Atomistry » Zinc » PDB 1do5-1e08 » 1dth
Atomistry »
  Zinc »
    PDB 1do5-1e08 »
      1dth »

Zinc in PDB 1dth: Metalloprotease

Enzymatic activity of Metalloprotease

All present enzymatic activity of Metalloprotease:
3.4.24.42;

Protein crystallography data

The structure of Metalloprotease, PDB code: 1dth was solved by I.Botos, L.Scapozza, D.Zhang, L.A.Liotta, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 97.210, 97.210, 87.910, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / n/a

Other elements in 1dth:

The structure of Metalloprotease also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Metalloprotease (pdb code 1dth). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Metalloprotease, PDB code: 1dth:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1dth

Go back to Zinc Binding Sites List in 1dth
Zinc binding site 1 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metalloprotease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:5.0
occ:1.00
O4 A:BAT972 1.9 29.7 0.9
NE2 A:HIS142 2.0 29.9 1.0
NE2 A:HIS152 2.0 16.7 1.0
NE2 A:HIS146 2.0 31.5 1.0
CD2 A:HIS142 2.9 5.8 1.0
CE1 A:HIS152 3.0 31.9 1.0
CE1 A:HIS142 3.0 5.0 1.0
C15 A:BAT972 3.0 28.1 0.9
CE1 A:HIS146 3.0 8.2 1.0
CD2 A:HIS146 3.1 28.6 1.0
CD2 A:HIS152 3.1 14.7 1.0
C16 A:BAT972 3.4 32.9 0.9
N3 A:BAT972 3.7 21.1 0.9
CG A:HIS142 4.1 5.0 1.0
ND1 A:HIS142 4.1 15.7 1.0
ND1 A:HIS152 4.1 20.0 1.0
OE2 A:GLU143 4.2 18.7 1.0
CG A:HIS152 4.2 7.8 1.0
ND1 A:HIS146 4.2 16.1 1.0
CG A:HIS146 4.2 6.1 1.0
C14 A:BAT972 4.3 33.8 0.9
N2 A:BAT972 4.3 30.7 0.9
C13 A:BAT972 4.4 18.3 0.9
OE1 A:GLU143 4.7 46.9 1.0
O3 A:BAT972 4.7 25.3 0.9
CE A:MET166 4.8 5.0 1.0
CD A:GLU143 4.8 15.4 1.0

Zinc binding site 2 out of 2 in 1dth

Go back to Zinc Binding Sites List in 1dth
Zinc binding site 2 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metalloprotease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:7.9
occ:1.00
NE2 B:HIS142 2.0 24.7 1.0
O4 B:BAT973 2.0 36.2 0.9
NE2 B:HIS152 2.0 5.7 1.0
NE2 B:HIS146 2.1 31.0 1.0
CE1 B:HIS152 2.9 5.0 1.0
CD2 B:HIS142 2.9 5.0 1.0
CE1 B:HIS142 3.0 5.0 1.0
C15 B:BAT973 3.0 31.3 0.9
CD2 B:HIS146 3.1 8.4 1.0
CD2 B:HIS152 3.1 5.0 1.0
CE1 B:HIS146 3.1 22.3 1.0
C16 B:BAT973 3.2 31.4 0.9
N3 B:BAT973 3.5 29.4 0.9
ND1 B:HIS152 4.1 10.9 1.0
CG B:HIS142 4.1 5.0 1.0
ND1 B:HIS142 4.1 7.2 1.0
CG B:HIS152 4.2 6.5 1.0
CG B:HIS146 4.2 9.2 1.0
ND1 B:HIS146 4.2 11.1 1.0
C14 B:BAT973 4.3 27.1 0.9
N2 B:BAT973 4.3 36.4 0.9
OE2 B:GLU143 4.5 28.3 1.0
CE B:MET166 4.6 19.3 1.0
C13 B:BAT973 4.6 38.0 0.9
O B:ARG167 4.7 41.3 1.0
OE1 B:GLU143 4.9 30.8 1.0
O3 B:BAT973 4.9 25.5 0.9

Reference:

I.Botos, L.Scapozza, D.Zhang, L.A.Liotta, E.F.Meyer. Batimastat, A Potent Matrix Mealloproteinase Inhibitor, Exhibits An Unexpected Mode of Binding. Proc.Natl.Acad.Sci.Usa V. 93 2749 1996.
ISSN: ISSN 0027-8424
PubMed: 8610113
DOI: 10.1073/PNAS.93.7.2749
Page generated: Mon Jan 25 16:09:06 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy