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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

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