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Zinc in PDB 6b9p: Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor

Enzymatic activity of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor

All present enzymatic activity of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor:
3.2.1.24;

Protein crystallography data

The structure of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor, PDB code: 6b9p was solved by E.Howard, A.Cousido-Siah, M.Lepage, A.Bodlenner, A.Mitschler, A.Meli, F.Dericcardis, I.Izzo, A.Podjarny, P.Compain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.274, 119.761, 277.050, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor (pdb code 6b9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor, PDB code: 6b9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6b9p

Go back to Zinc Binding Sites List in 6b9p
Zinc binding site 1 out of 2 in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:18.3
occ:1.00
NE2 A:HIS386 2.1 18.6 1.0
NE2 A:HIS23 2.1 18.1 1.0
OD1 A:ASP25 2.1 18.7 1.0
OD2 A:ASP145 2.1 22.1 1.0
O3A A:D0J1001 2.3 18.3 1.0
O2A A:D0J1001 2.3 19.2 1.0
C2A A:D0J1001 2.9 21.0 1.0
CE1 A:HIS23 3.0 20.6 1.0
CE1 A:HIS386 3.1 17.1 1.0
CD2 A:HIS386 3.1 18.9 1.0
CD2 A:HIS23 3.1 15.5 1.0
C3A A:D0J1001 3.1 18.0 1.0
CG A:ASP25 3.1 19.3 1.0
CG A:ASP145 3.1 21.4 1.0
OD2 A:ASP25 3.4 18.1 1.0
CB A:ASP145 3.5 20.0 1.0
OD2 A:ASP387 4.1 18.2 1.0
ND1 A:HIS23 4.2 17.2 1.0
ND1 A:HIS386 4.2 19.5 1.0
CG A:HIS386 4.2 19.2 1.0
CG A:HIS23 4.2 18.6 1.0
OD1 A:ASP145 4.2 18.9 1.0
C4A A:D0J1001 4.3 20.5 1.0
C1A A:D0J1001 4.4 20.4 1.0
CB A:ASP25 4.5 16.3 1.0
OH A:TYR210 4.6 18.6 1.0
CE1 A:HIS385 4.6 19.0 1.0
CA A:ASP25 4.9 14.2 1.0

Zinc binding site 2 out of 2 in 6b9p

Go back to Zinc Binding Sites List in 6b9p
Zinc binding site 2 out of 2 in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:20.9
occ:1.00
OD2 B:ASP145 2.0 20.5 1.0
NE2 B:HIS386 2.1 21.8 1.0
OD1 B:ASP25 2.1 21.1 1.0
NE2 B:HIS23 2.1 21.8 1.0
O3A B:D0J1001 2.3 20.2 1.0
O2A B:D0J1001 2.3 22.3 1.0
C2A B:D0J1001 2.9 19.6 1.0
CD2 B:HIS386 3.0 21.8 1.0
CG B:ASP145 3.0 19.6 1.0
CG B:ASP25 3.1 23.5 1.0
CD2 B:HIS23 3.1 21.7 1.0
C3A B:D0J1001 3.1 21.2 1.0
CE1 B:HIS23 3.1 23.9 1.0
CE1 B:HIS386 3.1 17.5 1.0
OD2 B:ASP25 3.3 22.4 1.0
CB B:ASP145 3.5 20.9 1.0
OD1 B:ASP145 4.1 17.9 1.0
OD2 B:ASP387 4.1 20.8 1.0
CG B:HIS386 4.2 21.2 1.0
ND1 B:HIS386 4.2 19.8 1.0
ND1 B:HIS23 4.2 19.7 1.0
CG B:HIS23 4.2 21.2 1.0
C4A B:D0J1001 4.2 23.6 1.0
C1A B:D0J1001 4.4 21.8 1.0
CB B:ASP25 4.4 19.9 1.0
CE1 B:HIS385 4.5 20.3 1.0
OH B:TYR210 4.7 22.0 1.0
CA B:ASP25 4.9 19.5 1.0
O B:HOH1253 5.0 20.8 1.0

Reference:

E.Howard, A.Cousido-Siah, M.L.Lepage, J.P.Schneider, A.Bodlenner, A.Mitschler, A.Meli, I.Izzo, H.A.Alvarez, A.Podjarny, P.Compain. Structural Basis of Outstanding Multivalent Effects in Jack Bean Alpha-Mannosidase Inhibition. Angew. Chem. Int. Ed. Engl. V. 57 8002 2018.
ISSN: ESSN 1521-3773
PubMed: 29722924
DOI: 10.1002/ANIE.201801202
Page generated: Wed Dec 16 11:31:41 2020

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