Calcium in PDB 4dyz: Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1

All present enzymatic activity of Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1:
1.16.3.1;

The structure of Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1, PDB code: 4dyz 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)	90.54 / 2.30
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.066, 181.066, 181.066, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.2

The structure of Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1 also contains other interesting chemical elements:

Copper

(Cu)

1 atom

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

Calcium binding site 1 out of 4 in the Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1


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 Apo Form of Human H-Ferritin Variant MIC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:23.9 occ:0.25 NE2 A:HIS173 3.1 21.4 1.0 CD2 A:LEU169 3.8 18.0 1.0 CE1 A:HIS173 3.9 22.0 1.0 CD2 A:HIS173 4.1 20.3 1.0 CD1 A:LEU169 4.7 18.8 1.0 CG A:LEU169 4.9 19.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1


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 Apo Form of Human H-Ferritin Variant MIC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:32.6 occ:1.00 O A:HOH390 2.2 39.0 1.0 OE1 A:GLN58 2.4 23.5 1.0 O A:HOH315 2.4 23.6 1.0 O A:HOH322 2.5 33.1 1.0 O A:HOH302 2.6 22.0 1.0 OE1 A:GLU61 2.6 26.7 1.0 CD A:GLU61 3.4 26.5 1.0 CD A:GLN58 3.6 20.8 1.0 OE2 A:GLU62 3.8 27.6 1.0 CG A:GLU61 3.9 24.0 1.0 OE1 A:GLU140 4.1 31.2 1.0 O A:HOH337 4.1 23.4 1.0 O A:HOH333 4.2 27.7 1.0 OE2 A:GLU61 4.3 26.9 1.0 O A:HOH336 4.4 24.6 1.0 CB A:ALA144 4.4 18.0 1.0 CG A:GLN58 4.5 20.0 1.0 CB A:GLN58 4.5 20.3 1.0 NE2 A:GLN58 4.5 20.7 1.0 CB A:GLU61 4.6 21.8 1.0 CA A:GLN58 4.6 20.3 1.0 OE2 A:GLU107 4.6 29.9 1.0 O A:HOH313 4.8 26.7 1.0 CD A:GLU62 4.8 25.8 1.0 O A:GLN58 4.9 19.9 1.0 CE1 A:HIS65 4.9 21.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1


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 Apo Form of Human H-Ferritin Variant MIC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:46.1 occ:0.33 OD1 A:ASP131 2.7 29.7 1.0 OE1 A:GLU134 2.8 32.6 1.0 O A:HOH362 3.2 31.1 0.3 O A:HOH344 3.3 53.1 0.3 CG A:ASP131 3.9 27.1 1.0 CD A:GLU134 4.0 32.0 1.0 CB A:ASP131 4.7 25.0 1.0 CB A:GLU134 4.7 26.7 1.0 OE2 A:GLU134 4.8 33.8 1.0 CA A:ASP131 4.9 24.6 1.0 OD2 A:ASP131 4.9 29.4 1.0 CG A:GLU134 4.9 29.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Apo Form of Human H-Ferritin Variant MIC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:40.5 occ:0.50 OD2 A:ASP84 2.5 30.7 1.0 O A:HOH356 2.9 37.6 1.0 OD1 A:ASP84 3.1 31.4 1.0 CG A:ASP84 3.2 30.6 1.0 O A:HOH381 4.5 47.3 0.5 CB A:ASP84 4.6 29.9 1.0 O A:HOH310 4.7 21.6 1.0

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