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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

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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

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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

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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

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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

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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: Thu Aug 21 17:20:41 2025

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