Atomistry » Cadmium » PDB 8i77-8yr4 » 8kh2
Atomistry »
  Cadmium »
    PDB 8i77-8yr4 »
      8kh2 »

Cadmium in PDB 8kh2: Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).

Protein crystallography data

The structure of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42)., PDB code: 8kh2 was solved by B.Maity, J.Tian, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.69 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.935, 181.935, 181.935, 90, 90, 90
R / Rfree (%) 21.5 / 25.8

Other elements in 8kh2:

The structure of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). (pdb code 8kh2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42)., PDB code: 8kh2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 1 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:33.2
occ:0.30
O A:HOH522 2.4 31.5 1.0
OD1 A:ASP38 2.7 12.0 1.0
SG A:CYS48 2.8 13.7 1.0
CG A:ASP38 3.4 10.2 1.0
CB A:CYS48 3.6 10.0 1.0
CB A:ASP38 3.6 8.8 1.0
CA A:ASP38 4.2 8.8 1.0
O A:HOH528 4.3 38.5 1.0
OD2 A:ASP38 4.5 10.6 1.0
CG A:GLU45 4.5 26.4 1.0
CA A:GLU45 4.8 12.4 1.0
N A:ASP38 4.9 8.5 1.0
CB A:GLU45 4.9 18.1 1.0
O A:GLU45 4.9 9.1 1.0

Cadmium binding site 2 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 2 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:28.1
occ:0.20
OE1 A:GLU56 2.1 39.5 1.0
OE2 A:GLU53 2.3 68.7 1.0
OE1 A:GLU53 2.9 65.1 1.0
CD A:GLU53 3.0 49.6 1.0
CD A:GLU56 3.2 33.0 1.0
OE2 A:GLU56 3.5 39.2 1.0
CG A:GLU53 4.5 30.1 1.0
CG A:GLU56 4.6 25.9 1.0
CD A:CD308 4.7 25.4 0.2
O A:HOH436 4.9 38.6 1.0

Cadmium binding site 3 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 3 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:36.4
occ:0.17
OE1 A:GLU130 2.2 33.5 1.0
CD A:CD306 2.4 38.4 0.2
CD A:GLU130 3.2 20.4 1.0
OE2 A:GLU130 3.5 19.0 1.0
CD A:CD304 4.4 40.5 0.1
CG A:GLU130 4.6 19.5 1.0
CB A:GLU130 5.0 20.0 1.0

Cadmium binding site 4 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 4 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:40.5
occ:0.12
OD1 A:ASP127 3.4 21.3 1.0
OE1 A:GLU130 4.3 33.5 1.0
CD A:CD303 4.4 36.4 0.2
OG A:SER131 4.4 30.0 1.0
CG A:ASP127 4.6 18.6 1.0

Cadmium binding site 5 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 5 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:21.3
occ:0.50
OD2 A:ASP80 2.0 11.3 1.0
OD1 A:ASP80 2.6 12.5 1.0
CG A:ASP80 2.7 13.8 1.0
CL A:CL313 2.7 36.7 1.0
CB A:ASP80 4.2 14.4 1.0
O A:HOH467 4.3 18.3 1.0
O A:HOH488 4.5 20.1 1.0

Cadmium binding site 6 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 6 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:38.4
occ:0.20
CD A:CD303 2.4 36.4 0.2
OE2 A:GLU130 3.0 19.0 1.0
OE1 A:GLU130 3.3 33.5 1.0
CD A:GLU130 3.5 20.4 1.0
CG A:GLU130 4.9 19.5 1.0

Cadmium binding site 7 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 7 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:13.8
occ:0.20
O A:HOH475 2.1 28.1 1.0
NE2 A:HIS132 2.2 27.0 1.0
O A:HOH538 2.5 40.5 1.0
CE1 A:HIS132 2.8 29.2 1.0
CD2 A:HIS132 3.5 24.2 1.0
ND1 A:HIS132 4.1 26.8 1.0
CG A:HIS132 4.4 20.3 1.0
NH2 A:ARG64 4.8 44.6 1.0

Cadmium binding site 8 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 8 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:25.4
occ:0.20
CD A:CD309 2.2 31.9 0.2
OE2 A:GLU60 2.2 35.8 1.0
OE2 A:GLU56 2.7 39.2 1.0
OE1 A:GLU60 2.8 31.5 1.0
CD A:GLU60 2.8 29.0 1.0
CD A:GLU56 3.1 33.0 1.0
CG A:GLU56 3.6 25.9 1.0
OE1 A:GLU56 3.6 39.5 1.0
CG A:GLU60 4.3 21.1 1.0
CD A:CD302 4.7 28.1 0.2
O A:HOH436 5.0 38.6 1.0
CB A:GLU56 5.0 16.6 1.0

Cadmium binding site 9 out of 9 in 8kh2

Go back to Cadmium Binding Sites List in 8kh2
Cadmium binding site 9 out of 9 in the Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42).


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Horse-Spleen L-Ferritin Fused with Amyloid Beta Peptide (1-42). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:31.9
occ:0.20
CD A:CD308 2.2 25.4 0.2
OE1 A:GLU60 2.4 31.5 1.0
CD A:GLU60 3.3 29.0 1.0
OE2 A:GLU60 3.5 35.8 1.0
O A:HOH436 4.2 38.6 1.0
CG A:GLU57 4.6 32.7 1.0
CG A:GLU60 4.7 21.1 1.0
CD A:GLU56 4.8 33.0 1.0
OE2 A:GLU56 4.8 39.2 1.0
CG A:GLU56 4.9 25.9 1.0

Reference:

B.Maity, S.Kameyama, J.Tian, T.T.Pham, S.Abe, E.Chatani, K.Murata, T.Ueno. Fusion of Amyloid Beta with Ferritin Yields An Isolated Oligomeric Beta-Sheet-Rich Aggregate Inside the Ferritin Cage. Biomater Sci 2024.
ISSN: ISSN 2047-4849
PubMed: 38511491
DOI: 10.1039/D4BM00173G
Page generated: Fri Jul 19 20:34:59 2024

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy