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Calcium in PDB 2z6m: Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis

Enzymatic activity of Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis

All present enzymatic activity of Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis, PDB code: 2z6m was solved by L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.72
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.294, 171.294, 190.455, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.2

Other elements in 2z6m:

The structure of Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis (pdb code 2z6m). 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 Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis, PDB code: 2z6m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2z6m

Go back to Calcium Binding Sites List in 2z6m
Calcium binding site 1 out of 4 in the Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis


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 Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca812

b:60.4
occ:1.00
 OE1 A:GLU134 2.4 54.9 1.0
OE2 E:GLU134 2.5 50.0 1.0
OE1 C:GLU134 2.7 48.2 1.0
OD1 E:ASP131 2.8 46.3 1.0
OD1 C:ASP131 2.8 48.4 1.0
OD1 A:ASP131 3.0 49.8 1.0
O E:HOH656 3.1 29.8 1.0
CD A:GLU134 3.7 54.7 1.0
CD E:GLU134 3.8 48.5 1.0
CD C:GLU134 3.8 46.8 1.0
CG C:ASP131 4.0 47.5 1.0
CG E:ASP131 4.0 44.1 1.0
CG A:ASP131 4.1 48.3 1.0
OE2 A:GLU134 4.5 54.9 1.0
OE1 E:GLU134 4.5 49.7 1.0
OE2 C:GLU134 4.5 47.1 1.0
CB C:ASP131 4.6 44.3 1.0
CB A:GLU134 4.6 51.5 1.0
CB E:GLU134 4.6 45.0 1.0
OG1 A:THR135 4.6 54.1 1.0
CG A:GLU134 4.7 52.3 1.0
CB C:GLU134 4.7 44.6 1.0
CB A:ASP131 4.8 46.4 1.0
CA C:ASP131 4.8 41.8 1.0
CB E:ASP131 4.8 41.5 1.0
CG C:GLU134 4.8 44.7 1.0
CG E:GLU134 4.8 47.4 1.0
CA E:ASP131 4.9 39.2 1.0
OD2 E:ASP131 4.9 45.1 1.0
CA A:ASP131 4.9 44.8 1.0

Calcium binding site 2 out of 4 in 2z6m

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Calcium binding site 2 out of 4 in the Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis


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 Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca813

b:59.5
occ:1.00
 OD1 F:ASP131 2.5 44.7 1.0
OE1 D:GLU134 2.6 54.1 1.0
OE1 F:GLU134 2.7 55.3 1.0
OD1 D:ASP131 2.9 46.9 1.0
OE1 B:GLU134 3.1 47.1 1.0
OD1 B:ASP131 3.1 48.4 1.0
O D:HOH185 3.5 44.1 1.0
O B:HOH816 3.7 45.2 1.0
CD F:GLU134 3.7 54.6 1.0
CG F:ASP131 3.7 44.7 1.0
CD D:GLU134 3.8 52.8 1.0
CD B:GLU134 4.0 48.0 1.0
CG B:ASP131 4.2 46.9 1.0
CG D:ASP131 4.2 45.8 1.0
OE2 F:GLU134 4.3 54.8 1.0
CB F:GLU134 4.4 50.9 1.0
CB F:ASP131 4.4 42.0 1.0
OE2 B:GLU134 4.5 50.4 1.0
OE2 D:GLU134 4.6 53.9 1.0
CA F:ASP131 4.6 40.4 1.0
CB D:GLU134 4.6 49.4 1.0
CG F:GLU134 4.7 53.4 1.0
OG1 F:THR135 4.7 50.1 1.0
OD2 F:ASP131 4.7 45.5 1.0
CG D:GLU134 4.7 51.0 1.0
CB B:ASP131 4.8 44.3 1.0
OD2 D:ASP131 4.9 47.2 1.0
CB B:GLU134 5.0 45.6 1.0

Calcium binding site 3 out of 4 in 2z6m

Go back to Calcium Binding Sites List in 2z6m
Calcium binding site 3 out of 4 in the Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis


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 Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca814

b:48.8
occ:1.00
 OE2 K:GLU134 2.5 49.3 1.0
OE1 G:GLU134 2.6 55.7 1.0
OD1 K:ASP131 2.7 45.6 1.0
OD1 G:ASP131 2.8 49.4 1.0
OE1 I:GLU134 2.8 47.5 1.0
OD1 I:ASP131 2.9 45.3 1.0
O I:HOH718 3.0 46.3 1.0
CD K:GLU134 3.8 48.4 1.0
CD G:GLU134 3.8 54.7 1.0
CG K:ASP131 4.0 43.5 1.0
CD I:GLU134 4.0 47.6 1.0
CG G:ASP131 4.0 48.9 1.0
CG I:ASP131 4.0 45.1 1.0
OG1 G:THR135 4.5 54.5 1.0
CB K:GLU134 4.5 44.7 1.0
OE1 K:GLU134 4.6 48.6 1.0
OE2 G:GLU134 4.6 54.9 1.0
CB G:GLU134 4.6 52.3 1.0
CB I:ASP131 4.7 43.3 1.0
CB G:ASP131 4.7 45.5 1.0
OE2 I:GLU134 4.7 49.2 1.0
CG G:GLU134 4.8 53.3 1.0
CB I:GLU134 4.8 46.5 1.0
CG K:GLU134 4.8 47.1 1.0
CB K:ASP131 4.8 39.9 1.0
OG1 K:THR135 4.8 46.8 1.0
CA K:ASP131 4.9 37.5 1.0
OD2 K:ASP131 4.9 44.3 1.0
CA G:ASP131 4.9 43.4 1.0
CA I:ASP131 4.9 43.4 1.0
OD2 G:ASP131 4.9 49.7 1.0
OG1 I:THR135 5.0 50.3 1.0
CG I:GLU134 5.0 47.1 1.0

Calcium binding site 4 out of 4 in 2z6m

Go back to Calcium Binding Sites List in 2z6m
Calcium binding site 4 out of 4 in the Crystal Structure of Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis


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 Human Ferritin H8 As Biotemplate For Noble Metal Nanoparticle Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca811

b:65.9
occ:1.00
 OE1 J:GLU134 2.4 56.6 1.0
OD1 J:ASP131 2.7 46.0 1.0
OD1 L:ASP131 2.7 47.8 1.0
OE1 L:GLU134 2.8 57.0 1.0
OE1 H:GLU134 2.8 51.9 1.0
O J:HOH194 2.9 22.1 1.0
OD1 H:ASP131 3.3 48.0 1.0
CD J:GLU134 3.6 55.0 1.0
CD H:GLU134 3.8 50.2 1.0
CD L:GLU134 3.8 55.6 1.0
CG J:ASP131 3.9 45.5 1.0
CG L:ASP131 3.9 46.2 1.0
OE2 H:GLU134 4.2 50.5 1.0
OE2 J:GLU134 4.3 55.1 1.0
CG H:ASP131 4.4 46.5 1.0
OE2 L:GLU134 4.4 56.1 1.0
CB J:GLU134 4.5 50.0 1.0
CG J:GLU134 4.6 52.9 1.0
CB L:ASP131 4.6 43.5 1.0
CB L:GLU134 4.7 51.3 1.0
OD2 J:ASP131 4.7 46.3 1.0
CB H:GLU134 4.7 46.5 1.0
CA L:ASP131 4.8 42.4 1.0
CB J:ASP131 4.8 43.9 1.0
CG H:GLU134 4.9 48.2 1.0
OD2 L:ASP131 4.9 46.7 1.0
CG L:GLU134 4.9 53.6 1.0
CB H:ASP131 4.9 44.2 1.0
CA J:ASP131 5.0 42.3 1.0
OG1 L:THR135 5.0 50.7 1.0

Reference:

C.A.Butts, J.Swift, S.G.Kang, L.Di Costanzo, D.W.Christianson, J.G.Saven, I.J.Dmochowski. Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein Biochemistry V. 47 12729 2008.
ISSN: ISSN 0006-2960
PubMed: 18991401
DOI: 10.1021/BI8016735
Page generated: Fri Jul 12 19:49:41 2024

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