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Cadmium in PDB 6ec0: Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10)

Protein crystallography data

The structure of Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10), PDB code: 6ec0 was solved by S.A.Eldirany, I.B.Lomakin, C.G.Bunick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.20 / 2.98
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.685, 106.685, 70.321, 90.00, 90.00, 120.00
R / Rfree (%) 28.1 / 30

Other elements in 6ec0:

The structure of Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Cobalt (Co) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) (pdb code 6ec0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10), PDB code: 6ec0:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 6ec0

Go back to Cadmium Binding Sites List in 6ec0
Cadmium binding site 1 out of 4 in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10)


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 the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:0.4
occ:1.00
HE1 B:HIS287 2.3 0.5 1.0
OE2 A:GLU322 2.6 89.5 1.0
CE1 B:HIS287 2.9 0.8 1.0
CD A:GLU322 3.5 91.4 1.0
NE2 B:HIS287 3.6 0.6 1.0
OE1 A:GLU322 3.7 93.1 1.0
ND1 B:HIS287 3.7 0.2 1.0
HD1 B:HIS287 3.9 0.6 1.0
HE1 A:TYR319 4.0 0.5 1.0
CD2 B:HIS287 4.7 0.5 1.0
CG B:HIS287 4.8 1.0 1.0
CE1 A:TYR319 4.8 90.4 1.0
CG A:GLU322 4.9 92.0 1.0

Cadmium binding site 2 out of 4 in 6ec0

Go back to Cadmium Binding Sites List in 6ec0
Cadmium binding site 2 out of 4 in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10)


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 the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:92.6
occ:1.00
OD2 A:ASP265 2.6 94.0 1.0
OD2 A:ASP261 2.7 0.3 1.0
CG A:ASP265 3.5 86.2 1.0
CG A:ASP261 3.8 1.0 1.0
OD1 A:ASP265 3.9 84.0 1.0
OD1 A:ASP261 4.3 0.7 1.0
HA A:MET262 4.5 0.6 1.0
HB2 A:ASP265 4.6 0.5 1.0
O A:ASP261 4.6 0.1 1.0
CB A:ASP265 4.6 86.3 1.0
C A:ASP261 4.9 0.4 1.0
HB3 A:ASP261 5.0 0.3 1.0
HB3 A:ASP265 5.0 0.5 1.0
CB A:ASP261 5.0 0.4 1.0

Cadmium binding site 3 out of 4 in 6ec0

Go back to Cadmium Binding Sites List in 6ec0
Cadmium binding site 3 out of 4 in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10)


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 the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:0.4
occ:1.00
HE2 A:MET225 2.4 1.0 1.0
O A:MET225 2.6 0.3 1.0
SD A:MET225 2.8 89.8 1.0
C A:MET225 2.9 0.6 1.0
HG2 A:MET225 2.9 0.9 1.0
CE A:MET225 3.0 91.7 1.0
N A:MET225 3.2 0.9 1.0
CG A:MET225 3.3 89.9 1.0
HA A:ASN226 3.3 0.7 1.0
HE1 A:MET225 3.3 1.0 1.0
CA A:MET225 3.4 0.7 1.0
N A:ASN226 3.5 0.5 1.0
CB A:MET225 3.8 89.9 1.0
HE3 A:MET225 3.8 1.0 1.0
OE2 A:GLU228 3.8 0.1 1.0
CA A:ASN226 3.9 0.6 1.0
HB2 A:MET225 4.0 0.9 1.0
H A:ASN226 4.1 0.8 1.0
HG3 A:MET225 4.2 0.9 1.0
OE1 A:GLU228 4.2 0.1 1.0
HA A:MET225 4.3 0.2 1.0
HB2 A:ASN226 4.4 0.3 1.0
HD12 A:LEU227 4.5 0.3 1.0
CD A:GLU228 4.5 0.2 1.0
H A:LEU227 4.5 0.9 1.0
HB3 A:MET225 4.6 0.9 1.0
HD22 A:ASN226 4.8 0.9 1.0
CB A:ASN226 4.8 0.9 1.0

Cadmium binding site 4 out of 4 in 6ec0

Go back to Cadmium Binding Sites List in 6ec0
Cadmium binding site 4 out of 4 in the Crystal Structure of the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10)


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 the Wild-Type Heterocomplex Between Coil 1B Domains of Human Intermediate Filament Proteins Keratin 1 (KRT1) and Keratin 10 (KRT10) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:0.0
occ:1.00
OE1 A:GLU283 2.8 0.5 1.0
OE2 B:GLU249 3.0 0.8 1.0
OE1 B:GLU249 3.0 0.6 1.0
CD B:GLU249 3.0 0.0 1.0
HD12 B:ILE252 3.7 0.7 1.0
HG3 B:GLU249 3.9 0.4 1.0
CD A:GLU283 4.0 0.6 1.0
CG B:GLU249 4.0 0.2 1.0
HG21 B:ILE252 4.2 0.8 1.0
HB2 B:GLU249 4.3 0.5 1.0
HD13 B:ILE252 4.5 0.7 1.0
HB2 A:GLU283 4.5 0.5 1.0
HA B:GLU249 4.5 0.5 1.0
HB3 A:GLU283 4.5 0.5 1.0
CD1 B:ILE252 4.5 97.2 1.0
HA A:ALA280 4.6 0.0 1.0
OE2 A:GLU283 4.7 0.3 1.0
CB B:GLU249 4.7 0.1 1.0
HB1 A:ALA280 4.8 0.4 1.0
HG2 B:GLU249 4.8 0.4 1.0
HB2 A:ALA280 4.9 0.4 1.0
CB A:GLU283 4.9 0.9 1.0
HH22 B:ARG245 4.9 0.8 1.0

Reference:

S.A.Eldirany, M.Ho, A.J.Hinbest, I.B.Lomakin, C.G.Bunick. Human Keratin 1/10-1B Tetramer Structures Reveal A Knob-Pocket Mechanism in Intermediate Filament Assembly. Embo J. V. 38 2019.
ISSN: ESSN 1460-2075
PubMed: 31036554
DOI: 10.15252/EMBJ.2018100741
Page generated: Sat Dec 12 08:28:16 2020

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