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Calcium in PDB 1z6o: Crystal Structure of Trichoplusia Ni Secreted Ferritin

Protein crystallography data

The structure of Crystal Structure of Trichoplusia Ni Secreted Ferritin, PDB code: 1z6o was solved by A.E.Hamburger, A.P.West Jr., Z.A.Hamburger, P.Hamburger, P.J.Bjorkman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 1.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 206.880, 145.697, 209.158, 90.00, 94.93, 90.00
R / Rfree (%) 18.9 / 19.4

Other elements in 1z6o:

The structure of Crystal Structure of Trichoplusia Ni Secreted Ferritin also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trichoplusia Ni Secreted Ferritin (pdb code 1z6o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Trichoplusia Ni Secreted Ferritin, PDB code: 1z6o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1z6o

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Calcium binding site 1 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


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 Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5302

b:18.5
occ:1.00
 OE1 A:GLU164 2.3 20.1 1.0
OE1 L:GLU164 2.3 20.1 1.0
OE1 L:GLN161 2.4 28.4 1.0
OE1 E:GLU164 2.5 20.1 1.0
OE1 A:GLN161 2.5 28.4 1.0
OE1 E:GLN161 2.6 28.4 1.0
CD A:GLU164 3.5 23.2 1.0
CD L:GLU164 3.5 23.2 1.0
CD L:GLN161 3.5 37.9 1.0
CD E:GLN161 3.7 37.9 1.0
CD A:GLN161 3.7 37.9 1.0
CD E:GLU164 3.7 23.2 1.0
O L:HOH213 3.7 20.5 1.0
NE2 L:GLN161 4.2 32.5 1.0
OE2 A:GLU164 4.2 22.1 1.0
NE2 E:GLN161 4.3 32.5 1.0
OE2 L:GLU164 4.3 22.1 1.0
NE2 A:GLN161 4.3 32.5 1.0
CB L:GLU164 4.4 16.8 1.0
CB A:GLU164 4.4 16.8 1.0
OE2 E:GLU164 4.4 22.1 1.0
CG A:GLU164 4.5 15.9 1.0
CG L:GLU164 4.5 15.9 1.0
CB E:GLU164 4.6 16.8 1.0
CG E:GLU164 4.7 15.9 1.0
CG L:GLN161 4.8 29.5 1.0
OE2 L:GLU165 4.9 37.1 1.0
CB L:GLN161 4.9 17.7 1.0
CA L:GLN161 4.9 16.1 1.0
CG A:GLN161 4.9 29.5 1.0
CG E:GLN161 4.9 29.5 1.0
OE2 E:GLU165 4.9 37.1 1.0
CA A:GLN161 5.0 16.1 1.0
CB A:GLN161 5.0 17.7 1.0
OE2 A:GLU165 5.0 37.1 1.0

Calcium binding site 2 out of 8 in 1z6o

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Calcium binding site 2 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


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 Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5303

b:63.9
occ:1.00
 O L:HOH213 1.8 20.5 1.0
O A:HOH5324 2.1 28.7 1.0
O L:HOH254 2.2 28.7 1.0
O E:HOH247 2.3 28.7 1.0
OE2 L:GLU164 3.3 22.1 1.0
OE2 A:GLU164 3.4 22.1 1.0
OE2 E:GLU164 3.5 22.1 1.0
CD L:GLU164 4.3 23.2 1.0
CD A:GLU164 4.4 23.2 1.0
CD E:GLU164 4.4 23.2 1.0
O E:HOH214 4.5 20.6 1.0
NE2 L:HIS144 4.5 15.9 1.0
CE1 L:HIS144 4.5 19.1 1.0
O L:HOH223 4.5 20.6 1.0
CE1 A:HIS144 4.5 19.1 1.0
OE1 L:GLU164 4.5 20.1 1.0
NE2 A:HIS144 4.5 15.9 1.0
O A:HOH5448 4.6 20.6 1.0
OE1 E:GLU164 4.6 20.1 1.0
OE1 A:GLU164 4.6 20.1 1.0
NE2 E:HIS144 4.7 15.9 1.0
CE1 E:HIS144 4.7 19.1 1.0

Calcium binding site 3 out of 8 in 1z6o

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Calcium binding site 3 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


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 Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6302

b:18.5
occ:1.00
 OE1 B:GLU164 2.3 20.1 1.0
OE1 D:GLU164 2.3 20.1 1.0
OE1 K:GLU164 2.4 20.1 1.0
OE1 D:GLN161 2.5 28.4 1.0
OE1 B:GLN161 2.5 28.4 1.0
OE1 K:GLN161 2.6 28.4 1.0
CD B:GLU164 3.5 23.2 1.0
CD D:GLU164 3.5 23.2 1.0
CD K:GLU164 3.6 23.2 1.0
CD D:GLN161 3.6 37.9 1.0
CD B:GLN161 3.7 37.9 1.0
O D:HOH376 3.7 20.5 1.0
CD K:GLN161 3.8 37.9 1.0
OE2 B:GLU164 4.2 22.1 1.0
OE2 D:GLU164 4.2 22.1 1.0
OE2 K:GLU164 4.3 22.1 1.0
NE2 D:GLN161 4.3 32.5 1.0
NE2 B:GLN161 4.3 32.5 1.0
NE2 K:GLN161 4.4 32.5 1.0
CB B:GLU164 4.4 16.8 1.0
CB D:GLU164 4.5 16.8 1.0
CG B:GLU164 4.5 15.9 1.0
CG D:GLU164 4.6 15.9 1.0
CB K:GLU164 4.6 16.8 1.0
CG K:GLU164 4.7 15.9 1.0
CG D:GLN161 4.8 29.5 1.0
CB D:GLN161 4.9 17.7 1.0
CA D:GLN161 4.9 16.1 1.0
CG B:GLN161 4.9 29.5 1.0
CA B:GLN161 5.0 16.1 1.0
CB B:GLN161 5.0 17.7 1.0
OE2 B:GLU165 5.0 37.1 1.0
CG K:GLN161 5.0 29.5 1.0

Calcium binding site 4 out of 8 in 1z6o

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Calcium binding site 4 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


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 Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6303

b:63.9
occ:1.00
 O D:HOH376 1.8 20.5 1.0
O B:HOH6326 2.1 28.7 1.0
O K:HOH3797 2.2 28.7 1.0
O D:HOH1201 2.3 28.7 1.0
OE2 B:GLU164 3.4 22.1 1.0
OE2 D:GLU164 3.5 22.1 1.0
OE2 K:GLU164 3.6 22.1 1.0
O B:HOH6443 4.3 20.6 1.0
O D:HOH3745 4.4 20.6 1.0
CD B:GLU164 4.4 23.2 1.0
O K:HOH405 4.5 20.6 1.0
CD D:GLU164 4.5 23.2 1.0
CE1 B:HIS144 4.5 19.1 1.0
NE2 B:HIS144 4.5 15.9 1.0
CE1 D:HIS144 4.6 19.1 1.0
NE2 D:HIS144 4.6 15.9 1.0
CD K:GLU164 4.6 23.2 1.0
CE1 K:HIS144 4.6 19.1 1.0
OE1 B:GLU164 4.6 20.1 1.0
NE2 K:HIS144 4.7 15.9 1.0
OE1 D:GLU164 4.7 20.1 1.0
OE1 K:GLU164 4.8 20.1 1.0

Calcium binding site 5 out of 8 in 1z6o

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Calcium binding site 5 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7302

b:18.5
occ:1.00
 OE1 C:GLU164 2.3 20.1 1.0
OE1 I:GLU164 2.3 20.1 1.0
OE1 H:GLU164 2.3 20.1 1.0
OE1 C:GLN161 2.5 28.4 1.0
OE1 H:GLN161 2.5 28.4 1.0
OE1 I:GLN161 2.6 28.4 1.0
CD C:GLU164 3.5 23.2 1.0
CD I:GLU164 3.5 23.2 1.0
CD H:GLU164 3.6 23.2 1.0
CD H:GLN161 3.7 37.9 1.0
CD C:GLN161 3.7 37.9 1.0
O H:HOH748 3.7 20.5 1.0
CD I:GLN161 3.8 37.9 1.0
OE2 C:GLU164 4.2 22.1 1.0
OE2 I:GLU164 4.2 22.1 1.0
OE2 H:GLU164 4.3 22.1 1.0
NE2 H:GLN161 4.3 32.5 1.0
NE2 C:GLN161 4.3 32.5 1.0
CB C:GLU164 4.4 16.8 1.0
NE2 I:GLN161 4.4 32.5 1.0
CB H:GLU164 4.5 16.8 1.0
CB I:GLU164 4.5 16.8 1.0
CG C:GLU164 4.5 15.9 1.0
CG I:GLU164 4.6 15.9 1.0
CG H:GLU164 4.6 15.9 1.0
CG C:GLN161 4.9 29.5 1.0
CG H:GLN161 4.9 29.5 1.0
CA C:GLN161 5.0 16.1 1.0
CB C:GLN161 5.0 17.7 1.0
OE2 H:GLU165 5.0 37.1 1.0
CB H:GLN161 5.0 17.7 1.0
OE2 C:GLU165 5.0 37.1 1.0

Calcium binding site 6 out of 8 in 1z6o

Go back to Calcium Binding Sites List in 1z6o
Calcium binding site 6 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7303

b:63.9
occ:1.00
 O H:HOH748 1.8 20.5 1.0
O I:HOH3059 2.1 28.7 1.0
O C:HOH829 2.1 28.7 1.0
O H:HOH2690 2.2 28.7 1.0
OE2 C:GLU164 3.4 22.1 1.0
OE2 H:GLU164 3.4 22.1 1.0
OE2 I:GLU164 3.5 22.1 1.0
CD C:GLU164 4.4 23.2 1.0
CD H:GLU164 4.4 23.2 1.0
O C:HOH3007 4.4 20.6 1.0
O I:HOH2638 4.5 20.6 1.0
O H:HOH777 4.5 20.6 1.0
CD I:GLU164 4.5 23.2 1.0
CE1 C:HIS144 4.5 19.1 1.0
NE2 C:HIS144 4.5 15.9 1.0
CE1 I:HIS144 4.5 19.1 1.0
NE2 H:HIS144 4.6 15.9 1.0
CE1 H:HIS144 4.6 19.1 1.0
NE2 I:HIS144 4.6 15.9 1.0
OE1 H:GLU164 4.6 20.1 1.0
OE1 C:GLU164 4.6 20.1 1.0
OE1 I:GLU164 4.7 20.1 1.0

Calcium binding site 7 out of 8 in 1z6o

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Calcium binding site 7 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca8302

b:18.5
occ:1.00
 OE1 F:GLU164 2.3 20.1 1.0
OE1 J:GLU164 2.3 20.1 1.0
OE1 G:GLU164 2.4 20.1 1.0
OE1 J:GLN161 2.5 28.4 1.0
OE1 F:GLN161 2.5 28.4 1.0
OE1 G:GLN161 2.6 28.4 1.0
CD F:GLU164 3.5 23.2 1.0
CD J:GLU164 3.5 23.2 1.0
CD G:GLU164 3.6 23.2 1.0
CD J:GLN161 3.7 37.9 1.0
CD F:GLN161 3.7 37.9 1.0
CD G:GLN161 3.7 37.9 1.0
O F:HOH1863 3.7 20.5 1.0
OE2 F:GLU164 4.2 22.1 1.0
OE2 J:GLU164 4.2 22.1 1.0
OE2 G:GLU164 4.3 22.1 1.0
NE2 J:GLN161 4.3 32.5 1.0
NE2 G:GLN161 4.3 32.5 1.0
NE2 F:GLN161 4.3 32.5 1.0
CB F:GLU164 4.4 16.8 1.0
CG F:GLU164 4.5 15.9 1.0
CB J:GLU164 4.5 16.8 1.0
CB G:GLU164 4.5 16.8 1.0
CG J:GLU164 4.6 15.9 1.0
CG G:GLU164 4.6 15.9 1.0
CG J:GLN161 4.9 29.5 1.0
CG F:GLN161 4.9 29.5 1.0
CB J:GLN161 4.9 17.7 1.0
CG G:GLN161 4.9 29.5 1.0
CA J:GLN161 5.0 16.1 1.0
CA F:GLN161 5.0 16.1 1.0
CB F:GLN161 5.0 17.7 1.0
OE2 F:GLU165 5.0 37.1 1.0
CB G:GLN161 5.0 17.7 1.0

Calcium binding site 8 out of 8 in 1z6o

Go back to Calcium Binding Sites List in 1z6o
Calcium binding site 8 out of 8 in the Crystal Structure of Trichoplusia Ni Secreted Ferritin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Trichoplusia Ni Secreted Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca8303

b:63.9
occ:1.00
 O F:HOH1863 1.8 20.5 1.0
O F:HOH1944 2.1 28.7 1.0
O G:HOH2318 2.2 28.7 1.0
O J:HOH3428 2.2 28.7 1.0
OE2 F:GLU164 3.4 22.1 1.0
OE2 G:GLU164 3.5 22.1 1.0
OE2 J:GLU164 3.5 22.1 1.0
O F:HOH3376 4.4 20.6 1.0
O J:HOH2266 4.4 20.6 1.0
CD F:GLU164 4.4 23.2 1.0
O G:HOH1892 4.5 20.6 1.0
CD G:GLU164 4.5 23.2 1.0
CD J:GLU164 4.5 23.2 1.0
CE1 F:HIS144 4.5 19.1 1.0
NE2 F:HIS144 4.5 15.9 1.0
CE1 J:HIS144 4.6 19.1 1.0
NE2 J:HIS144 4.6 15.9 1.0
CE1 G:HIS144 4.6 19.1 1.0
NE2 G:HIS144 4.6 15.9 1.0
OE1 F:GLU164 4.6 20.1 1.0
OE1 G:GLU164 4.7 20.1 1.0
OE1 J:GLU164 4.7 20.1 1.0

Reference:

A.E.Hamburger, A.P.West, Z.A.Hamburger, P.Hamburger, P.J.Bjorkman. Crystal Structure of A Secreted Insect Ferritin Reveals A Symmetrical Arrangement of Heavy and Light Chains. J.Mol.Biol. V. 349 558 2005.
ISSN: ISSN 0022-2836
PubMed: 15896348
DOI: 10.1016/J.JMB.2005.03.074
Page generated: Sat Dec 12 03:29:51 2020

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