Copper in PDB 3umk: X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper, PDB code: 3umk was solved by S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 2.60
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	39.760, 39.760, 126.420, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.9

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper also contains other interesting chemical elements:

Cadmium

(Cd)

8 atoms

The binding sites of Copper atom in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper (pdb code 3umk). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper, PDB code: 3umk:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1 b:48.3 occ:0.68 NE2 A:HIS432 1.9 39.2 1.0 NE2 A:HIS313 2.0 60.0 1.0 NE2 A:HIS382 2.0 42.4 1.0 NE2 A:HIS436 2.1 40.6 1.0 CD2 A:HIS432 2.9 40.0 1.0 CE1 A:HIS313 2.9 63.7 1.0 CE1 A:HIS432 2.9 32.8 1.0 CE1 A:HIS382 3.0 39.1 1.0 CE1 A:HIS436 3.0 40.1 1.0 CD2 A:HIS313 3.0 61.0 1.0 CD2 A:HIS382 3.0 39.8 1.0 CD2 A:HIS436 3.1 37.3 1.0 ND1 A:HIS432 4.0 36.4 1.0 CG A:HIS432 4.0 33.8 1.0 ND1 A:HIS313 4.0 62.3 1.0 ND1 A:HIS382 4.1 39.3 1.0 CG A:HIS313 4.1 63.0 1.0 ND1 A:HIS436 4.1 37.9 1.0 CG A:HIS382 4.1 39.7 1.0 CG A:HIS436 4.2 33.2 1.0 CG2 A:VAL386 4.7 35.2 1.0 CD2 A:PHE316 4.9 44.1 1.0 SD A:MET383 5.0 43.3 1.0

Copper binding site 2 out of 2 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu5 b:37.2 occ:0.66 NE2 A:HIS327 2.0 34.6 1.0 O A:HOH713 2.3 38.6 1.0 OE2 A:GLU368 2.4 37.9 1.0 OE1 A:GLU368 2.7 39.4 1.0 CD A:GLU368 2.9 37.7 1.0 CD2 A:HIS327 3.0 31.5 1.0 CE1 A:HIS327 3.1 31.1 1.0 CE A:MET331 3.9 48.1 1.0 CG A:HIS327 4.1 32.3 1.0 ND1 A:HIS327 4.2 30.2 1.0 CG A:GLU368 4.4 34.1 1.0 O A:HOH718 4.5 41.7 1.0 CG A:MET331 4.8 46.9 1.0 SD A:MET331 4.9 50.9 1.0

S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.C.Mayer, D.Kaden, G.Multhaup, M.E.Than. Metal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (App) E2 Domain. J.Mol.Biol. V. 416 438 2012.
ISSN: ISSN 0022-2836
PubMed: 22245578
DOI: 10.1016/J.JMB.2011.12.057