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Zinc in PDB 5e9a: Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3

Enzymatic activity of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3

All present enzymatic activity of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3, PDB code: 5e9a was solved by Y.Z.Zhang, Y.T.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 138.45 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 146.426, 106.831, 164.244, 90.00, 109.00, 90.00
R / Rfree (%) 19.9 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 (pdb code 5e9a). 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 Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3, PDB code: 5e9a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5e9a

Go back to Zinc Binding Sites List in 5e9a
Zinc binding site 1 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:24.8
occ:1.00
 SG A:CYS162 2.3 23.3 1.0
SG A:CYS167 2.3 22.8 1.0
SG A:CYS164 2.4 24.1 1.0
SG A:CYS122 2.4 26.1 1.0
CB A:CYS162 3.2 23.6 1.0
CB A:CYS122 3.3 26.4 1.0
CB A:CYS167 3.4 25.0 1.0
CB A:CYS164 3.5 28.1 1.0
N A:CYS164 3.9 30.2 1.0
CA A:CYS122 4.1 28.2 1.0
N A:CYS167 4.1 26.3 1.0
CA A:CYS164 4.2 29.6 1.0
CA A:CYS167 4.4 25.4 1.0
CA A:CYS162 4.4 24.7 1.0
C A:CYS162 4.4 25.6 1.0
N A:MET123 4.6 33.5 1.0
CB A:SER124 4.6 36.2 1.0
O A:CYS164 4.6 30.1 1.0
O A:CYS162 4.6 24.5 1.0
OG A:SER124 4.6 33.4 1.0
C A:CYS164 4.7 30.2 1.0
C A:CYS122 4.7 29.3 1.0
N A:HIS163 4.7 28.1 1.0
N A:SER124 4.8 36.6 1.0

Zinc binding site 2 out of 6 in 5e9a

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Zinc binding site 2 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:32.8
occ:1.00
 SG B:CYS167 2.2 33.9 1.0
SG B:CYS122 2.3 23.8 1.0
SG B:CYS164 2.4 35.6 1.0
SG B:CYS162 2.4 35.5 1.0
CB B:CYS162 3.4 33.3 1.0
CB B:CYS167 3.4 34.1 1.0
CB B:CYS164 3.6 33.7 1.0
CB B:CYS122 3.6 25.8 1.0
N B:CYS167 4.0 36.6 1.0
N B:CYS164 4.0 33.0 1.0
CA B:CYS164 4.2 34.1 1.0
CA B:CYS167 4.3 33.5 1.0
CA B:CYS122 4.3 27.6 1.0
O B:CYS164 4.4 36.2 1.0
CB B:SER124 4.4 37.7 1.0
C B:CYS162 4.5 31.1 1.0
CA B:CYS162 4.6 32.1 1.0
C B:CYS164 4.6 35.1 1.0
OG B:SER124 4.7 43.0 1.0
N B:HIS163 4.7 31.0 1.0
N B:MET123 4.8 34.4 1.0
N B:SER124 4.8 40.2 1.0
C B:CYS122 4.9 29.5 1.0
O B:CYS162 4.9 30.5 1.0

Zinc binding site 3 out of 6 in 5e9a

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Zinc binding site 3 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:34.7
occ:1.00
 SG C:CYS167 2.2 32.8 1.0
SG C:CYS122 2.3 33.0 1.0
SG C:CYS164 2.4 25.8 1.0
SG C:CYS162 2.4 33.2 1.0
CB C:CYS162 3.4 31.0 1.0
CB C:CYS167 3.4 34.1 1.0
CB C:CYS122 3.4 38.5 1.0
CB C:CYS164 3.5 27.2 1.0
N C:CYS167 4.0 35.5 1.0
N C:CYS164 4.0 31.4 1.0
CA C:CYS164 4.2 30.2 1.0
CA C:CYS167 4.3 34.9 1.0
CA C:CYS122 4.3 38.8 1.0
C C:CYS162 4.5 30.6 1.0
O C:CYS164 4.5 34.9 1.0
CB C:SER124 4.5 40.1 1.0
CA C:CYS162 4.5 30.0 1.0
OG C:SER124 4.6 39.7 1.0
C C:CYS164 4.6 33.2 1.0
O C:CYS162 4.7 28.8 1.0
N C:MET123 4.7 45.7 1.0
N C:HIS163 4.8 31.7 1.0
N C:SER124 4.8 43.0 1.0
C C:CYS122 4.8 41.8 1.0
CB C:THR166 4.9 35.5 1.0
O C:HOH856 4.9 27.3 1.0

Zinc binding site 4 out of 6 in 5e9a

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Zinc binding site 4 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:27.3
occ:1.00
 SG D:CYS167 2.2 26.9 1.0
SG D:CYS162 2.3 25.7 1.0
SG D:CYS122 2.4 27.0 1.0
SG D:CYS164 2.5 25.7 1.0
CB D:CYS162 3.1 26.1 1.0
CB D:CYS167 3.4 31.5 1.0
CB D:CYS122 3.5 28.4 1.0
CB D:CYS164 3.6 28.7 1.0
N D:CYS164 4.0 31.6 1.0
O D:HOH846 4.1 26.5 1.0
N D:CYS167 4.1 33.6 1.0
CA D:CYS122 4.2 29.6 1.0
CA D:CYS164 4.3 30.2 1.0
CA D:CYS167 4.3 31.2 1.0
CA D:CYS162 4.4 25.3 1.0
C D:CYS162 4.4 26.2 1.0
CB D:SER124 4.5 36.1 1.0
O D:CYS164 4.5 36.5 1.0
OG D:SER124 4.6 34.2 1.0
N D:MET123 4.6 33.1 1.0
O D:CYS162 4.6 24.1 1.0
C D:CYS164 4.7 32.6 1.0
N D:HIS163 4.7 30.3 1.0
C D:CYS122 4.7 29.4 1.0
N D:SER124 4.7 38.5 1.0
CB D:THR166 5.0 36.6 1.0

Zinc binding site 5 out of 6 in 5e9a

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Zinc binding site 5 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:37.6
occ:1.00
 SG E:CYS122 2.2 32.0 1.0
SG E:CYS164 2.3 38.7 1.0
SG E:CYS167 2.3 41.3 1.0
SG E:CYS162 2.4 43.8 1.0
CB E:CYS162 3.3 38.5 1.0
CB E:CYS167 3.4 40.9 1.0
CB E:CYS164 3.4 36.9 1.0
CB E:CYS122 3.5 34.2 1.0
N E:CYS164 4.0 34.1 1.0
N E:CYS167 4.0 41.8 1.0
CA E:CYS122 4.2 34.0 1.0
CA E:CYS164 4.2 36.8 1.0
CA E:CYS167 4.3 40.4 1.0
O E:CYS164 4.4 38.6 1.0
CB E:SER124 4.5 47.4 1.0
CA E:CYS162 4.5 36.5 1.0
OG E:SER124 4.5 47.9 1.0
C E:CYS164 4.6 39.8 1.0
C E:CYS162 4.6 35.0 1.0
N E:HIS163 4.7 34.5 1.0
N E:MET123 4.7 40.9 1.0
C E:CYS122 4.8 35.6 1.0
N E:SER124 4.8 46.6 1.0
CB E:THR166 4.9 43.3 1.0

Zinc binding site 6 out of 6 in 5e9a

Go back to Zinc Binding Sites List in 5e9a
Zinc binding site 6 out of 6 in the Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of the Cold-Adamped Beta-Galactosidase From Rahnella Sp. R3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:36.5
occ:1.00
 SG F:CYS167 2.2 37.3 1.0
SG F:CYS162 2.3 39.7 1.0
SG F:CYS164 2.4 31.9 1.0
SG F:CYS122 2.4 38.8 1.0
CB F:CYS162 3.2 35.0 1.0
CB F:CYS122 3.4 45.2 1.0
CB F:CYS167 3.4 38.1 1.0
CB F:CYS164 3.5 32.4 1.0
N F:CYS164 3.9 35.4 1.0
N F:CYS167 4.0 38.4 1.0
CA F:CYS122 4.2 46.5 1.0
CA F:CYS164 4.2 33.6 1.0
CA F:CYS167 4.3 38.0 1.0
C F:CYS162 4.4 32.8 1.0
CA F:CYS162 4.4 32.7 1.0
O F:CYS164 4.6 34.4 1.0
N F:HIS163 4.6 33.8 1.0
O F:CYS162 4.6 29.9 1.0
N F:MET123 4.7 50.2 1.0
C F:CYS164 4.7 34.0 1.0
C F:CYS122 4.7 48.3 1.0
CB F:SER124 4.7 43.6 1.0
N F:SER124 4.9 53.4 1.0
CB F:THR166 5.0 37.4 1.0

Reference:

Y.Fan, X.Hua, Y.Zhang, Y.Feng, Q.Shen, J.Dong, W.Zhao, W.Zhang, Z.Jin, R.Yang. Cloning, Expression and Structural Stability of A Cold-Adapted Beta-Galactosidase From Rahnella Sp. R3. Protein Expr.Purif. V. 115 158 2015.
ISSN: ESSN 1096-0279
PubMed: 26145832
DOI: 10.1016/J.PEP.2015.07.001
Page generated: Sun Oct 27 15:06:53 2024

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