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Sodium in PDB 5u1a: Ferritin with Gc Mtre Loop 1 Inserted at HIS34

Enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34

All present enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34:
1.16.3.2;

Protein crystallography data

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a was solved by S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 128.412, 128.412, 165.041, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.6

Other elements in 5u1a:

The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Sodium atom in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34 (pdb code 5u1a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 30 binding sites of Sodium where determined in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 30 in 5u1a

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Sodium binding site 1 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:22.7
occ:1.00
 OE1 A:GLU145 2.2 21.5 1.0
O A:HOH310 2.2 41.2 1.0
OE1 A:GLU65 2.2 35.2 1.0
OE2 A:GLU109 2.4 26.9 1.0
OE1 A:GLN142 2.5 23.2 1.0
CD A:GLU65 3.0 31.5 1.0
OE2 A:GLU65 3.0 43.3 1.0
CD A:GLU109 3.2 24.8 1.0
OE1 A:GLU109 3.2 31.9 1.0
CD A:GLU145 3.4 26.7 1.0
CD A:GLN142 3.4 24.2 1.0
NE2 A:GLN142 3.7 23.6 1.0
CE1 A:HIS61 4.0 21.0 1.0
NE2 A:HIS61 4.0 20.8 1.0
CB A:GLU145 4.1 21.4 1.0
OE2 A:GLU145 4.3 28.0 1.0
CG A:GLU145 4.3 23.1 1.0
CG A:GLU65 4.5 29.3 1.0
CG2 A:ILE112 4.5 21.7 1.0
CD2 A:HIS68 4.6 23.8 1.0
CG A:GLU109 4.6 22.4 1.0
NE2 A:HIS68 4.7 26.1 1.0
CG A:GLN142 4.8 24.5 1.0
CB A:ILE112 4.9 22.5 1.0
OE2 A:GLU17 4.9 32.6 1.0
OE1 A:GLU17 5.0 31.3 1.0

Sodium binding site 2 out of 30 in 5u1a

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Sodium binding site 2 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:41.3
occ:1.00
 O A:TYR49 2.1 42.3 1.0
O A:CYS31 2.8 18.8 1.0
O A:TRP30 2.9 16.6 1.0
N A:GLY34 3.2 37.0 1.0
O A:GLY34 3.3 45.1 1.0
C A:TYR49 3.4 41.1 1.0
C A:CYS31 3.5 19.7 1.0
N A:THR33 3.7 26.1 1.0
C A:THR33 3.8 35.8 1.0
CA A:GLY34 3.8 40.5 1.0
C A:TYR32 3.9 24.2 1.0
N A:TYR49 3.9 44.8 1.0
C A:GLY34 4.0 46.4 1.0
CA A:THR33 4.0 29.6 1.0
C A:TRP30 4.0 16.8 1.0
O A:TYR32 4.1 32.2 1.0
CA A:CYS31 4.1 18.2 1.0
CA A:TYR49 4.2 44.5 1.0
N A:TYR32 4.3 19.3 1.0
C A:SER48 4.3 39.2 1.0
N A:SER50 4.3 30.0 1.0
CA A:SER50 4.4 27.9 1.0
N A:SER48 4.5 45.0 1.0
CA A:TYR32 4.5 23.0 1.0
N A:CYS31 4.6 17.2 1.0
N A:LEU51 4.6 19.0 1.0
O A:THR33 4.7 38.8 1.0
CA A:SER48 4.7 46.5 1.0
CG A:LEU51 4.8 20.4 1.0
O A:SER48 4.9 42.8 1.0
CB A:TYR49 4.9 41.2 1.0
CE3 A:TRP30 5.0 22.7 1.0

Sodium binding site 3 out of 30 in 5u1a

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Sodium binding site 3 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:23.5
occ:1.00
 OE1 B:GLU145 2.2 23.9 1.0
OE2 B:GLU109 2.3 23.6 1.0
OE1 B:GLU65 2.4 42.0 1.0
OE1 B:GLN142 2.5 24.4 1.0
CD B:GLU65 3.1 34.8 1.0
CD B:GLU109 3.2 26.7 1.0
OE2 B:GLU65 3.2 46.6 1.0
OE1 B:GLU109 3.2 30.6 1.0
CD B:GLN142 3.4 27.0 1.0
CD B:GLU145 3.4 25.8 1.0
NE2 B:GLN142 3.6 30.5 1.0
CE1 B:HIS61 4.0 21.5 1.0
CB B:GLU145 4.0 23.3 1.0
NE2 B:HIS61 4.0 19.7 1.0
CD1 B:ILE112 4.1 27.4 1.0
CG B:GLU145 4.3 23.9 1.0
OE2 B:GLU145 4.3 29.3 1.0
CG2 B:ILE112 4.5 21.0 1.0
CG B:GLU109 4.6 24.2 1.0
CG B:GLU65 4.6 32.1 1.0
CD2 B:HIS68 4.7 26.4 1.0
CG B:GLN142 4.8 30.5 1.0
NE2 B:HIS68 4.8 26.6 1.0
CB B:ILE112 4.9 22.3 1.0

Sodium binding site 4 out of 30 in 5u1a

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Sodium binding site 4 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:46.4
occ:1.00
 O B:HOH376 2.4 34.3 1.0
O B:CYS31 2.8 15.4 1.0
O B:TYR49 3.0 46.6 1.0
O B:TRP30 3.1 15.5 1.0
N B:GLY34 3.2 36.8 1.0
C B:CYS31 3.6 17.8 1.0
N B:THR33 3.6 25.3 1.0
C B:THR33 3.7 33.4 1.0
C B:TYR32 3.8 26.0 1.0
CA B:GLY34 3.9 37.2 1.0
CA B:THR33 3.9 30.3 1.0
O B:TYR32 3.9 28.7 1.0
C B:GLY34 4.0 43.9 1.0
CE1 B:TYR49 4.0 58.0 1.0
C B:TYR49 4.1 39.6 1.0
CD1 B:TYR49 4.2 48.2 1.0
C B:TRP30 4.3 15.7 1.0
CA B:CYS31 4.3 16.3 1.0
N B:TYR32 4.3 19.5 1.0
CA B:SER50 4.4 29.9 1.0
CA B:TYR32 4.5 21.7 1.0
N B:LEU51 4.5 21.1 1.0
O B:THR33 4.6 34.8 1.0
N B:SER50 4.7 31.2 1.0
N B:CYS31 4.8 16.2 1.0
CG B:LEU51 4.9 22.4 1.0
C B:SER50 5.0 24.6 1.0

Sodium binding site 5 out of 30 in 5u1a

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Sodium binding site 5 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:23.9
occ:1.00
 OE1 C:GLU145 2.2 22.2 1.0
OE1 C:GLN142 2.4 23.9 1.0
OE2 C:GLU109 2.4 25.8 1.0
OE1 C:GLU65 2.4 36.1 1.0
O C:HOH310 2.6 34.2 1.0
CD C:GLU65 3.2 26.5 1.0
OE2 C:GLU65 3.2 31.9 1.0
CD C:GLU109 3.2 22.8 1.0
OE1 C:GLU109 3.3 25.2 1.0
CD C:GLN142 3.4 21.3 1.0
CD C:GLU145 3.4 21.7 1.0
O C:HOH308 3.4 47.7 1.0
NE2 C:GLN142 3.6 21.5 1.0
CB C:GLU145 3.9 18.2 1.0
CE1 C:HIS61 4.0 21.2 1.0
NE2 C:HIS61 4.0 22.6 1.0
CG C:GLU145 4.3 19.2 1.0
OE2 C:GLU145 4.3 22.4 1.0
CG2 C:ILE112 4.5 21.8 1.0
CG C:GLU65 4.6 22.4 1.0
CG C:GLU109 4.7 20.9 1.0
CD2 C:HIS68 4.7 24.1 1.0
CG C:GLN142 4.8 21.1 1.0
NE2 C:HIS68 4.8 27.6 1.0
CB C:ILE112 4.9 20.9 1.0
OE2 C:GLU17 4.9 28.5 1.0
CA C:GLN142 5.0 20.1 1.0
OE1 C:GLU17 5.0 34.4 1.0

Sodium binding site 6 out of 30 in 5u1a

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Sodium binding site 6 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:26.7
occ:1.00
 OE1 D:GLU145 2.2 21.9 1.0
OE1 D:GLN142 2.3 20.8 1.0
OE2 D:GLU109 2.4 25.7 1.0
OE2 D:GLU65 2.5 38.3 1.0
O D:HOH316 2.6 32.9 1.0
CD D:GLU65 3.2 32.0 1.0
CD D:GLU109 3.3 23.8 1.0
CD D:GLN142 3.3 23.1 1.0
OE1 D:GLU65 3.3 40.4 1.0
OE1 D:GLU109 3.4 24.5 1.0
CD D:GLU145 3.4 25.5 1.0
NE2 D:GLN142 3.6 21.8 1.0
CB D:GLU145 3.9 22.4 1.0
CE1 D:HIS61 4.0 23.4 1.0
NE2 D:HIS61 4.1 24.1 1.0
CG D:GLU145 4.2 22.7 1.0
OE2 D:GLU145 4.3 26.9 1.0
CG2 D:ILE112 4.4 21.9 1.0
CG D:GLN142 4.7 22.5 1.0
CG D:GLU109 4.7 21.6 1.0
CG D:GLU65 4.7 24.9 1.0
CD2 D:HIS68 4.7 24.3 1.0
NE2 D:HIS68 4.8 26.3 1.0
CB D:ILE112 4.9 22.2 1.0
CA D:GLN142 4.9 22.8 1.0
OE2 D:GLU17 5.0 34.4 1.0

Sodium binding site 7 out of 30 in 5u1a

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Sodium binding site 7 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:22.8
occ:1.00
 OE1 E:GLU145 2.2 22.6 1.0
OE1 E:GLN142 2.3 22.9 1.0
OE2 E:GLU109 2.4 21.8 1.0
OE1 E:GLU65 2.4 30.6 1.0
O E:HOH308 2.6 35.7 1.0
CD E:GLU109 3.2 23.2 1.0
CD E:GLU65 3.2 31.3 1.0
OE1 E:GLU109 3.3 20.5 1.0
OE2 E:GLU65 3.3 35.1 1.0
CD E:GLN142 3.4 23.2 1.0
NA E:NA203 3.5 47.0 1.0
CD E:GLU145 3.5 23.8 1.0
NE2 E:GLN142 3.6 21.7 1.0
CB E:GLU145 3.9 22.1 1.0
CE1 E:HIS61 4.0 22.4 1.0
NE2 E:HIS61 4.0 22.5 1.0
CG E:GLU145 4.3 21.6 1.0
OE2 E:GLU145 4.4 29.6 1.0
CG2 E:ILE112 4.5 21.3 1.0
CG E:GLU109 4.7 20.6 1.0
CG E:GLU65 4.7 24.1 1.0
CG E:GLN142 4.8 23.1 1.0
CD2 E:HIS68 4.8 24.6 1.0
NE2 E:HIS68 4.9 26.2 1.0
CB E:ILE112 4.9 20.0 1.0
CA E:GLN142 5.0 22.0 1.0
OE2 E:GLU17 5.0 32.5 1.0

Sodium binding site 8 out of 30 in 5u1a

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Sodium binding site 8 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:29.6
occ:1.00
 O E:HOH307 2.2 24.8 1.0
O E:THR33 2.2 50.3 1.0
O E:TYR49 2.2 32.5 1.0
O E:CYS31 2.5 17.1 1.0
O E:TRP30 2.6 15.8 1.0
C E:CYS31 3.2 19.2 1.0
O E:SER47 3.3 43.1 1.0
C E:THR33 3.4 48.9 1.0
C E:TYR49 3.4 37.3 1.0
N E:THR33 3.6 34.9 1.0
O E:HOH323 3.6 33.7 1.0
C E:TRP30 3.8 17.5 1.0
CA E:CYS31 3.8 17.2 1.0
C E:TYR32 3.8 29.6 1.0
O E:SER46 4.0 44.4 1.0
CA E:THR33 4.0 38.5 1.0
N E:TYR49 4.1 37.2 1.0
C E:SER47 4.1 51.7 1.0
N E:TYR32 4.1 21.6 1.0
O E:TYR32 4.2 36.1 1.0
CA E:TYR49 4.2 39.2 1.0
N E:CYS31 4.3 16.1 1.0
N E:SER50 4.3 27.4 1.0
CA E:SER50 4.4 26.0 1.0
CA E:TYR32 4.4 26.1 1.0
N E:GLY34 4.4 49.3 1.0
N E:LEU51 4.4 20.0 1.0
OG1 E:THR33 4.6 34.0 1.0
C E:SER48 4.7 40.7 1.0
CA E:SER47 4.7 52.9 1.0
CG E:LEU51 4.7 21.3 1.0
CA E:GLY34 4.7 48.0 1.0
CE3 E:TRP30 4.9 18.8 1.0
CB E:TYR49 4.9 38.2 1.0
N E:SER48 4.9 43.5 1.0
C E:SER50 4.9 23.3 1.0
CB E:THR33 5.0 36.3 1.0

Sodium binding site 9 out of 30 in 5u1a

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Sodium binding site 9 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:47.0
occ:1.00
 OE1 E:GLU65 2.3 30.6 1.0
OE1 E:GLU17 2.8 34.3 1.0
OG E:SER20 3.0 29.1 1.0
CB E:SER20 3.1 22.7 1.0
CD E:GLU65 3.2 31.3 1.0
NA E:NA201 3.5 22.8 1.0
O E:HOH308 3.5 35.7 1.0
CD E:GLU17 3.5 28.2 1.0
CG1 E:ILE112 3.6 22.1 1.0
OE2 E:GLU17 3.6 32.5 1.0
CG E:GLU65 3.7 24.1 1.0
CG2 E:ILE112 3.9 21.3 1.0
CD1 E:ILE112 3.9 24.3 1.0
OE2 E:GLU65 4.2 35.1 1.0
CB E:GLU65 4.2 20.8 1.0
CB E:ILE112 4.3 20.0 1.0
OE1 E:GLU109 4.4 20.5 1.0
NE2 E:HIS108 4.5 23.3 1.0
OE2 E:GLU109 4.7 21.8 1.0
CA E:SER20 4.7 20.3 1.0
CA E:GLU17 4.7 16.8 1.0
OE1 E:GLN142 4.8 22.9 1.0
CG E:GLU17 4.8 23.2 1.0
CE2 E:TYR24 4.9 24.9 1.0
CD2 E:HIS108 4.9 22.4 1.0
CD E:GLU109 4.9 23.2 1.0
O E:LYS16 5.0 17.4 1.0

Sodium binding site 10 out of 30 in 5u1a

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Sodium binding site 10 out of 30 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:22.2
occ:1.00
 OE1 F:GLU145 2.3 20.6 1.0
OE1 F:GLN142 2.3 20.1 1.0
OE2 F:GLU109 2.3 21.6 1.0
OE1 F:GLU65 2.4 27.7 1.0
O F:HOH318 2.4 33.8 1.0
CD F:GLU109 3.2 20.5 1.0
CD F:GLU65 3.3 25.7 1.0
OE1 F:GLU109 3.3 21.8 1.0
CD F:GLN142 3.3 19.1 1.0
OE2 F:GLU65 3.3 29.9 1.0
CD F:GLU145 3.5 20.7 1.0
NE2 F:GLN142 3.6 17.2 1.0
CB F:GLU145 4.0 17.9 1.0
CE1 F:HIS61 4.0 20.1 1.0
NE2 F:HIS61 4.1 22.0 1.0
CG F:GLU145 4.3 18.8 1.0
CG2 F:ILE112 4.4 21.0 1.0
OE2 F:GLU145 4.5 22.3 1.0
CG F:GLU109 4.6 17.8 1.0
CG F:GLU65 4.7 20.7 1.0
CG F:GLN142 4.8 17.9 1.0
CB F:ILE112 4.8 19.5 1.0
OE2 F:GLU17 4.9 24.9 1.0
CD2 F:HIS68 4.9 19.3 1.0
CA F:GLN142 5.0 18.2 1.0
NE2 F:HIS68 5.0 21.3 1.0
OE1 F:GLU17 5.0 27.1 1.0

Reference:

L.Wang, D.Xing, A.Le Van, A.E.Jerse, S.Wang. Structure-Based Design of Ferritin Nanoparticle Immunogens Displaying Antigenic Loops of Neisseria Gonorrhoeae. Febs Open Bio V. 7 1196 2017.
ISSN: ESSN 2211-5463
PubMed: 28781959
DOI: 10.1002/2211-5463.12267
Page generated: Tue Oct 8 00:20:33 2024

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