Atomistry » Zinc » PDB 5e8c-5ehe » 5e9a
Atomistry »
  Zinc »
    PDB 5e8c-5ehe »
      5e9a »

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

Go back to Zinc Binding Sites List in 5e9a
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

Go back to Zinc Binding Sites List in 5e9a
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

Go back to Zinc Binding Sites List in 5e9a
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

Go back to Zinc Binding Sites List in 5e9a
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: Wed Dec 16 06:09:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy