Copper in PDB 2fk3: Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form

The structure of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form, PDB code: 2fk3 was solved by G.K.-W.Kong, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.623, 67.437, 127.656, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Copper atom in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form (pdb code 2fk3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 19 binding sites of Copper where determined in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form, PDB code: 2fk3:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu204 b:36.1 occ:0.81 O A:HOH237 1.9 32.4 1.0 OE2 A:GLU139 2.1 42.0 1.0 N G:GLU131 2.2 33.8 1.0 NE2 A:HIS137 2.3 31.4 1.0 O G:GLU131 2.5 34.5 1.0 C G:GLU131 2.9 33.6 1.0 CA G:GLU131 3.0 34.3 1.0 CD2 A:HIS137 3.0 30.6 1.0 CD A:GLU139 3.3 40.4 1.0 CE1 A:HIS137 3.4 32.2 1.0 OE1 A:GLU139 3.9 43.6 1.0 N G:ALA132 4.0 30.5 1.0 CG A:HIS137 4.3 30.1 1.0 CG A:GLU139 4.3 37.1 1.0 CB G:GLU131 4.4 35.5 1.0 ND1 A:HIS137 4.4 31.5 1.0 CB G:ALA132 4.6 26.1 1.0 CA G:ALA132 4.7 28.7 1.0 CU A:CU211 4.8 65.0 0.9

Copper binding site 2 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu208 b:35.1 occ:1.00 O A:HOH218 2.7 18.1 1.0 O A:HOH214 2.7 25.3 1.0 O F:HOH221 2.7 22.3 1.0 O A:HOH217 2.7 18.1 1.0 O F:HOH220 2.9 16.1 1.0 CU A:CU213 4.5 17.9 0.6 CE A:LYS155 4.7 36.7 1.0 CE1 A:HIS151 4.9 23.6 1.0 CE1 F:HIS151 4.9 20.6 1.0

Copper binding site 3 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu211 b:65.0 occ:0.86 O A:HOH235 1.9 43.3 1.0 O A:HOH236 1.9 40.9 1.0 O A:HOH237 3.0 32.4 1.0 CE1 A:HIS137 4.7 32.2 1.0 CU A:CU204 4.8 36.1 0.8

Copper binding site 4 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu213 b:17.9 occ:0.57 O F:HIS166 2.8 15.1 1.0 O F:LEU165 2.8 16.7 1.0 O A:LEU165 2.9 17.9 1.0 O A:HIS166 3.1 14.2 1.0 O F:HOH220 3.1 16.1 1.0 O A:HOH217 3.3 18.1 1.0 C F:HIS166 3.6 14.9 1.0 C F:LEU165 3.6 15.9 1.0 C A:LEU165 3.7 15.6 1.0 CA F:HIS166 3.8 16.6 1.0 C A:HIS166 3.9 14.6 1.0 CA A:HIS166 3.9 13.9 1.0 CG F:LEU165 4.0 12.0 1.0 N F:HIS166 4.1 15.2 1.0 CG A:LEU165 4.3 10.7 1.0 N A:HIS166 4.3 14.9 1.0 CD2 F:LEU165 4.3 11.3 1.0 CU A:CU208 4.5 35.1 1.0 CB F:LEU165 4.5 14.0 1.0 CE1 A:TYR168 4.5 14.1 1.0 CB A:LEU165 4.6 13.5 1.0 CE1 F:TYR168 4.6 17.0 1.0 CA F:LEU165 4.7 15.2 1.0 CD2 A:LEU165 4.7 9.2 1.0 CD1 F:TYR168 4.8 15.6 1.0 CA A:LEU165 4.8 15.4 1.0 N F:ASP167 4.8 14.6 1.0 CD1 A:TYR168 4.8 13.9 1.0

Copper binding site 5 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu203 b:35.9 occ:0.66 NE2 B:HIS137 2.1 22.2 1.0 NE2 D:HIS137 2.2 25.1 1.0 CE1 B:HIS137 3.1 20.2 1.0 CD2 B:HIS137 3.1 22.4 1.0 CE1 D:HIS137 3.1 22.1 1.0 CD2 D:HIS137 3.2 23.8 1.0 ND1 B:HIS137 4.2 22.0 1.0 CG B:HIS137 4.2 22.2 1.0 ND1 D:HIS137 4.2 22.9 1.0 CG D:HIS137 4.3 24.3 1.0 O B:HOH233 4.8 33.9 1.0

Copper binding site 6 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu214 b:22.4 occ:0.40 O B:TYR168 2.8 18.8 1.0 O C:TYR168 2.8 17.8 1.0 O C:HOH237 3.3 14.3 1.0 O B:HOH236 3.5 34.4 1.0 C C:TYR168 3.8 18.6 1.0 C B:TYR168 3.8 20.1 1.0 CA B:GLY169 4.1 19.9 1.0 CA C:GLY169 4.2 18.4 1.0 N B:GLY169 4.4 20.6 1.0 N C:GLY169 4.4 18.9 1.0 N C:TYR168 4.7 18.9 1.0 O B:HOH235 4.8 33.4 1.0 N B:TYR168 4.8 19.6 1.0 CA C:TYR168 4.8 18.5 1.0 CA B:TYR168 4.9 19.7 1.0

Copper binding site 7 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu201 b:21.5 occ:0.63 NE2 G:HIS137 1.9 14.4 1.0 NE2 C:HIS137 2.0 21.7 1.0 O G:HOH190 2.8 39.2 1.0 CE1 G:HIS137 2.8 14.5 1.0 CD2 G:HIS137 2.9 16.8 1.0 CD2 C:HIS137 2.9 19.4 1.0 CE1 C:HIS137 3.0 19.6 1.0 O C:HOH244 3.2 70.6 1.0 O G:HOH196 3.5 43.7 1.0 ND1 G:HIS137 3.9 16.2 1.0 CG G:HIS137 4.0 17.7 1.0 CG C:HIS137 4.1 18.4 1.0 ND1 C:HIS137 4.1 20.0 1.0 O C:HOH215 4.3 29.5 1.0 O G:HOH195 4.4 29.5 1.0

Copper binding site 8 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu202 b:22.4 occ:0.67 N C:GLU131 2.0 26.5 1.0 NE2 H:HIS137 2.1 11.3 1.0 O C:GLU131 2.1 29.3 1.0 OE1 H:GLU139 2.5 47.5 1.0 C C:GLU131 2.8 27.7 1.0 CA C:GLU131 2.9 29.2 1.0 CD2 H:HIS137 3.1 16.3 1.0 CE1 H:HIS137 3.1 15.1 1.0 CD H:GLU139 3.5 47.4 1.0 CG H:GLU139 4.0 45.2 1.0 CB C:GLU131 4.0 31.5 1.0 O H:HOH217 4.1 25.4 1.0 N C:ALA132 4.1 26.1 1.0 ND1 H:HIS137 4.2 17.4 1.0 CG H:HIS137 4.2 16.5 1.0 OE2 H:GLU139 4.6 47.5 1.0 CA C:ALA132 4.9 24.4 1.0 CB C:ALA132 5.0 22.4 1.0 CG C:GLU131 5.0 36.4 1.0

Copper binding site 9 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu210 b:59.4 occ:0.66 O C:HOH244 1.9 70.6 1.0 O G:HOH214 4.7 41.8 1.0

Copper binding site 10 out of 19 in the Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu215 b:24.7 occ:0.40 O D:HOH229 2.1 26.2 1.0 O G:TYR168 2.6 20.2 1.0 O D:TYR168 2.8 19.2 1.0 O G:HOH209 3.1 18.7 1.0 O G:HOH210 3.3 18.9 1.0 C G:TYR168 3.5 19.7 1.0 C D:TYR168 3.8 19.8 1.0 CA G:GLY169 4.0 18.7 1.0 N G:GLY169 4.1 19.8 1.0 CA D:GLY169 4.1 19.0 1.0 N D:GLY169 4.4 19.8 1.0 N G:TYR168 4.5 21.1 1.0 CA G:TYR168 4.7 19.2 1.0 OE1 G:GLU183 4.8 33.7 1.0 N D:TYR168 4.9 20.0 1.0 CA D:TYR168 5.0 18.9 1.0 O G:HOH192 5.0 16.8 1.0

G.K.Kong, J.J.Adams, H.H.Harris, J.F.Boas, C.C.Curtain, D.Galatis, C.L.Masters, K.J.Barnham, W.J.Mckinstry, R.Cappai, M.W.Parker. Structural Studies of the Alzheimer'S Amyloid Precursor Protein Copper-Binding Domain Reveal How It Binds Copper Ions J.Mol.Biol. V. 367 148 2007.
ISSN: ISSN 0022-2836
PubMed: 17239395
DOI: 10.1016/J.JMB.2006.12.041