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Zinc in PDB 3edz: Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor:
3.4.24.86;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor, PDB code: 3edz was solved by R.D.Mazzola, Z.Zhu, L.Sinning, B.Mckittrick, B.Lavey, J.Spitler, J.Kozlowski, S.Neng-Yang, G.Zhou, Z.Guo, P.Orth, V.Madison, J.Sun, D.Lundell, X.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.83 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.796, 75.702, 102.877, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor (pdb code 3edz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor, PDB code: 3edz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3edz

Go back to Zinc Binding Sites List in 3edz
Zinc binding site 1 out of 2 in the Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:16.7
occ:1.00
NE2 A:HIS405 2.0 14.0 1.0
O A:INN2 2.0 20.1 1.0
NE2 A:HIS415 2.1 18.6 1.0
NE2 A:HIS409 2.1 17.0 1.0
O4 A:INN2 2.2 15.3 1.0
O A:HOH648 2.2 38.9 1.0
C A:INN2 2.7 15.1 1.0
N A:INN2 2.9 19.6 1.0
CE1 A:HIS405 2.9 14.3 1.0
CD2 A:HIS405 3.0 14.4 1.0
CE1 A:HIS415 3.0 19.2 1.0
CD2 A:HIS409 3.0 17.1 1.0
CD2 A:HIS415 3.1 18.1 1.0
CE1 A:HIS409 3.1 16.6 1.0
O A:HOH508 3.9 18.5 1.0
ND1 A:HIS405 4.0 15.0 1.0
CG A:HIS405 4.1 13.9 1.0
ND1 A:HIS415 4.1 20.2 1.0
C0 A:INN2 4.2 22.0 1.0
CG A:HIS415 4.2 18.3 1.0
CG A:HIS409 4.2 15.3 1.0
ND1 A:HIS409 4.2 16.5 1.0
O A:HOH649 4.3 45.4 1.0
OE1 A:GLU406 4.4 15.7 1.0
O A:HOH651 4.5 21.8 1.0
CB A:INN2 4.7 21.2 1.0
CA A:INN2 4.7 29.4 1.0
CE A:MET435 4.8 15.2 1.0
OE2 A:GLU406 4.9 15.1 1.0

Zinc binding site 2 out of 2 in 3edz

Go back to Zinc Binding Sites List in 3edz
Zinc binding site 2 out of 2 in the Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Domain of Tace with Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:20.1
occ:1.00
NE2 B:HIS415 2.1 17.4 1.0
O2 B:5501 2.1 19.4 1.0
O1 B:5501 2.1 26.8 1.0
NE2 B:HIS405 2.1 16.1 1.0
NE2 B:HIS409 2.1 18.8 1.0
C6 B:5501 2.9 25.4 1.0
N1 B:5501 3.0 24.0 1.0
CE1 B:HIS415 3.0 17.8 1.0
CD2 B:HIS405 3.0 17.3 1.0
CD2 B:HIS409 3.0 19.0 1.0
CD2 B:HIS415 3.1 17.6 1.0
CE1 B:HIS405 3.1 15.7 1.0
CE1 B:HIS409 3.2 18.2 1.0
O B:HOH827 4.0 29.4 1.0
ND1 B:HIS415 4.1 18.8 1.0
CG B:HIS405 4.2 15.2 1.0
CG B:HIS415 4.2 17.6 1.0
ND1 B:HIS405 4.2 16.7 1.0
CG B:HIS409 4.2 16.9 1.0
ND1 B:HIS409 4.2 17.6 1.0
C1 B:5501 4.3 26.6 1.0
C5 B:5501 4.3 27.3 1.0
C8 B:5501 4.4 27.6 1.0
C13 B:5501 4.6 26.5 1.0
CE B:MET435 4.6 16.3 1.0
OE1 B:GLU406 4.7 16.5 1.0
O B:HOH821 4.7 53.4 1.0
O B:HOH832 4.7 33.9 1.0
C2 B:5501 4.8 28.0 1.0
OE2 B:GLU406 4.9 18.1 1.0
C9 B:5501 4.9 25.9 1.0

Reference:

R.D.Mazzola, Z.Zhu, L.Sinning, B.Mckittrick, B.Lavey, J.Spitler, J.Kozlowski, S.Neng-Yang, G.Zhou, Z.Guo, P.Orth, V.Madison, J.Sun, D.Lundell, X.Niu. Discovery of Novel Hydroxamates As Highly Potent Tumor Necrosis Factor-Alpha Converting Enzyme Inhibitors. Part II: Optimization of the S3' Pocket. Bioorg.Med.Chem.Lett. V. 18 5809 2008.
ISSN: ISSN 0960-894X
PubMed: 18835710
DOI: 10.1016/J.BMCL.2008.09.045
Page generated: Wed Dec 16 04:15:43 2020

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