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Copper in PDB 4dyx: Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star

Enzymatic activity of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star

All present enzymatic activity of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star, PDB code: 4dyx was solved by F.A.Tezcan, D.J.E.Huard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.78 / 1.85
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 179.268, 179.268, 179.268, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.7

Other elements in 4dyx:

The structure of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star (pdb code 4dyx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star, PDB code: 4dyx:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 4dyx

Go back to Copper Binding Sites List in 4dyx
Copper binding site 1 out of 4 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:20.4
occ:1.00
 NE2 A:HIS63 2.1 17.3 1.0
NE2 A:HIS67 2.1 16.7 1.0
CD2 A:HIS63 3.0 16.5 1.0
CD2 A:HIS67 3.1 16.1 1.0
CE1 A:HIS63 3.1 16.9 1.0
CE1 A:HIS67 3.1 16.9 1.0
CG A:HIS63 4.2 15.5 1.0
ND1 A:HIS63 4.2 16.9 1.0
ND1 A:HIS67 4.2 16.0 1.0
CG A:HIS67 4.2 14.8 1.0

Copper binding site 2 out of 4 in 4dyx

Go back to Copper Binding Sites List in 4dyx
Copper binding site 2 out of 4 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:19.0
occ:0.25
 NE2 A:HIS173 2.2 17.6 1.0
O A:HOH456 2.6 34.3 0.2
O A:HOH502 2.7 30.3 0.2
CE1 A:HIS173 3.1 17.9 1.0
CD2 A:HIS173 3.2 17.1 1.0
ND1 A:HIS173 4.2 17.4 1.0
CG A:HIS173 4.3 16.2 1.0
O A:HOH497 4.9 45.2 1.0

Copper binding site 3 out of 4 in 4dyx

Go back to Copper Binding Sites List in 4dyx
Copper binding site 3 out of 4 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:14.1
occ:1.00
 O A:HOH399 1.9 18.7 1.0
OE1 A:GLU27 2.0 13.3 1.0
OE1 A:GLU62 2.1 15.1 1.0
ND1 A:HIS65 2.2 15.2 1.0
O A:HOH341 2.3 14.7 1.0
CD A:GLU27 3.0 13.5 1.0
CE1 A:HIS65 3.1 16.2 1.0
CD A:GLU62 3.2 15.0 1.0
CG A:HIS65 3.2 14.1 1.0
OE2 A:GLU27 3.4 13.4 1.0
CU A:CU204 3.4 18.5 1.0
CB A:HIS65 3.5 13.6 1.0
OE2 A:GLU62 3.6 16.3 1.0
OE1 A:GLN141 3.8 18.0 1.0
NE2 A:HIS65 4.2 16.1 1.0
CD2 A:HIS65 4.3 15.5 1.0
CG1 A:VAL110 4.3 14.0 1.0
CG A:GLU27 4.4 12.6 1.0
O A:HOH355 4.4 19.9 1.0
CG A:GLU62 4.5 13.9 1.0
CA A:GLU62 4.5 13.6 1.0
CB A:GLU62 4.7 13.6 1.0
CB A:GLU27 4.7 12.6 1.0
CD A:GLN141 4.9 16.3 1.0
OE1 A:GLU107 5.0 14.7 1.0
CA A:GLU27 5.0 12.3 1.0

Copper binding site 4 out of 4 in 4dyx

Go back to Copper Binding Sites List in 4dyx
Copper binding site 4 out of 4 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant 4HIS- Delta C-Star within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu204

b:18.5
occ:1.00
 OE2 A:GLU62 1.9 16.3 1.0
O A:HOH399 2.0 18.7 1.0
O A:HOH355 2.0 19.9 1.0
OE2 A:GLU107 2.1 16.5 1.0
OE1 A:GLU107 2.3 14.7 1.0
CD A:GLU107 2.5 15.2 1.0
CD A:GLU62 2.9 15.0 1.0
OE1 A:GLU62 3.2 15.1 1.0
CU A:CU203 3.4 14.1 1.0
CG A:GLU107 4.0 14.7 1.0
OE1 A:GLN141 4.0 18.0 1.0
O A:HOH431 4.1 38.4 1.0
CG A:GLU62 4.2 13.9 1.0
CE1 A:HIS65 4.3 16.2 1.0
ND1 A:HIS65 4.4 15.2 1.0
NE2 A:GLN141 4.4 16.2 1.0
CE2 A:TYR34 4.5 13.2 1.0
O A:HOH455 4.5 38.5 1.0
CD A:GLN141 4.6 16.3 1.0
OH A:TYR34 4.6 14.7 1.0
O A:HOH341 4.7 14.7 1.0
CB A:ALA144 4.9 12.3 1.0
CB A:GLU107 4.9 14.7 1.0

Reference:

D.J.Huard, K.M.Kane, F.A.Tezcan. Re-Engineering Protein Interfaces Yields Copper-Inducible Ferritin Cage Assembly. Nat.Chem.Biol. V. 9 169 2013.
ISSN: ISSN 1552-4450
PubMed: 23340339
DOI: 10.1038/NCHEMBIO.1163
Page generated: Wed Jul 31 02:43:51 2024

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