Atomistry » Zinc » PDB 6dit-6dxq » 6dkh
Atomistry »
  Zinc »
    PDB 6dit-6dxq »
      6dkh »

Zinc in PDB 6dkh: The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655

Enzymatic activity of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655

All present enzymatic activity of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655:
1.1.1.264;

Protein crystallography data

The structure of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655, PDB code: 6dkh was solved by K.Tan, E.Evdokimova, C.Mcchesney, A.Savchenko, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.99 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.055, 77.646, 128.350, 90.00, 92.62, 90.00
R / Rfree (%) 20 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 (pdb code 6dkh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655, PDB code: 6dkh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dkh

Go back to Zinc Binding Sites List in 6dkh
Zinc binding site 1 out of 4 in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:57.5
occ:1.00
 SG A:CYS107 2.3 59.5 1.0
SG A:CYS93 2.4 64.0 1.0
SG A:CYS99 2.4 62.2 1.0
SG A:CYS96 2.4 61.7 1.0
CB A:CYS96 3.1 44.9 1.0
CB A:CYS99 3.2 60.3 1.0
CB A:CYS107 3.3 56.9 1.0
CB A:CYS93 3.7 59.8 1.0
N A:CYS93 3.8 57.7 1.0
CA A:CYS107 3.8 56.8 1.0
O A:CYS93 3.9 79.5 1.0
N A:CYS96 4.0 65.8 1.0
N A:THR108 4.1 67.4 1.0
CA A:CYS93 4.1 60.9 1.0
C A:CYS93 4.1 74.9 1.0
CA A:CYS96 4.1 54.8 1.0
N A:CYS99 4.3 51.6 1.0
CA A:CYS99 4.3 56.0 1.0
C A:CYS107 4.4 63.1 1.0
N A:ASP109 4.6 64.1 1.0
C A:CYS96 4.8 63.3 1.0
CB A:PRO92 4.8 52.8 1.0
C A:PRO92 4.9 60.5 1.0
N A:GLY94 4.9 83.7 1.0
O A:ASP109 4.9 71.0 1.0
N A:HIS95 5.0 96.7 1.0

Zinc binding site 2 out of 4 in 6dkh

Go back to Zinc Binding Sites List in 6dkh
Zinc binding site 2 out of 4 in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:48.5
occ:1.00
 SG B:CYS107 2.3 51.0 1.0
SG B:CYS99 2.4 58.0 1.0
SG B:CYS93 2.4 57.9 1.0
SG B:CYS96 2.4 61.0 1.0
CB B:CYS107 3.1 45.0 1.0
CB B:CYS99 3.4 54.2 1.0
CB B:CYS96 3.4 49.0 1.0
CB B:CYS93 3.5 48.5 1.0
CA B:CYS107 3.6 35.8 1.0
N B:CYS93 3.6 36.7 1.0
N B:GLY94 3.8 47.2 1.0
N B:THR108 3.9 44.4 1.0
N B:CYS96 4.0 57.2 1.0
CA B:CYS93 4.0 42.5 1.0
C B:CYS107 4.2 42.7 1.0
CA B:CYS96 4.2 54.9 1.0
N B:CYS99 4.3 44.8 1.0
C B:CYS93 4.4 39.1 1.0
CA B:CYS99 4.4 42.5 1.0
N B:ASP109 4.5 59.1 1.0
OG1 B:THR108 4.6 58.7 1.0
N B:HIS95 4.6 59.7 1.0
C B:PRO92 4.7 56.4 1.0
CA B:GLY94 4.8 52.8 1.0
C B:CYS96 4.8 52.9 1.0
N B:CYS107 4.9 42.2 1.0
CB B:PRO92 4.9 48.5 1.0
O B:CYS96 4.9 55.1 1.0
CA B:PRO92 5.0 57.0 1.0

Zinc binding site 3 out of 4 in 6dkh

Go back to Zinc Binding Sites List in 6dkh
Zinc binding site 3 out of 4 in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:65.3
occ:1.00
 SG C:CYS99 2.3 62.9 1.0
SG C:CYS107 2.4 69.0 1.0
SG C:CYS93 2.4 87.1 1.0
SG C:CYS96 2.5 66.6 1.0
CB C:CYS96 3.0 60.6 1.0
CB C:CYS107 3.2 51.8 1.0
CB C:CYS99 3.2 68.3 1.0
CA C:CYS107 3.7 51.7 1.0
CB C:CYS93 3.9 71.9 1.0
N C:CYS96 3.9 79.7 1.0
CA C:CYS96 4.0 74.0 1.0
N C:CYS93 4.1 56.8 1.0
N C:THR108 4.1 60.5 1.0
N C:CYS99 4.2 46.3 1.0
C C:CYS93 4.2 79.0 1.0
CA C:CYS93 4.3 62.3 1.0
CA C:CYS99 4.3 66.8 1.0
O C:CYS93 4.3 95.8 1.0
C C:CYS107 4.4 55.2 1.0
N C:GLY94 4.7 78.4 1.0
OG1 C:THR108 4.7 79.5 1.0
C C:CYS96 4.7 82.4 1.0
N C:HIS95 4.9 71.1 1.0
CB C:PRO92 4.9 51.6 1.0
N C:CYS107 5.0 55.6 1.0
N C:ASP109 5.0 72.9 1.0

Zinc binding site 4 out of 4 in 6dkh

Go back to Zinc Binding Sites List in 6dkh
Zinc binding site 4 out of 4 in the The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.6
occ:1.00
 SG D:CYS107 2.4 59.3 1.0
SG D:CYS99 2.4 71.0 1.0
SG D:CYS93 2.4 63.7 1.0
SG D:CYS96 2.5 69.2 1.0
CB D:CYS96 3.2 60.1 1.0
O D:CYS93 3.3 92.4 1.0
CB D:CYS107 3.3 54.0 1.0
CB D:CYS99 3.4 56.5 1.0
N D:CYS93 3.7 53.3 1.0
CB D:CYS93 3.8 64.0 1.0
C D:CYS93 3.8 72.5 1.0
CA D:CYS107 3.8 45.4 1.0
CA D:CYS93 4.0 61.5 1.0
N D:CYS96 4.0 83.4 1.0
N D:THR108 4.2 64.0 1.0
CA D:CYS96 4.2 68.8 1.0
N D:CYS99 4.4 43.9 1.0
C D:CYS107 4.5 51.9 1.0
CA D:CYS99 4.5 53.5 1.0
CB D:PRO92 4.5 55.7 1.0
OG1 D:THR108 4.7 68.7 1.0
C D:PRO92 4.7 51.9 1.0
N D:ASP109 4.8 54.6 1.0
N D:GLY94 4.8 61.0 1.0
C D:CYS96 4.8 61.8 1.0
N D:HIS95 4.9 69.7 1.0
CA D:PRO92 5.0 55.9 1.0
O D:CYS96 5.0 61.2 1.0

Reference:

K.Tan, E.Evdokimova, C.Mcchesney, A.Savchenko, A.Joachimiak. The Crystal Structure of L-Idonate 5-Dehydrogenase From Escherichia Coli Str. K-12 Substr. MG1655 To Be Published.
Page generated: Mon Oct 28 19:37:56 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy