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Sodium in PDB 6l55: Recombinant Tegillarca Granosa Ferritin

Enzymatic activity of Recombinant Tegillarca Granosa Ferritin

All present enzymatic activity of Recombinant Tegillarca Granosa Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Recombinant Tegillarca Granosa Ferritin, PDB code: 6l55 was solved by Q.Q.Jiang, X.R.Su, T.H.Ming, H.S.Huan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.04 / 1.78
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 214.623, 214.905, 151.902, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.1

Other elements in 6l55:

The structure of Recombinant Tegillarca Granosa Ferritin also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Recombinant Tegillarca Granosa Ferritin (pdb code 6l55). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Recombinant Tegillarca Granosa Ferritin, PDB code: 6l55:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 6l55

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Sodium binding site 1 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:12.9
occ:1.00
 O A:ASP40 2.2 7.0 1.0
OD1 A:ASP40 2.6 9.3 1.0
O A:HOH457 2.8 23.1 1.0
CG A:ASP40 3.0 11.0 1.0
C A:ASP40 3.3 6.0 1.0
OD2 A:ASP40 3.3 10.8 1.0
O A:HOH339 3.5 9.0 1.0
CA A:ASP40 3.8 4.7 1.0
CB A:ASP40 4.0 7.0 1.0
O A:HOH471 4.0 15.0 1.0
O A:HOH344 4.2 15.1 1.0
O A:HOH479 4.2 12.3 1.0
C A:ARG41 4.4 2.4 1.0
N A:ARG41 4.4 3.8 1.0
O A:ARG41 4.6 6.2 1.0
CB B:ASN72 4.6 4.3 1.0
N A:ASP42 4.6 3.6 1.0
CA A:ARG41 4.7 5.0 1.0
CA A:ASP42 5.0 6.8 1.0

Sodium binding site 2 out of 11 in 6l55

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Sodium binding site 2 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:12.2
occ:1.00
 O A:HOH450 2.2 22.0 1.0
O A:HOH341 2.4 14.6 1.0
OE2 A:GLU144 3.9 18.5 1.0
OD2 A:ASP148 4.1 12.4 1.0
OD1 A:ASP148 4.3 11.9 1.0
O A:HOH342 4.4 16.0 1.0
O A:HOH372 4.6 18.1 1.0
CG A:ASP148 4.7 12.0 1.0
O A:HOH411 4.7 19.1 1.0
CD A:GLU144 4.8 17.3 1.0
CG A:GLU144 4.8 7.7 1.0

Sodium binding site 3 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 3 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:14.0
occ:1.00
 O B:HOH445 2.2 21.1 1.0
O B:HOH324 2.4 11.8 1.0
O B:HOH359 2.4 10.6 1.0
O B:HOH438 2.7 20.4 1.0
OD2 B:ASP148 4.1 13.1 1.0
OE2 B:GLU144 4.1 13.5 1.0
OD1 B:ASP148 4.1 6.7 1.0
O B:HOH312 4.5 19.2 1.0
CG B:ASP148 4.6 10.0 1.0
O B:HOH334 4.7 13.7 1.0
CG B:GLU144 4.8 9.7 1.0
CD B:GLU144 4.9 15.1 1.0

Sodium binding site 4 out of 11 in 6l55

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Sodium binding site 4 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:15.2
occ:1.00
 O B:ASP40 2.2 4.0 1.0
OD1 B:ASP40 2.6 7.7 1.0
CG B:ASP40 3.2 7.5 1.0
C B:ASP40 3.3 5.8 1.0
O B:HOH349 3.5 13.7 1.0
OD2 B:ASP40 3.6 7.6 1.0
CA B:ASP40 3.9 5.9 1.0
O B:HOH365 4.0 17.9 1.0
CB B:ASP40 4.1 4.1 1.0
O B:HOH461 4.1 17.0 1.0
O B:HOH383 4.2 15.8 1.0
O A:HOH443 4.3 23.7 1.0
C B:ARG41 4.4 6.2 1.0
N B:ARG41 4.4 5.8 1.0
O B:ARG41 4.4 6.2 1.0
O B:HOH435 4.5 10.3 1.0
N B:ASP42 4.7 3.8 1.0
CB A:ASN72 4.7 3.9 1.0
CA B:ARG41 4.7 5.1 1.0

Sodium binding site 5 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 5 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:12.8
occ:1.00
 O C:ASP40 2.2 5.0 1.0
O C:HOH457 2.2 19.5 1.0
OD1 C:ASP40 2.7 8.5 1.0
CG C:ASP40 3.1 8.5 1.0
C C:ASP40 3.3 6.1 1.0
OD2 C:ASP40 3.5 8.3 1.0
O C:HOH346 3.6 9.2 1.0
CA C:ASP40 3.8 4.2 1.0
CB C:ASP40 4.1 4.7 1.0
O C:HOH354 4.2 14.5 1.0
O C:HOH475 4.3 14.3 1.0
O C:HOH448 4.3 20.5 1.0
O C:HOH384 4.3 19.0 1.0
N C:ARG41 4.4 4.0 1.0
C C:ARG41 4.4 2.8 1.0
O J:HOH439 4.5 21.3 1.0
O C:ARG41 4.5 5.1 1.0
CB J:ASN72 4.6 3.1 1.0
N C:ASP42 4.6 3.8 1.0
CA C:ARG41 4.7 3.5 1.0

Sodium binding site 6 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 6 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:14.0
occ:1.00
 O E:HOH355 2.3 12.4 1.0
O E:HOH311 2.4 12.2 1.0
OE2 E:GLU144 3.9 21.2 1.0
OD1 E:ASP148 4.2 11.5 1.0
OD2 E:ASP148 4.2 13.5 1.0
O E:HOH318 4.6 17.1 1.0
CG E:ASP148 4.6 13.1 1.0
O E:HOH338 4.7 17.6 1.0
CD E:GLU144 4.8 17.9 1.0
CG E:GLU144 4.8 12.9 1.0

Sodium binding site 7 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 7 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:14.1
occ:1.00
 O E:ASP40 2.3 8.1 1.0
O D:HOH320 2.4 13.1 1.0
O D:HOH382 2.4 12.6 1.0
O E:HOH447 2.4 25.0 1.0
OD1 E:ASP40 2.6 9.2 1.0
CG E:ASP40 3.1 11.5 1.0
C E:ASP40 3.3 7.2 1.0
OD2 E:ASP40 3.5 11.0 1.0
O E:HOH339 3.6 10.3 1.0
OE2 D:GLU144 3.8 23.4 1.0
CA E:ASP40 3.9 8.1 1.0
O E:HOH453 4.1 13.2 1.0
CB E:ASP40 4.1 7.6 1.0
OD2 D:ASP148 4.2 16.0 1.0
O E:HOH332 4.2 18.1 1.0
OD1 D:ASP148 4.2 11.8 1.0
C E:ARG41 4.4 7.5 1.0
O E:HOH436 4.4 16.2 1.0
N E:ARG41 4.4 6.2 1.0
O D:HOH314 4.5 19.2 1.0
O E:ARG41 4.5 6.9 1.0
CG D:ASP148 4.6 12.3 1.0
N E:ASP42 4.6 6.6 1.0
CB H:ASN72 4.7 6.0 1.0
O D:HOH310 4.7 16.9 1.0
CA E:ARG41 4.7 6.7 1.0
CD D:GLU144 4.7 19.0 1.0
CG D:GLU144 4.8 10.6 1.0

Sodium binding site 8 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 8 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na203

b:14.5
occ:1.00
 O F:ASP40 2.2 3.7 1.0
O C:HOH452 2.2 16.5 1.0
O C:HOH371 2.4 9.7 1.0
O C:HOH338 2.4 14.4 1.0
OD1 F:ASP40 2.6 6.9 1.0
O C:HOH454 2.7 26.7 1.0
CG F:ASP40 3.1 8.3 1.0
C F:ASP40 3.3 4.5 1.0
O F:HOH363 3.5 9.3 1.0
OD2 F:ASP40 3.5 7.2 1.0
CA F:ASP40 3.8 3.5 1.0
CB F:ASP40 4.0 5.0 1.0
OD2 C:ASP148 4.1 11.1 1.0
OE2 C:GLU144 4.1 13.8 1.0
O F:HOH408 4.2 20.9 1.0
O F:HOH417 4.2 11.7 1.0
O F:HOH449 4.2 16.2 1.0
O F:HOH469 4.2 13.6 1.0
OD1 C:ASP148 4.3 7.9 1.0
N F:ARG41 4.4 4.1 1.0
C F:ARG41 4.4 2.8 1.0
O C:HOH316 4.5 15.4 1.0
O F:ARG41 4.5 5.3 1.0
O C:HOH404 4.6 16.4 1.0
O G:HOH440 4.6 19.4 1.0
CG C:ASP148 4.6 8.6 1.0
N F:ASP42 4.7 4.0 1.0
CB G:ASN72 4.7 3.0 1.0
CA F:ARG41 4.7 3.0 1.0
CG C:GLU144 4.8 9.5 1.0
O C:HOH441 4.9 17.4 1.0
CD C:GLU144 4.9 16.2 1.0

Sodium binding site 9 out of 11 in 6l55

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Sodium binding site 9 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na202

b:12.4
occ:1.00
 O G:ASP40 2.3 4.9 1.0
OD1 G:ASP40 2.6 7.6 1.0
CG G:ASP40 3.1 7.3 1.0
C G:ASP40 3.3 4.1 1.0
O G:HOH347 3.5 9.8 1.0
OD2 G:ASP40 3.5 10.8 1.0
CA G:ASP40 3.8 6.6 1.0
O G:HOH461 4.0 16.5 1.0
CB G:ASP40 4.1 4.6 1.0
O G:HOH429 4.1 22.1 1.0
O G:HOH470 4.1 12.7 1.0
O G:HOH425 4.3 13.4 1.0
C G:ARG41 4.4 4.5 1.0
N G:ARG41 4.4 4.0 1.0
O G:ARG41 4.5 5.7 1.0
CB F:ASN72 4.7 2.6 1.0
N G:ASP42 4.7 3.5 1.0
CA G:ARG41 4.8 2.7 1.0
O F:HOH444 4.8 16.3 1.0

Sodium binding site 10 out of 11 in 6l55

Go back to Sodium Binding Sites List in 6l55
Sodium binding site 10 out of 11 in the Recombinant Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Recombinant Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na202

b:13.7
occ:1.00
 O H:ASP40 2.2 6.2 1.0
O H:HOH447 2.3 18.9 1.0
O H:HOH369 2.4 11.3 1.0
OD1 H:ASP40 2.7 10.3 1.0
CG H:ASP40 3.2 11.6 1.0
C H:ASP40 3.3 9.3 1.0
O H:HOH338 3.5 8.6 1.0
OD2 H:ASP40 3.5 7.7 1.0
CA H:ASP40 3.9 5.4 1.0
O H:HOH321 4.1 16.3 1.0
CB H:ASP40 4.1 5.4 1.0
O H:HOH467 4.2 15.1 1.0
C H:ARG41 4.4 3.0 1.0
N H:ARG41 4.4 5.2 1.0
O H:HOH445 4.4 15.7 1.0
O H:HOH324 4.4 22.6 1.0
O H:ARG41 4.5 5.3 1.0
CB E:ASN72 4.6 5.3 1.0
N H:ASP42 4.6 5.5 1.0
CA H:ARG41 4.7 5.1 1.0

Reference:

Q.Q.Jian, X.R.Su, T.H.Ming, H.S.Huan. Crystal Structure Analysis Unravels How CU2+ in CU2+-Ferritin Nanocage Perturb the Functions of Tegillarca Granosa Ferritin To Be Published.
Page generated: Tue Oct 8 11:36:21 2024

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