Sodium in PDB 6kzy: Cu(II) Loaded Tegillarca Granosa Ferritin

All present enzymatic activity of Cu(II) Loaded Tegillarca Granosa Ferritin:
1.16.3.1;

The structure of Cu(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6kzy 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)	32.72 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	217.054, 217.054, 132.874, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 19.5

The structure of Cu(II) Loaded Tegillarca Granosa Ferritin also contains other interesting chemical elements:

Copper

(Cu)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Sodium atom in the Cu(II) Loaded Tegillarca Granosa Ferritin (pdb code 6kzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 37 binding sites of Sodium where determined in the Cu(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6kzy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:52.1 occ:1.00 OE1 A:GLU13 2.3 31.6 1.0 CD A:GLU13 3.0 37.1 1.0 CB A:GLU13 3.5 26.7 1.0 CG A:GLU13 3.6 39.6 1.0 OE2 A:GLU13 3.8 36.6 1.0 CE1 A:HIS11 3.9 29.4 1.0 NE2 A:HIS122 4.1 27.1 1.0 CE1 A:HIS122 4.4 28.4 1.0 ND1 A:HIS11 4.5 25.2 1.0 NE2 A:HIS11 4.8 26.8 1.0 CA A:GLU13 4.8 25.3 1.0

Sodium binding site 2 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:39.0 occ:1.00 NA A:NA205 2.6 37.9 1.0 O A:LEU88 2.6 29.9 1.0 OG A:SER34 2.8 28.8 1.0 CG A:PRO86 3.5 22.7 1.0 CB A:SER34 3.6 22.0 1.0 CB A:PRO86 3.7 26.1 1.0 CD A:PRO86 3.7 20.1 1.0 C A:LEU88 3.7 30.4 1.0 O A:HOH349 3.7 27.9 1.0 CA A:ASP89 3.8 28.4 1.0 OD1 A:ASP89 4.0 30.6 1.0 N A:ASP89 4.2 29.2 1.0 CZ2 A:TRP91 4.2 24.4 1.0 O A:HOH348 4.3 36.3 1.0 C A:ASP89 4.5 29.7 1.0 O A:ASP89 4.5 27.8 1.0 N A:PRO86 4.5 26.3 1.0 CA A:PRO86 4.6 26.2 1.0 O A:PRO86 4.6 31.6 1.0 NE1 A:TRP91 4.7 22.9 1.0 CB A:ASP89 4.8 28.1 1.0 C A:PRO86 4.8 28.1 1.0 CG A:ASP89 4.8 35.2 1.0 CE2 A:TRP91 4.8 26.0 1.0 CA A:SER34 4.9 21.9 1.0

Sodium binding site 3 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:37.9 occ:1.00 O A:HOH349 2.6 27.9 1.0 NA A:NA204 2.6 39.0 1.0 OD1 A:ASP89 2.7 30.6 1.0 CG A:ASP89 3.5 35.2 1.0 CA A:ASP89 3.7 28.4 1.0 CB A:ASP89 3.8 28.1 1.0 O A:HOH330 3.9 33.4 1.0 O A:LEU88 4.3 29.9 1.0 O A:ASP89 4.4 27.8 1.0 OG A:SER34 4.5 28.8 1.0 OD2 A:ASP89 4.5 37.6 1.0 C A:ASP89 4.6 29.7 1.0 N A:ASP89 4.6 29.2 1.0 O A:HOH348 4.6 36.3 1.0 C A:LEU88 4.9 30.4 1.0

Sodium binding site 4 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:35.6 occ:1.00 O A:HOH343 2.6 22.8 1.0 O A:HOH322 2.9 28.4 1.0 O A:MET37 3.3 26.8 1.0 CA A:TYR38 3.3 23.3 1.0 CD A:ARG41 3.4 26.6 1.0 N A:TYR38 3.5 24.1 1.0 C A:MET37 3.5 26.2 1.0 CG A:ARG41 3.7 23.2 1.0 CB A:TYR38 3.9 25.5 1.0 O A:HOH349 4.0 27.9 1.0 CB A:MET37 4.3 19.7 1.0 O A:ASP89 4.5 27.8 1.0 C A:TYR38 4.5 25.0 1.0 CA A:MET37 4.5 27.9 1.0 O A:SER34 4.5 24.7 1.0 CD1 A:TYR38 4.6 24.3 1.0 O A:TYR38 4.7 27.6 1.0 CG A:TYR38 4.8 22.1 1.0 NE A:ARG41 4.8 23.6 1.0 NH1 A:ARG41 4.8 22.2 1.0

Sodium binding site 5 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:44.4 occ:1.00 OE2 A:GLU13 2.7 36.6 1.0 O A:HOH351 2.9 26.8 1.0 CG A:GLU13 3.4 39.6 1.0 CD A:GLU13 3.4 37.1 1.0 CD1 A:ILE118 3.5 23.9 1.0 CG1 A:ILE118 4.2 26.9 1.0 O A:HOH396 4.2 35.9 1.0 O A:HOH355 4.2 43.8 1.0 OE1 A:GLU13 4.6 31.6 1.0 NZ A:LYS121 4.8 32.8 1.0 CB A:GLU13 4.9 26.7 1.0 O A:GLU13 5.0 24.7 1.0

Sodium binding site 6 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:46.5 occ:1.00 O A:SER107 3.0 31.2 1.0 OG A:SER107 3.2 45.1 1.0 C A:SER107 3.8 26.9 1.0 CA A:SER107 3.9 27.5 1.0 CB A:GLN110 4.0 26.4 1.0 N A:ALA111 4.1 23.3 1.0 CB A:SER107 4.1 25.7 1.0 CE A:MET24 4.2 36.9 1.0 CB A:ALA111 4.3 18.5 1.0 CG A:GLN110 4.4 24.1 1.0 CA A:ALA111 4.6 23.4 1.0 C A:GLN110 4.6 29.6 1.0 CA A:GLN110 4.9 23.6 1.0

Sodium binding site 7 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:51.8 occ:1.00 NE2 A:GLN99 2.6 33.6 1.0 O D:HOH305 2.6 36.3 1.0 NZ A:LYS154 3.1 43.7 1.0 O A:HOH390 3.1 39.1 1.0 CE A:LYS154 3.7 31.9 1.0 CD A:GLN99 3.7 36.8 1.0 CG2 A:ILE150 4.0 21.1 1.0 CG A:GLN99 4.0 25.3 1.0 OE1 D:GLN5 4.4 35.7 1.0 OE1 A:GLN99 4.7 34.0 1.0 CD A:LYS154 5.0 35.0 1.0

Sodium binding site 8 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:34.9 occ:1.00 O B:HOH317 2.9 26.1 1.0 CD1 B:ILE78 4.2 23.8 1.0 CB B:ILE78 4.2 30.0 1.0 O B:HOH320 4.3 29.6 1.0 OD1 B:ASN72 4.5 25.5 1.0 CG1 B:ILE78 4.6 24.5 1.0 N B:ILE78 4.6 24.3 1.0 O B:ILE78 4.7 27.1 1.0 ND2 B:ASN72 4.8 20.8 1.0 CA B:ILE78 4.9 24.5 1.0

Sodium binding site 9 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:38.4 occ:1.00 OD1 B:ASP89 2.5 26.0 1.0 O B:HOH307 2.6 29.2 1.0 O B:HOH328 2.9 29.4 1.0 CG B:ASP89 3.4 32.9 1.0 CA B:ASP89 3.6 28.6 1.0 O B:HOH326 3.7 31.7 1.0 CB B:ASP89 3.7 29.9 1.0 O B:LEU88 4.2 29.4 1.0 O B:ASP89 4.4 26.2 1.0 OD2 B:ASP89 4.5 39.2 1.0 OG B:SER34 4.5 27.9 1.0 N B:ASP89 4.5 28.4 1.0 C B:ASP89 4.6 29.4 1.0 C B:LEU88 4.8 29.3 1.0

Sodium binding site 10 out of 37 in the Cu(II) Loaded 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 Cu(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:47.8 occ:1.00 OE2 B:GLU13 2.7 36.0 1.0 O B:HOH358 2.8 28.1 1.0 O B:HOH396 3.2 44.6 1.0 CG B:GLU13 3.4 35.3 1.0 CD B:GLU13 3.5 38.4 1.0 CD1 B:ILE118 3.5 24.5 1.0 CG1 B:ILE118 4.1 29.5 1.0 O B:HOH379 4.2 41.2 1.0 O B:HOH399 4.2 33.9 1.0 OE1 B:GLU13 4.7 30.4 1.0 NZ B:LYS121 4.8 34.2 1.0 CB B:GLU13 4.9 27.0 1.0 O B:GLU13 5.0 26.1 1.0

Q.Q.Jiang, 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.