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Calcium in PDB 4dz0: Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore

Enzymatic activity of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore

All present enzymatic activity of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore, PDB code: 4dz0 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) 36.84 / 2.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.434, 180.434, 180.434, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 30

Other elements in 4dz0:

The structure of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore also contains other interesting chemical elements:

Copper (Cu) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore (pdb code 4dz0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore, PDB code: 4dz0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4dz0

Go back to Calcium Binding Sites List in 4dz0
Calcium binding site 1 out of 3 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:53.3
occ:0.33
 OD1 A:ASP131 2.5 41.4 1.0
OE1 A:GLU134 2.6 42.0 1.0
O A:HOH339 2.8 46.9 0.3
O A:HOH301 3.1 44.4 0.3
CG A:ASP131 3.7 39.5 1.0
CD A:GLU134 3.9 40.6 1.0
CB A:ASP131 4.5 37.9 1.0
OE2 A:GLU134 4.5 42.5 1.0
OD2 A:ASP131 4.7 40.7 1.0
CB A:GLU134 4.7 36.4 1.0
CA A:ASP131 4.7 37.6 1.0
CG A:GLU134 4.9 37.9 1.0

Calcium binding site 2 out of 3 in 4dz0

Go back to Calcium Binding Sites List in 4dz0
Calcium binding site 2 out of 3 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:56.4
occ:0.50
 OD2 A:ASP84 2.4 47.4 1.0
CG A:ASP84 3.1 46.9 1.0
OD1 A:ASP84 3.2 47.9 1.0
O A:HOH310 4.5 23.7 0.2
CB A:ASP84 4.6 46.1 1.0

Calcium binding site 3 out of 3 in 4dz0

Go back to Calcium Binding Sites List in 4dz0
Calcium binding site 3 out of 3 in the Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Cu-Adduct of Human H-Ferritin Variant MIC1 Labeled with A Dansyl Fluorophore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:63.1
occ:1.00
 OE1 A:GLN58 2.7 36.7 1.0
OE1 A:GLU61 2.8 41.6 1.0
O A:HOH319 2.8 55.4 1.0
OE2 A:GLU62 2.9 37.0 1.0
O A:HOH305 2.9 41.0 1.0
OE2 A:GLU107 3.2 43.6 1.0
CD A:GLU61 3.6 40.2 1.0
CD A:GLN58 3.9 35.5 1.0
CD A:GLU62 4.1 35.6 1.0
OE2 A:GLU61 4.1 42.0 1.0
CD A:GLU107 4.1 42.8 1.0
CB A:ALA144 4.3 29.4 1.0
O A:HOH343 4.4 53.5 1.0
OE1 A:GLU107 4.5 43.5 1.0
CB A:GLU61 4.5 33.8 1.0
OH A:TYR34 4.6 33.6 1.0
CB A:GLN58 4.6 32.9 1.0
CG A:GLN58 4.6 33.3 1.0
CE2 A:TYR34 4.6 33.3 1.0
CE1 A:HIS65 4.7 35.5 1.0
CG A:GLU61 4.7 36.6 1.0
O A:GLN58 4.7 32.0 1.0
CG A:GLU62 4.7 34.1 1.0
CA A:GLN58 4.8 32.9 1.0
CZ A:TYR34 4.9 33.3 1.0
NE2 A:GLN58 5.0 35.6 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: Tue Jul 8 19:38:44 2025

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