Calcium in PDB 6be6: ADAM10 Extracellular Domain

All present enzymatic activity of ADAM10 Extracellular Domain:
3.4.24.81;

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

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

Zinc

(Zn)

4 atoms

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

Calcium binding site 1 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ADAM10 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:35.2 occ:1.00 OE2 A:GLU469 2.3 39.1 1.0 OD1 A:ASN462 2.4 51.5 1.0 OD2 A:ASP472 2.4 36.9 1.0 O A:ILE459 2.5 41.4 1.0 OE1 A:GLU469 3.0 48.5 1.0 CD A:GLU469 3.0 44.9 1.0 O A:MET464 3.0 31.1 1.0 OE2 A:GLU466 3.2 42.3 1.0 CG A:ASN462 3.3 41.4 1.0 CG A:ASP472 3.6 41.9 1.0 C A:ILE459 3.6 47.3 1.0 ND2 A:ASN462 3.7 27.2 1.0 CD A:GLU466 3.8 38.9 1.0 CG A:GLU466 3.9 57.3 1.0 CA A:CYS460 4.1 30.8 1.0 C A:MET464 4.3 39.2 1.0 N A:CYS460 4.3 38.3 1.0 CB A:GLU466 4.4 50.8 1.0 OD1 A:ASP472 4.4 37.8 1.0 N A:GLY461 4.5 35.7 1.0 CB A:ASP472 4.5 49.9 1.0 N A:ASN462 4.5 24.2 1.0 CG A:GLU469 4.5 42.4 1.0 CB A:ASN462 4.5 45.8 1.0 N A:ILE459 4.6 46.7 1.0 N A:GLU466 4.6 28.0 1.0 CB A:PRO458 4.7 47.3 1.0 C A:CYS460 4.8 41.0 1.0 CA A:ILE459 4.8 50.6 1.0 OE1 A:GLU466 4.8 64.7 1.0 N A:MET464 4.9 39.3 1.0 C A:PRO458 4.9 45.3 1.0

Calcium binding site 2 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ADAM10 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca708 b:40.7 occ:1.00 OE1 B:GLU469 2.4 39.5 1.0 OD1 B:ASN462 2.4 61.9 1.0 O B:ILE459 2.6 53.3 1.0 OD2 B:ASP472 2.6 59.4 1.0 O B:MET464 2.9 58.3 1.0 CD B:GLU469 3.2 47.7 1.0 CG B:ASN462 3.2 58.6 1.0 OE2 B:GLU469 3.4 50.0 1.0 C B:ILE459 3.5 58.8 1.0 ND2 B:ASN462 3.7 57.7 1.0 CG B:GLU466 3.7 62.4 1.0 CG B:ASP472 3.8 56.2 1.0 CA B:CYS460 3.8 46.5 1.0 OE1 B:GLU466 3.8 83.6 1.0 N B:CYS460 4.0 48.5 1.0 N B:GLY461 4.1 45.2 1.0 CD B:GLU466 4.1 80.4 1.0 C B:MET464 4.1 70.8 1.0 CB B:ASP472 4.3 45.6 1.0 N B:ASN462 4.3 46.7 1.0 CB B:GLU466 4.4 52.3 1.0 CB B:ASN462 4.4 40.6 1.0 N B:ILE459 4.5 65.2 1.0 C B:CYS460 4.5 60.7 1.0 N B:MET464 4.6 57.4 1.0 CA B:ILE459 4.6 60.4 1.0 CG B:GLU469 4.7 51.7 1.0 N B:GLU466 4.7 64.2 1.0 OD1 B:ASP472 4.8 51.3 1.0 CA B:ASN462 4.9 31.5 1.0 CA B:MET464 4.9 69.0 1.0 CB B:CYS460 4.9 58.0 1.0 C B:PRO458 5.0 63.1 1.0 SG B:CYS495 5.0 51.9 1.0

Calcium binding site 3 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of ADAM10 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca707 b:44.8 occ:1.00 O C:MET464 2.5 45.5 1.0 OD2 C:ASP472 2.5 71.8 1.0 OE1 C:GLU469 2.6 48.0 1.0 OD1 C:ASN462 2.6 70.7 1.0 O C:ILE459 2.6 74.2 1.0 CG C:ASP472 3.3 65.4 1.0 OE1 C:GLU466 3.4 88.5 1.0 CD C:GLU469 3.4 56.3 1.0 OE2 C:GLU469 3.5 43.7 1.0 CA C:CYS460 3.5 54.0 1.0 CG C:ASN462 3.5 58.7 1.0 C C:ILE459 3.6 60.9 1.0 C C:MET464 3.6 50.2 1.0 ND2 C:ASN462 3.7 48.4 1.0 CB C:ASP472 3.9 67.9 1.0 N C:CYS460 4.0 46.4 1.0 OD1 C:ASP472 4.0 52.3 1.0 N C:MET464 4.2 50.5 1.0 CB C:CYS460 4.2 63.2 1.0 CD C:GLU466 4.3 95.8 1.0 N C:GLY461 4.4 43.9 1.0 CA C:MET464 4.4 43.6 1.0 C C:CYS460 4.4 55.4 1.0 N C:VAL465 4.6 52.2 1.0 N C:ASN462 4.6 42.6 1.0 N C:GLU466 4.7 54.1 1.0 CG C:GLU466 4.7 87.5 1.0 CA C:VAL465 4.8 49.0 1.0 CB C:MET464 4.8 47.8 1.0 SG C:CYS460 4.8 77.4 1.0 CG C:GLU469 4.9 61.7 1.0 CB C:ASN462 4.9 57.2 1.0 CB C:GLU466 4.9 88.6 1.0 CA C:ILE459 4.9 62.0 1.0

Calcium binding site 4 out of 4 in the ADAM10 Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of ADAM10 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca709 b:38.0 occ:1.00 O D:MET464 2.4 65.5 1.0 OD2 D:ASP472 2.4 55.2 1.0 OE1 D:GLU469 2.5 46.4 1.0 O D:ILE459 2.6 56.4 1.0 OD1 D:ASN462 2.7 54.6 1.0 CD D:GLU469 3.3 61.6 1.0 OE2 D:GLU469 3.4 86.9 1.0 OE1 D:GLU466 3.4 62.4 1.0 CG D:ASP472 3.5 59.3 1.0 C D:MET464 3.6 66.3 1.0 CA D:CYS460 3.6 56.0 1.0 C D:ILE459 3.6 60.1 1.0 CG D:ASN462 3.7 49.7 1.0 CD D:GLU466 3.8 69.3 1.0 CB D:ASP472 4.0 61.4 1.0 ND2 D:ASN462 4.0 43.5 1.0 N D:CYS460 4.0 45.3 1.0 N D:MET464 4.1 48.9 1.0 CA D:MET464 4.2 52.5 1.0 CG D:GLU466 4.3 66.6 1.0 CB D:MET464 4.3 62.4 1.0 CB D:CYS460 4.4 63.6 1.0 OE2 D:GLU466 4.4 67.7 1.0 C D:CYS460 4.5 59.1 1.0 CB D:GLU466 4.5 80.8 1.0 N D:GLU466 4.6 65.6 1.0 OD1 D:ASP472 4.6 47.7 1.0 N D:GLY461 4.6 46.3 1.0 N D:VAL465 4.6 73.8 1.0 CG D:GLU469 4.7 72.6 1.0 N D:ASN462 4.8 31.3 1.0 SG D:CYS460 4.8 0.8 1.0 CA D:VAL465 4.9 70.6 1.0 N D:ILE459 4.9 69.3 1.0 CA D:ILE459 4.9 68.8 1.0

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