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

Protein crystallography data

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc, PDB code: 3umi 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) 27.44 / 2.40
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 39.757, 39.757, 126.425, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.5

Other elements in 3umi:

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

Zinc (Zn) 1 atom

Cadmium 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 Zinc (pdb code 3umi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 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 Zinc, PDB code: 3umi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3umi

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Cadmium binding site 1 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:43.2
occ:0.50
 CD A:CD2 0.0 43.2 0.5
CD A:CD2 1.4 39.5 0.4
OD1 A:ASP429 2.2 35.6 1.0
OE1 A:GLU387 2.3 45.6 1.0
NE2 A:HIS458 2.4 30.7 1.0
O A:HOH33 2.4 29.4 1.0
CE1 A:HIS458 3.1 33.0 1.0
CG A:ASP429 3.1 31.0 1.0
CD A:GLU387 3.2 40.9 1.0
OD2 A:ASP429 3.3 33.9 1.0
OE2 A:GLU387 3.4 40.3 1.0
OD1 A:ASN391 3.4 34.8 1.0
CD2 A:HIS458 3.6 33.6 1.0
O A:HOH701 4.0 41.1 1.0
CD1 A:ILE462 4.3 19.0 1.0
ND1 A:HIS458 4.3 35.0 1.0
CG A:ASN391 4.4 31.5 1.0
CG1 A:ILE462 4.5 22.3 1.0
CB A:ASP429 4.5 29.9 1.0
NH2 A:ARG465 4.5 23.7 1.0
CG A:GLU387 4.6 37.8 1.0
CG A:HIS458 4.6 32.2 1.0
ND2 A:ASN391 4.8 29.2 1.0

Cadmium binding site 2 out of 9 in 3umi

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Cadmium binding site 2 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:39.5
occ:0.37
 CD A:CD2 0.0 39.5 0.4
CD A:CD2 1.4 43.2 0.5
NE2 A:HIS458 2.1 30.7 1.0
CE1 A:HIS458 2.2 33.0 1.0
OD1 A:ASP429 2.4 35.6 1.0
OD2 A:ASP429 2.4 33.9 1.0
OE1 A:GLU387 2.4 45.6 1.0
OE2 A:GLU387 2.6 40.3 1.0
CG A:ASP429 2.7 31.0 1.0
CD A:GLU387 2.9 40.9 1.0
CD2 A:HIS458 3.5 33.6 1.0
ND1 A:HIS458 3.5 35.0 1.0
O A:HOH33 3.6 29.4 1.0
CG A:HIS458 4.1 32.2 1.0
CD1 A:ILE462 4.1 19.0 1.0
CB A:ASP429 4.2 29.9 1.0
OG1 A:THR433 4.2 27.7 1.0
CG A:GLU387 4.4 37.8 1.0
OD1 A:ASN391 4.4 34.8 1.0
O A:HOH774 4.7 51.8 1.0
CG1 A:ILE462 4.8 22.3 1.0
O A:HOH701 4.9 41.1 1.0
O A:ASP429 4.9 26.2 1.0

Cadmium binding site 3 out of 9 in 3umi

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Cadmium binding site 3 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3

b:34.8
occ:1.00
 OD2 A:ASP444 2.2 35.0 1.0
O A:HOH732 2.5 29.9 1.0
OD1 A:ASP444 2.8 25.9 1.0
CG A:ASP444 2.9 29.5 1.0
CB A:LYS447 4.3 25.3 1.0
CB A:ASP444 4.3 28.7 1.0
O A:HOH736 4.4 37.5 1.0
NZ A:LYS447 4.6 37.3 1.0
N A:LYS447 4.6 27.8 1.0
O A:HOH710 4.6 30.3 1.0
O A:HOH758 4.8 69.9 1.0
CA A:LYS447 4.9 25.3 1.0
CB A:LYS446 5.0 32.7 1.0

Cadmium binding site 4 out of 9 in 3umi

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Cadmium binding site 4 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd4

b:35.6
occ:0.75
 NE2 A:HIS439 2.2 30.2 1.0
CE1 A:HIS439 3.1 27.7 1.0
CD2 A:HIS439 3.3 25.8 1.0
ND1 A:HIS439 4.3 30.8 1.0
CG A:HIS439 4.4 27.5 1.0
CG2 A:VAL443 4.9 32.4 1.0

Cadmium binding site 5 out of 9 in 3umi

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Cadmium binding site 5 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5

b:45.1
occ:0.67
 NE2 A:HIS327 2.1 27.1 1.0
O A:HOH711 2.1 40.0 1.0
OE2 A:GLU368 2.3 41.0 1.0
OE1 A:GLU368 2.4 33.1 1.0
CD A:GLU368 2.7 34.3 1.0
CE1 A:HIS327 3.0 27.4 1.0
CD2 A:HIS327 3.1 23.4 1.0
ND1 A:HIS327 4.1 24.9 1.0
CE A:MET331 4.2 46.2 1.0
CG A:HIS327 4.2 28.1 1.0
CG A:GLU368 4.2 32.0 1.0
O A:HOH716 4.3 38.8 1.0
NH2 A:ARG375 4.8 36.8 1.0

Cadmium binding site 6 out of 9 in 3umi

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Cadmium binding site 6 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd6

b:27.7
occ:1.00
 O A:ACT601 2.2 34.6 1.0
OE1 A:GLU365 2.3 30.3 1.0
OE1 A:GLU362 2.5 23.3 1.0
OXT A:ACT601 2.5 34.6 1.0
C A:ACT601 2.7 34.8 1.0
OE2 A:GLU362 2.8 31.4 1.0
OE2 A:GLU365 2.8 28.2 1.0
CD A:GLU365 2.9 29.2 1.0
CD A:GLU362 3.0 24.3 1.0
CH3 A:ACT601 4.2 27.5 1.0
O A:HOH760 4.2 44.6 1.0
CG A:GLU365 4.4 24.4 1.0
CG A:GLU362 4.5 22.5 1.0
O A:HOH767 4.6 44.6 1.0
CB A:GLU365 4.9 26.8 1.0

Cadmium binding site 7 out of 9 in 3umi

Go back to Cadmium Binding Sites List in 3umi
Cadmium binding site 7 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd7

b:50.2
occ:0.63
 OD1 A:ASP488 2.2 48.7 1.0
CG A:ASP488 2.9 42.7 1.0
OD2 A:ASP488 2.9 43.5 1.0
OE1 A:GLN484 3.4 50.1 1.0
CD A:GLN484 3.8 48.1 1.0
CG A:GLN484 4.0 40.2 1.0
CB A:ASP488 4.3 34.5 1.0
NE2 A:GLN484 4.6 47.6 1.0
O A:GLN484 4.9 27.1 1.0

Cadmium binding site 8 out of 9 in 3umi

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Cadmium binding site 8 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd8

b:46.6
occ:0.28
 ND1 A:HIS359 2.0 37.6 1.0
CE1 A:HIS359 2.7 38.4 1.0
CG A:HIS359 3.2 34.2 1.0
CB A:HIS359 3.8 28.5 1.0
O A:HOH771 3.9 41.9 1.0
NE2 A:HIS359 3.9 37.4 1.0
CD2 A:HIS359 4.2 37.3 1.0
CA A:HIS359 4.4 28.5 1.0

Cadmium binding site 9 out of 9 in 3umi

Go back to Cadmium Binding Sites List in 3umi
Cadmium binding site 9 out of 9 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd9

b:46.0
occ:0.35
 OE2 A:GLU321 2.2 59.2 1.0
OE2 A:GLU324 2.8 36.0 0.0
CD A:GLU321 3.3 55.8 1.0
OE1 A:GLU321 3.6 59.6 1.0
CD A:GLU324 3.7 35.7 0.0
OE1 A:GLU324 3.9 36.0 0.0
CG A:GLU321 4.6 45.4 1.0

Reference:

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
Page generated: Sun Jan 24 09:56:05 2021

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