Atomistry » Calcium » PDB 2yi1-2z8s » 2z6m
Atomistry »
  Calcium »
    PDB 2yi1-2z8s »
      2z6m »

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

Go back to Calcium Binding Sites List in 2z6m
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy