34 / 2.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 226.000, 226.000, 246.400, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus (pdb code 3tts). 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, PDB code: 3tts:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3tts

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Zinc binding site 1 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn676

b:21.8
occ:1.00
 SG A:CYS155 2.3 19.3 1.0
SG A:CYS160 2.4 21.2 1.0
SG A:CYS115 2.4 18.0 1.0
SG A:CYS157 2.5 20.0 1.0
CB A:CYS155 3.2 15.3 1.0
CB A:CYS160 3.3 16.2 1.0
CB A:CYS115 3.4 17.9 1.0
CB A:CYS157 3.5 19.5 1.0
N A:CYS157 3.9 16.7 1.0
N A:CYS160 3.9 18.6 1.0
CA A:CYS157 4.2 19.0 1.0
CD A:PRO116 4.2 18.7 1.0
CA A:CYS160 4.2 16.7 1.0
CA A:CYS115 4.2 20.6 1.0
CA A:CYS155 4.4 16.8 1.0
C A:CYS155 4.5 18.1 1.0
O A:HOH689 4.5 23.0 1.0
C A:CYS157 4.7 22.7 1.0
N A:TYR156 4.7 16.2 1.0
O A:CYS157 4.7 16.1 1.0
C A:CYS115 4.8 18.8 1.0
N A:PRO116 4.8 19.8 1.0
O A:CYS155 4.8 14.5 1.0
N A:ASN117 4.9 18.4 1.0
O A:HOH1552 4.9 31.3 1.0
C A:ASN159 5.0 22.9 1.0

Zinc binding site 2 out of 6 in 3tts

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn676

b:22.7
occ:1.00
 SG B:CYS155 2.3 17.5 1.0
SG B:CYS157 2.4 24.5 1.0
SG B:CYS115 2.4 18.4 1.0
SG B:CYS160 2.5 20.1 1.0
CB B:CYS155 3.3 16.6 1.0
CB B:CYS115 3.4 20.3 1.0
CB B:CYS160 3.4 16.6 1.0
CB B:CYS157 3.6 21.6 1.0
N B:CYS157 4.0 15.8 1.0
N B:CYS160 4.0 23.7 1.0
CD B:PRO116 4.2 16.6 1.0
CA B:CYS160 4.2 17.8 1.0
CA B:CYS115 4.2 20.4 1.0
CA B:CYS157 4.3 19.8 1.0
C B:CYS155 4.4 19.7 1.0
O B:HOH681 4.4 19.2 1.0
CA B:CYS155 4.5 16.1 1.0
O B:CYS157 4.6 20.1 1.0
O B:CYS155 4.7 18.6 1.0
N B:TYR156 4.7 19.1 1.0
C B:CYS157 4.7 19.6 1.0
C B:CYS115 4.8 19.3 1.0
N B:PRO116 4.8 19.0 1.0
N B:ASN117 4.9 19.9 1.0
C B:ASN159 5.0 20.6 1.0

Zinc binding site 3 out of 6 in 3tts

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn676

b:20.2
occ:1.00
 SG C:CYS155 2.3 19.1 1.0
SG C:CYS160 2.4 20.5 1.0
SG C:CYS115 2.4 18.1 1.0
SG C:CYS157 2.5 21.2 1.0
CB C:CYS155 3.3 16.5 1.0
CB C:CYS115 3.3 15.6 1.0
CB C:CYS160 3.4 15.7 1.0
CB C:CYS157 3.6 17.0 1.0
N C:CYS160 3.8 16.7 1.0
N C:CYS157 3.9 20.4 1.0
CA C:CYS160 4.1 19.1 1.0
CA C:CYS115 4.2 21.0 1.0
CA C:CYS157 4.3 18.7 1.0
CD C:PRO116 4.5 17.6 1.0
C C:CYS155 4.5 19.4 1.0
O C:HOH684 4.5 22.6 1.0
CA C:CYS155 4.5 16.0 1.0
N C:TYR156 4.7 17.4 1.0
O C:CYS157 4.7 20.4 1.0
C C:CYS157 4.7 18.0 1.0
C C:CYS115 4.8 17.2 1.0
O C:CYS155 4.8 15.9 1.0
N C:PRO116 4.8 16.4 1.0
C C:ASN159 4.8 18.3 1.0
CB C:ASN159 4.9 20.7 1.0
N C:ASN117 4.9 14.2 1.0

Zinc binding site 4 out of 6 in 3tts

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn676

b:21.6
occ:1.00
 SG D:CYS155 2.3 17.5 1.0
SG D:CYS160 2.4 20.3 1.0
SG D:CYS115 2.4 17.1 1.0
SG D:CYS157 2.5 21.7 1.0
CB D:CYS155 3.3 22.7 1.0
CB D:CYS160 3.4 16.3 1.0
CB D:CYS115 3.5 18.5 1.0
CB D:CYS157 3.6 21.9 1.0
N D:CYS160 3.8 18.6 1.0
N D:CYS157 4.0 17.3 1.0
CA D:CYS160 4.1 18.1 1.0
CA D:CYS115 4.2 20.0 1.0
CA D:CYS157 4.3 19.7 1.0
O D:HOH789 4.4 26.4 1.0
CD D:PRO116 4.4 19.1 1.0
C D:CYS155 4.5 16.7 1.0
CA D:CYS155 4.5 17.7 1.0
N D:TYR156 4.7 14.2 1.0
C D:CYS157 4.7 24.2 1.0
C D:CYS115 4.8 21.5 1.0
O D:CYS157 4.8 20.2 1.0
O D:CYS155 4.8 15.8 1.0
N D:ASN117 4.8 18.3 1.0
N D:PRO116 4.8 22.7 1.0
C D:ASN159 4.9 22.4 1.0
CB D:ASN117 4.9 21.2 1.0

Zinc binding site 5 out of 6 in 3tts

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn676

b:24.0
occ:1.00
 SG E:CYS155 2.3 21.2 1.0
SG E:CYS160 2.4 22.3 1.0
SG E:CYS115 2.4 19.7 1.0
SG E:CYS157 2.4 24.1 1.0
CB E:CYS155 3.3 19.2 1.0
CB E:CYS160 3.4 18.3 1.0
CB E:CYS115 3.5 16.2 1.0
CB E:CYS157 3.5 18.0 1.0
N E:CYS157 3.8 20.0 1.0
N E:CYS160 3.9 20.6 1.0
CA E:CYS160 4.2 18.7 1.0
CA E:CYS157 4.2 18.6 1.0
CA E:CYS115 4.3 19.8 1.0
O E:HOH771 4.4 25.1 1.0
CD E:PRO116 4.4 13.6 1.0
C E:CYS155 4.4 18.2 1.0
CA E:CYS155 4.5 18.6 1.0
N E:TYR156 4.6 18.1 1.0
C E:CYS157 4.7 19.6 1.0
O E:CYS155 4.8 21.6 1.0
O E:CYS157 4.9 25.8 1.0
C E:ASN159 4.9 24.8 1.0
C E:CYS115 4.9 18.8 1.0
N E:PRO116 5.0 15.2 1.0
C E:TYR156 5.0 22.1 1.0
N E:ASN117 5.0 16.3 1.0

Zinc binding site 6 out of 6 in 3tts

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn676

b:22.1
occ:1.00
 SG F:CYS160 2.3 17.6 1.0
SG F:CYS155 2.3 19.2 1.0
SG F:CYS115 2.4 21.2 1.0
SG F:CYS157 2.4 24.4 1.0
CB F:CYS160 3.3 17.4 1.0
CB F:CYS155 3.3 21.6 1.0
CB F:CYS115 3.4 18.6 1.0
CB F:CYS157 3.4 20.1 1.0
N F:CYS160 3.8 20.0 1.0
N F:CYS157 3.9 18.7 1.0
CA F:CYS160 4.1 19.0 1.0
CA F:CYS157 4.2 18.4 1.0
CD F:PRO116 4.2 17.8 1.0
CA F:CYS115 4.2 21.1 1.0
C F:CYS155 4.4 18.0 1.0
CA F:CYS155 4.5 19.9 1.0
O F:HOH727 4.5 22.1 1.0
N F:TYR156 4.6 19.6 1.0
C F:CYS157 4.6 21.9 1.0
O F:CYS157 4.7 21.1 1.0
O F:CYS155 4.8 20.5 1.0
C F:CYS115 4.8 18.2 1.0
N F:PRO116 4.8 20.6 1.0
N F:ASN117 4.9 17.6 1.0
C F:ASN159 4.9 21.1 1.0
CB F:ASN159 5.0 19.7 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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