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

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium, PDB code: 3umh 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)	27.40 / 2.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	39.692, 39.692, 126.215, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium (pdb code 3umh). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium, PDB code: 3umh:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:36.4 occ:0.33 CD A:CD1 0.0 36.4 0.3 CD A:CD1 1.5 38.7 0.3 CD A:CD1 1.5 42.0 0.3 NE2 A:HIS432 2.0 28.8 0.5 NE2 A:HIS382 2.3 37.1 0.5 NE2 A:HIS436 2.3 39.7 1.0 CE1 A:HIS432 2.7 23.7 0.5 NE2 A:HIS382 2.7 40.7 0.5 CD2 A:HIS432 3.0 28.6 0.5 CD2 A:HIS382 3.1 40.7 0.5 CE1 A:HIS436 3.2 43.9 1.0 CE1 A:HIS382 3.2 34.8 0.5 CD2 A:HIS382 3.2 36.0 0.5 CD2 A:HIS436 3.3 39.7 1.0 ND1 A:HIS313 3.5 61.8 1.0 ND1 A:HIS432 3.6 26.7 0.5 ND1 A:HIS432 3.7 25.9 0.5 CE1 A:HIS382 3.9 38.4 0.5 CG A:HIS432 3.9 27.4 0.5 CE1 A:HIS432 3.9 22.4 0.5 O A:HOH745 4.1 50.6 1.0 CE1 A:HIS313 4.2 61.2 1.0 ND1 A:HIS382 4.3 33.9 0.5 ND1 A:HIS436 4.4 41.1 1.0 CG A:HIS382 4.4 36.0 0.5 CG A:HIS382 4.5 38.6 0.5 CG A:HIS436 4.5 39.8 1.0 CD2 A:PHE316 4.6 49.6 1.0 CE2 A:PHE316 4.7 51.9 1.0 CG A:HIS313 4.7 63.2 1.0 ND1 A:HIS382 4.8 37.8 0.5 CG A:HIS432 4.9 24.0 0.5

Cadmium binding site 2 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:42.0 occ:0.33 CD A:CD1 0.0 42.0 0.3 CD A:CD1 1.5 36.4 0.3 CD A:CD1 2.2 38.7 0.3 ND1 A:HIS313 2.3 61.8 1.0 NE2 A:HIS432 2.3 28.8 0.5 NE2 A:HIS382 2.3 40.7 0.5 NE2 A:HIS382 2.4 37.1 0.5 CE1 A:HIS382 2.8 34.8 0.5 O A:HOH745 3.2 50.6 1.0 CE1 A:HIS382 3.2 38.4 0.5 CE1 A:HIS313 3.3 61.2 1.0 CE1 A:HIS432 3.3 23.7 0.5 CD2 A:HIS432 3.3 28.6 0.5 CG A:HIS313 3.3 63.2 1.0 CD2 A:HIS382 3.4 40.7 0.5 CB A:HIS313 3.6 60.8 1.0 CD2 A:HIS382 3.7 36.0 0.5 NE2 A:HIS436 3.8 39.7 1.0 ND1 A:HIS382 4.1 33.9 0.5 ND1 A:HIS432 4.3 26.7 0.5 CD2 A:PHE316 4.3 49.6 1.0 ND1 A:HIS382 4.4 37.8 0.5 NE2 A:HIS313 4.4 65.4 1.0 ND1 A:HIS432 4.4 25.9 0.5 CD2 A:HIS313 4.4 64.4 1.0 CG A:HIS432 4.5 27.4 0.5 CG A:HIS382 4.5 38.6 0.5 CG A:HIS382 4.5 36.0 0.5 CA A:HIS313 4.6 60.4 1.0 CE1 A:HIS436 4.6 43.9 1.0 CE1 A:HIS432 4.7 22.4 0.5 CD2 A:HIS436 4.8 39.7 1.0 CG A:PHE316 4.8 46.3 1.0 CE2 A:PHE316 4.9 51.9 1.0 CB A:PHE316 4.9 48.5 1.0 CG2 A:VAL386 5.0 34.5 1.0

Cadmium binding site 3 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:38.7 occ:0.33 CD A:CD1 0.0 38.7 0.3 NE2 A:HIS432 0.7 28.8 0.5 CE1 A:HIS432 1.3 23.7 0.5 CD A:CD1 1.5 36.4 0.3 CD2 A:HIS432 1.9 28.6 0.5 CD A:CD1 2.2 42.0 0.3 ND1 A:HIS432 2.2 26.7 0.5 ND1 A:HIS432 2.3 25.9 0.5 CG A:HIS432 2.6 27.4 0.5 CE1 A:HIS432 2.6 22.4 0.5 NE2 A:HIS436 2.7 39.7 1.0 NE2 A:HIS382 2.7 37.1 0.5 NE2 A:HIS382 3.2 40.7 0.5 CD2 A:HIS436 3.2 39.7 1.0 ND1 A:HIS313 3.4 61.8 1.0 CE1 A:HIS382 3.4 34.8 0.5 CG A:HIS432 3.5 24.0 0.5 CE1 A:HIS313 3.6 61.2 1.0 CD2 A:HIS382 3.6 40.7 0.5 CD2 A:HIS382 3.7 36.0 0.5 CE1 A:HIS436 3.9 43.9 1.0 NE2 A:HIS432 3.9 31.1 0.5 CB A:HIS432 4.1 28.1 0.5 CE1 A:HIS382 4.2 38.4 0.5 CB A:HIS432 4.2 28.1 0.5 O A:HOH745 4.3 50.6 1.0 CD2 A:HIS432 4.4 25.6 0.5 CG A:HIS436 4.5 39.8 1.0 O A:HIS432 4.5 28.7 0.5 ND1 A:HIS382 4.5 33.9 0.5 CG2 A:VAL386 4.6 34.5 1.0 CA A:HIS432 4.7 27.6 0.5 CG A:HIS382 4.7 36.0 0.5 CA A:HIS432 4.7 28.1 0.5 O A:HIS432 4.8 28.4 0.5 CG A:HIS313 4.8 63.2 1.0 ND1 A:HIS436 4.8 41.1 1.0 CG A:HIS382 4.8 38.6 0.5 CG1 A:VAL386 4.8 36.0 1.0 SD A:MET383 4.9 44.1 1.0 NE2 A:HIS313 4.9 65.4 1.0 C A:HIS432 4.9 29.7 0.5

Cadmium binding site 4 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2 b:30.1 occ:0.50 CD A:CD2 0.0 30.1 0.5 CD A:CD2 1.8 33.6 0.5 OE1 A:GLU387 2.0 48.5 1.0 OD1 A:ASP429 2.2 30.7 1.0 CE1 A:HIS458 2.5 38.0 1.0 O A:HOH33 2.6 32.3 1.0 NE2 A:HIS458 2.6 36.6 1.0 CD A:GLU387 2.7 42.3 1.0 OE2 A:GLU387 2.9 42.2 1.0 CG A:ASP429 2.9 29.5 1.0 OD2 A:ASP429 3.0 31.6 1.0 OD1 A:ASN391 3.5 37.0 1.0 ND1 A:HIS458 3.8 34.7 1.0 CD2 A:HIS458 4.0 43.0 1.0 CG A:GLU387 4.2 39.6 1.0 O A:HOH703 4.2 41.4 1.0 CD1 A:ILE462 4.4 28.5 1.0 CB A:ASP429 4.4 29.2 1.0 CG A:HIS458 4.6 36.6 1.0 CG A:ASN391 4.6 43.9 1.0 CG1 A:ILE462 4.7 29.6 1.0 NH2 A:ARG465 4.8 30.4 1.0 NH2 A:ARG394 4.9 48.3 1.0 ND2 A:ASN391 5.0 47.7 1.0

Cadmium binding site 5 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2 b:33.6 occ:0.50 CD A:CD2 0.0 33.6 0.5 NE2 A:HIS458 1.8 36.6 1.0 CD A:CD2 1.8 30.1 0.5 OD2 A:ASP429 2.2 31.6 1.0 OE2 A:GLU387 2.3 42.2 1.0 CE1 A:HIS458 2.6 38.0 1.0 OE1 A:GLU387 2.7 48.5 1.0 CD A:GLU387 2.8 42.3 1.0 CG A:ASP429 2.9 29.5 1.0 CD2 A:HIS458 2.9 43.0 1.0 OD1 A:ASP429 3.0 30.7 1.0 OG1 A:THR433 3.7 32.3 1.0 ND1 A:HIS458 3.8 34.7 1.0 CG A:HIS458 3.9 36.6 1.0 CD1 A:ILE462 4.2 28.5 1.0 O A:HOH33 4.2 32.3 1.0 CG A:GLU387 4.3 39.6 1.0 CB A:ASP429 4.4 29.2 1.0 O A:ASP429 4.6 29.1 1.0 CA A:ASP429 4.9 27.9 1.0 CB A:GLU387 5.0 36.4 1.0 C A:ASP429 5.0 31.0 1.0 CB A:THR433 5.0 27.5 1.0

Cadmium binding site 6 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd3 b:39.4 occ:1.00 O A:HOH787 2.3 47.2 1.0 OD2 A:ASP444 2.3 28.5 1.0 OD1 A:ASP444 2.6 27.5 1.0 CG A:ASP444 2.8 27.0 1.0 CB A:LYS447 4.2 34.8 1.0 CB A:ASP444 4.3 32.5 1.0 O A:HOH711 4.4 40.5 1.0 NZ A:LYS447 4.4 51.9 1.0 N A:LYS447 4.5 33.2 1.0 CE A:LYS446 4.7 54.8 1.0 CA A:LYS447 4.8 33.0 1.0 CB A:LYS446 4.9 43.0 1.0 O A:HOH782 5.0 66.1 1.0

Cadmium binding site 7 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd4 b:42.0 occ:1.00 O A:HOH774 1.9 34.1 1.0 OXT A:ACT601 2.1 56.5 1.0 NE2 A:HIS439 2.2 40.0 1.0 O A:ACT601 2.4 58.2 1.0 C A:ACT601 2.6 59.3 1.0 CE1 A:HIS439 2.9 37.2 1.0 CD2 A:HIS439 3.3 36.5 1.0 CH3 A:ACT601 4.1 57.2 1.0 ND1 A:HIS439 4.1 38.1 1.0 CG A:HIS439 4.4 35.1 1.0 CG2 A:VAL443 4.8 36.1 1.0 O A:HOH762 4.8 38.8 1.0

Cadmium binding site 8 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd5 b:43.5 occ:0.93 NE2 A:HIS327 2.2 37.2 1.0 O A:HOH718 2.3 41.6 1.0 OE1 A:GLU368 2.4 36.7 1.0 OE2 A:GLU368 2.5 39.0 1.0 CD A:GLU368 2.8 34.5 1.0 CD2 A:HIS327 3.1 39.3 1.0 CE1 A:HIS327 3.2 40.4 1.0 O A:HOH777 3.3 32.8 1.0 O A:HOH710 4.2 33.9 1.0 CG A:HIS327 4.2 40.6 1.0 ND1 A:HIS327 4.2 35.2 1.0 CG A:GLU368 4.3 33.7 1.0 NH2 A:ARG375 4.4 45.2 1.0 CE A:MET331 5.0 51.2 1.0

Cadmium binding site 9 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd6 b:29.0 occ:1.00 O A:ACT602 2.0 34.4 1.0 OE1 A:GLU365 2.3 30.3 1.0 OE2 A:GLU362 2.4 31.6 1.0 OE1 A:GLU362 2.5 32.7 1.0 OXT A:ACT602 2.5 34.7 1.0 OE2 A:GLU365 2.6 23.3 1.0 C A:ACT602 2.6 35.6 1.0 CD A:GLU365 2.8 27.4 1.0 CD A:GLU362 2.8 34.9 1.0 CH3 A:ACT602 4.1 34.7 1.0 CG A:GLU365 4.3 23.8 1.0 CG A:GLU362 4.3 32.0 1.0 O A:HOH760 4.4 52.4 1.0 O A:HOH766 4.5 47.9 1.0 O A:HOH736 4.6 36.5 1.0 O A:HOH765 4.8 32.7 1.0 CB A:GLU365 4.8 26.8 1.0 O A:HOH708 4.9 23.9 1.0

Cadmium binding site 10 out of 12 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd7 b:57.2 occ:0.55 O A:HOH779 1.9 44.7 1.0 ND1 A:HIS359 2.1 48.4 1.0 O A:HOH778 2.1 68.2 1.0 CE1 A:HIS359 3.0 49.1 1.0 CG A:HIS359 3.2 42.7 1.0 CB A:HIS359 3.8 41.4 1.0 O A:HOH753 3.8 40.3 1.0 NE2 A:HIS359 4.2 50.8 1.0 CD2 A:HIS359 4.3 43.0 1.0 CA A:HIS359 4.4 36.5 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