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Zinc in PDB 6be6: ADAM10 Extracellular Domain

Enzymatic activity of ADAM10 Extracellular Domain

All present enzymatic activity of ADAM10 Extracellular Domain:
3.4.24.81;

Protein crystallography data

The structure of ADAM10 Extracellular Domain, PDB code: 6be6 was solved by T.C.M.Seegar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.48 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.420, 188.780, 86.640, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28.5

Other elements in 6be6:

The structure of ADAM10 Extracellular Domain also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the ADAM10 Extracellular Domain (pdb code 6be6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the ADAM10 Extracellular Domain, PDB code: 6be6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6be6

Go back to Zinc Binding Sites List in 6be6
Zinc binding site 1 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ADAM10 Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn706

b:22.1
occ:1.00
NE2 A:HIS387 2.1 20.4 1.0
NE2 A:HIS383 2.1 32.0 1.0
NE2 A:HIS393 2.1 35.0 1.0
CE1 A:HIS387 2.9 22.6 1.0
CD2 A:HIS383 2.9 23.4 1.0
CD2 A:HIS393 3.0 24.5 1.0
C B:GLY655 3.1 60.9 1.0
CD2 A:HIS387 3.1 24.5 1.0
CE1 A:HIS383 3.2 22.2 1.0
CE1 A:HIS393 3.2 29.9 1.0
O B:GLY655 3.5 61.3 1.0
ND1 A:HIS387 4.0 25.9 1.0
CG A:HIS383 4.1 20.0 1.0
CG A:HIS393 4.2 24.0 1.0
CG A:HIS387 4.2 19.8 1.0
OE2 A:GLU384 4.2 31.8 1.0
ND1 A:HIS383 4.2 13.5 1.0
CA B:GLY655 4.3 45.6 1.0
ND1 A:HIS393 4.3 19.6 1.0
N B:GLY655 4.3 31.9 1.0
C B:LEU654 4.5 29.9 1.0
CB B:LEU654 4.6 19.7 1.0
CD A:GLU384 4.8 32.7 1.0
OE1 A:GLU384 4.8 27.7 1.0
CE A:MET417 4.9 20.8 1.0

Zinc binding site 2 out of 4 in 6be6

Go back to Zinc Binding Sites List in 6be6
Zinc binding site 2 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ADAM10 Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn709

b:20.0
occ:1.00
NE2 B:HIS387 2.1 20.4 1.0
NE2 B:HIS393 2.1 35.2 1.0
NE2 B:HIS383 2.2 20.0 1.0
CE1 B:HIS387 2.8 21.5 1.0
C A:GLY655 2.9 40.9 1.0
CE1 B:HIS383 2.9 26.9 1.0
CD2 B:HIS393 3.0 26.8 1.0
CE1 B:HIS393 3.1 45.6 1.0
O A:GLY655 3.2 60.9 1.0
CD2 B:HIS387 3.2 24.1 1.0
CD2 B:HIS383 3.3 28.4 1.0
ND1 B:HIS387 3.9 21.4 1.0
ND1 B:HIS383 4.1 22.6 1.0
CA A:GLY655 4.1 31.9 1.0
ND1 B:HIS393 4.2 55.6 1.0
CG B:HIS393 4.2 38.7 1.0
CG B:HIS387 4.2 23.1 1.0
N A:GLY655 4.3 40.7 1.0
CG B:HIS383 4.3 19.9 1.0
C A:LEU654 4.6 28.7 1.0
OE2 B:GLU384 4.6 28.9 1.0
O A:LEU654 4.7 33.7 1.0
CB A:LEU654 4.7 38.4 1.0

Zinc binding site 3 out of 4 in 6be6

Go back to Zinc Binding Sites List in 6be6
Zinc binding site 3 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ADAM10 Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn706

b:24.8
occ:1.00
NE2 C:HIS383 2.0 26.3 1.0
NE2 C:HIS387 2.1 18.8 1.0
NE2 C:HIS393 2.3 20.5 1.0
CD2 C:HIS387 2.9 18.9 1.0
CD2 C:HIS383 2.9 19.7 1.0
CE1 C:HIS383 3.0 30.0 1.0
CD2 C:HIS393 3.2 22.8 1.0
CE1 C:HIS387 3.2 16.4 1.0
C D:GLY655 3.3 43.6 1.0
CE1 C:HIS393 3.4 26.4 1.0
O D:GLY655 3.9 52.7 1.0
CG C:HIS383 4.0 20.8 1.0
ND1 C:HIS383 4.0 20.3 1.0
CG C:HIS387 4.1 16.2 1.0
ND1 C:HIS387 4.2 18.4 1.0
CB D:LEU654 4.3 33.1 1.0
N D:GLY655 4.4 27.5 1.0
CA D:GLY655 4.4 37.6 1.0
CG C:HIS393 4.4 25.6 1.0
C D:LEU654 4.4 29.2 1.0
ND1 C:HIS393 4.5 21.5 1.0
O D:LEU654 4.5 31.9 1.0
OE2 C:GLU384 4.6 28.8 1.0
O C:HIS383 4.8 35.0 1.0
OE1 C:GLU384 4.8 25.8 1.0
CE C:MET417 4.8 29.0 1.0

Zinc binding site 4 out of 4 in 6be6

Go back to Zinc Binding Sites List in 6be6
Zinc binding site 4 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ADAM10 Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn710

b:30.6
occ:1.00
O C:GLY655 1.9 43.1 1.0
NE2 D:HIS387 2.1 16.1 1.0
NE2 D:HIS383 2.1 32.4 1.0
NE2 D:HIS393 2.3 24.6 1.0
C C:GLY655 2.8 46.3 1.0
CE1 D:HIS387 3.0 16.7 1.0
CE1 D:HIS383 3.0 27.4 1.0
CD2 D:HIS383 3.1 23.9 1.0
CD2 D:HIS387 3.1 18.7 1.0
CE1 D:HIS393 3.2 17.8 1.0
CD2 D:HIS393 3.2 23.3 1.0
ND1 D:HIS383 4.1 25.6 1.0
ND1 D:HIS387 4.1 20.4 1.0
CG D:HIS383 4.2 15.7 1.0
CG D:HIS387 4.2 23.8 1.0
CA C:GLY655 4.2 39.5 1.0
ND1 D:HIS393 4.2 17.1 1.0
CG D:HIS393 4.3 21.5 1.0
OE2 D:GLU384 4.4 33.1 1.0
N C:GLY655 4.6 20.8 1.0
O C:LEU654 4.6 33.5 1.0
CG C:LEU654 4.7 32.9 1.0
C C:LEU654 4.8 27.0 1.0
CE D:MET417 4.9 22.4 1.0

Reference:

T.C.M.Seegar, L.B.Killingsworth, N.Saha, P.A.Meyer, D.Patra, B.Zimmerman, P.W.Janes, E.Rubinstein, D.B.Nikolov, G.Skiniotis, A.C.Kruse, S.C.Blacklow. Structural Basis For Regulated Proteolysis By the Alpha-Secretase ADAM10. Cell V. 171 1638 2017.
ISSN: ISSN 1097-4172
PubMed: 29224781
DOI: 10.1016/J.CELL.2017.11.014
Page generated: Wed Dec 16 11:31:52 2020

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