Atomistry » Zinc » PDB 6lux-6mbd » 6m61
Atomistry »
  Zinc »
    PDB 6lux-6mbd »
      6m61 »

Zinc in PDB 6m61: Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid

Enzymatic activity of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid

All present enzymatic activity of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid:
1.2.1.12;

Protein crystallography data

The structure of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid, PDB code: 6m61 was solved by Y.Yan, X.Zang, S.J.Cooper, H.Lin, J.Zhou, Y.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.358, 135.078, 146.227, 90, 90, 90
R / Rfree (%) 19.2 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid (pdb code 6m61). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid, PDB code: 6m61:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6m61

Go back to Zinc Binding Sites List in 6m61
Zinc binding site 1 out of 5 in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn404

b:67.3
occ:1.00
O O:HOH559 2.4 24.6 1.0
NE2 O:HIS57 2.5 42.2 1.0
CE1 O:HIS57 2.7 41.8 1.0
O O:HOH783 3.1 40.9 1.0
CD2 O:HIS57 3.5 42.8 1.0
ND1 O:HIS57 3.8 38.1 1.0
O O:LYS55 4.1 16.6 1.0
CG O:HIS57 4.2 35.1 1.0
O O:HIS53 4.4 15.5 1.0
O O:HOH670 4.7 28.2 1.0
N O:LYS55 4.9 13.8 1.0
CA O:GLY54 4.9 15.8 1.0

Zinc binding site 2 out of 5 in 6m61

Go back to Zinc Binding Sites List in 6m61
Zinc binding site 2 out of 5 in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn405

b:15.6
occ:0.40
ND1 O:HIS291 2.0 17.3 1.0
O O:HOH741 2.1 31.1 1.0
OD2 O:ASP289 2.1 19.4 1.0
OD1 O:ASP289 2.2 13.2 1.0
O O:HOH598 2.2 13.5 1.0
CG O:ASP289 2.4 16.0 1.0
CE1 O:HIS291 2.6 16.7 1.0
CG O:HIS291 3.2 14.7 1.0
CB O:HIS291 3.8 9.6 1.0
NE2 O:HIS291 3.8 15.4 1.0
CB O:ASP289 4.0 11.6 1.0
CD2 O:HIS291 4.1 13.7 1.0
O O:HOH716 4.1 18.2 1.0
OG1 O:THR294 4.1 12.9 1.0
N O:HIS291 4.2 12.5 1.0
O O:HOH524 4.4 23.9 1.0
CA O:HIS291 4.6 9.7 1.0
N O:THR290 4.6 11.7 1.0
CA O:ASP289 4.7 12.6 1.0
O O:HOH793 4.7 27.9 1.0
C O:ASP289 4.8 12.1 1.0
O O:HOH527 5.0 13.9 1.0
O O:HOH821 5.0 37.2 1.0

Zinc binding site 3 out of 5 in 6m61

Go back to Zinc Binding Sites List in 6m61
Zinc binding site 3 out of 5 in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn406

b:17.6
occ:0.45
ND1 Q:HIS291 1.9 16.0 1.0
O Q:HOH588 2.1 16.6 1.0
O Q:HOH735 2.2 33.1 1.0
OD2 Q:ASP289 2.2 17.3 1.0
OD1 Q:ASP289 2.2 15.0 1.0
O Q:HOH651 2.4 31.5 1.0
CG Q:ASP289 2.5 16.8 1.0
CE1 Q:HIS291 2.5 15.0 1.0
CG Q:HIS291 3.1 14.0 1.0
CB Q:HIS291 3.7 11.7 1.0
NE2 Q:HIS291 3.7 15.5 1.0
O Q:HOH738 3.9 31.7 1.0
CB Q:ASP289 4.0 11.9 1.0
CD2 Q:HIS291 4.0 13.6 1.0
OG1 Q:THR294 4.1 11.0 1.0
N Q:HIS291 4.2 11.6 1.0
O Q:HOH701 4.3 19.4 1.0
O Q:HOH753 4.5 30.8 1.0
O2 Q:EDO404 4.5 31.7 1.0
CA Q:HIS291 4.6 10.7 1.0
O Q:HOH582 4.6 23.6 1.0
O Q:HOH751 4.6 37.6 1.0
N Q:THR290 4.7 12.7 1.0
CA Q:ASP289 4.7 14.3 1.0
C Q:ASP289 4.9 14.1 1.0
C2 Q:EDO404 4.9 31.4 1.0

Zinc binding site 4 out of 5 in 6m61

Go back to Zinc Binding Sites List in 6m61
Zinc binding site 4 out of 5 in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn404

b:17.2
occ:1.00
O P:GLU335 2.0 11.2 1.0
O P:HOH666 2.1 15.5 1.0
C P:GLU335 2.9 14.8 1.0
O P:HOH624 3.0 26.4 1.0
CA P:GLU335 4.3 11.9 1.0
CB P:GLU335 4.8 12.1 1.0
CG P:GLU335 4.8 11.5 1.0

Zinc binding site 5 out of 5 in 6m61

Go back to Zinc Binding Sites List in 6m61
Zinc binding site 5 out of 5 in the Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) with Inhibitor Heptelidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn405

b:23.8
occ:0.40
ND1 P:HIS291 2.0 22.6 1.0
OD1 P:ASP289 2.2 16.8 1.0
OD2 P:ASP289 2.2 22.1 1.0
O P:HOH721 2.3 34.0 1.0
O P:HOH586 2.3 22.6 1.0
O P:HOH664 2.4 34.5 1.0
CG P:ASP289 2.5 21.5 1.0
CE1 P:HIS291 2.6 19.5 1.0
CG P:HIS291 3.1 19.2 1.0
CB P:HIS291 3.7 18.0 1.0
NE2 P:HIS291 3.8 21.2 1.0
O P:HOH708 3.9 38.3 1.0
CB P:ASP289 4.0 18.2 1.0
CD2 P:HIS291 4.0 20.4 1.0
N P:HIS291 4.1 16.2 1.0
OG1 P:THR294 4.1 19.0 1.0
O P:HOH681 4.2 21.3 1.0
O2 P:EDO401 4.5 39.9 1.0
O P:HOH531 4.5 34.4 1.0
CA P:HIS291 4.5 14.8 1.0
N P:THR290 4.6 15.7 1.0
O P:HOH740 4.6 32.9 1.0
CA P:ASP289 4.7 17.5 1.0
C P:ASP289 4.8 17.8 1.0

Reference:

Y.Yan, X.Zang, S.J.Cooper, H.Lin, J.Zhou, Y.Tang. Biosynthesis of the Fungal Glyceraldehyde-3-Phosphate Dehydrogenase Inhibitor Heptelidic Acid and Mechanism of Self-Resistance Chem Sci V. 11 9554 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC03805A
Page generated: Tue Oct 29 02:56:33 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy