Sodium in PDB 7zg7: Structure of Human Apoferritin Obtained From Ssdna Coated Grid

All present enzymatic activity of Structure of Human Apoferritin Obtained From Ssdna Coated Grid:
1.16.3.1;

The structure of Structure of Human Apoferritin Obtained From Ssdna Coated Grid also contains other interesting chemical elements:

Zinc

(Zn)

270 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 112;

Binding sites:

The binding sites of Sodium atom in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid (pdb code 7zg7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 112 binding sites of Sodium where determined in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid, PDB code: 7zg7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:25.5 occ:1.00 O F:HOH325 2.8 13.3 1.0 O S:HOH353 2.8 8.4 1.0 CD A:GLN7 4.0 5.4 1.0 NE2 A:GLN7 4.0 1.7 1.0 NH1 F:ARG156 4.2 11.4 0.5 ZN S:ZN202 4.2 73.4 1.0 CB S:ASP45 4.2 6.9 1.0 OE1 A:GLN7 4.3 7.8 1.0 CB A:GLN7 4.3 0.3 1.0 CG A:GLN7 4.4 1.2 1.0 O S:HOH359 4.4 14.8 1.0 OG1 F:THR153 4.6 5.4 1.0 OD2 S:ASP44 4.6 8.4 1.0 N A:GLN7 4.7 0.1 1.0 CA S:ASP45 4.8 6.4 1.0

Sodium binding site 2 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:23.7 occ:1.00 OD1 A:ASN109 2.4 2.1 0.5 O A:HIS105 2.7 3.9 1.0 CD2 A:HIS105 3.0 8.1 1.0 NE2 A:HIS105 3.2 10.6 1.0 CG A:ASN109 3.2 0.0 0.5 CG A:HIS105 3.3 4.8 1.0 C A:HIS105 3.5 0.0 1.0 CE1 A:HIS105 3.5 8.5 1.0 ND1 A:HIS105 3.6 11.8 1.0 CA A:HIS105 3.6 0.0 1.0 N A:ASN109 3.7 0.0 1.0 CB A:LYS108 3.8 0.0 1.0 ND2 A:ASN109 3.8 3.3 0.5 CB A:HIS105 4.0 1.9 1.0 CB A:ASN109 4.2 0.3 0.5 C A:LYS108 4.2 0.6 1.0 CB A:ASN109 4.2 0.4 0.5 CA A:ASN109 4.2 0.0 1.0 CA A:LYS108 4.5 1.5 1.0 N A:LEU106 4.7 0.0 1.0 N A:LYS108 4.9 0.0 1.0 CG A:LYS108 4.9 0.0 1.0 O A:LYS108 4.9 0.0 1.0 N A:HIS105 5.0 0.0 1.0 O A:LEU104 5.0 0.0 1.0

Sodium binding site 3 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:24.4 occ:1.00 O T:HOH325 2.6 21.9 1.0 O A:HOH365 2.8 14.9 1.0 CG A:LEU104 3.9 0.0 1.0 CD A:LYS108 4.0 2.5 1.0 CA A:HIS105 4.0 0.0 1.0 CD2 A:LEU104 4.0 0.0 1.0 N A:HIS105 4.1 0.0 1.0 CB A:HIS105 4.3 1.9 1.0 O A:HOH400 4.4 15.0 1.0 C A:LEU104 4.4 0.0 1.0 CD2 A:HIS105 4.5 8.1 1.0 O A:LEU104 4.6 0.0 1.0 CB A:LEU104 4.6 0.0 1.0 O T:GLN7 4.8 7.5 1.0 CG A:HIS105 4.8 4.8 1.0 CG A:LYS108 4.9 0.0 1.0 O A:GLU101 4.9 0.0 1.0 NZ A:LYS108 5.0 8.8 1.0

Sodium binding site 4 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:28.0 occ:1.00 O A:HOH335 2.5 11.1 1.0 O A:HOH410 2.6 16.6 1.0 CD1 A:LEU26 3.4 0.0 1.0 CD2 A:TYR29 3.8 0.0 1.0 CG A:TYR29 4.0 0.0 1.0 CB A:TYR29 4.2 0.0 1.0 CE2 A:TYR29 4.3 0.0 1.0 O A:HOH376 4.3 10.6 1.0 CA A:LEU26 4.5 0.0 1.0 CD1 A:TYR29 4.6 0.0 1.0 CG A:LEU26 4.6 0.0 1.0 O A:HOH336 4.7 12.8 1.0 OD1 A:ASN25 4.7 0.0 1.0 O A:HOH409 4.7 18.6 1.0 CB A:LEU26 4.8 0.0 1.0 CZ A:TYR29 4.9 0.0 1.0

Sodium binding site 5 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:26.1 occ:1.00 OE1 A:GLN112 2.2 15.5 1.0 NE2 T:GLN10 2.8 5.3 1.0 CD A:GLN112 3.2 7.2 1.0 CG A:GLN112 3.6 3.7 1.0 CD T:GLN10 3.8 7.8 1.0 CG T:GLN10 3.8 4.9 1.0 CB A:GLN112 3.8 3.1 1.0 NE2 A:GLN112 4.3 13.8 1.0 CA A:GLN112 4.8 0.0 1.0 O T:HOH308 4.9 17.2 1.0 OE1 T:GLN10 4.9 5.9 1.0 O A:LYS108 4.9 0.0 1.0

Sodium binding site 6 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:28.1 occ:1.00 O S:HOH326 2.8 12.6 1.0 O P:HOH354 2.8 12.5 1.0 CD B:GLN7 4.0 10.0 1.0 NE2 B:GLN7 4.0 1.6 1.0 NH1 S:ARG156 4.2 11.6 0.5 ZN P:ZN202 4.2 66.9 1.0 CB P:ASP45 4.2 4.4 1.0 OE1 B:GLN7 4.3 12.1 1.0 CB B:GLN7 4.3 1.0 1.0 CG B:GLN7 4.4 2.3 1.0 O P:HOH359 4.4 11.5 1.0 OG1 S:THR153 4.6 5.6 1.0 OD2 P:ASP44 4.6 7.7 1.0 N B:GLN7 4.7 1.5 1.0 CA P:ASP45 4.8 4.5 1.0

Sodium binding site 7 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:26.2 occ:1.00 OD1 B:ASN109 2.4 5.0 0.5 O B:HIS105 2.7 9.0 1.0 CD2 B:HIS105 3.0 12.4 1.0 NE2 B:HIS105 3.2 15.2 1.0 CG B:ASN109 3.2 1.2 0.5 CG B:HIS105 3.3 8.4 1.0 C B:HIS105 3.5 1.1 1.0 CE1 B:HIS105 3.5 13.7 1.0 ND1 B:HIS105 3.6 17.6 1.0 CA B:HIS105 3.6 0.0 1.0 N B:ASN109 3.7 1.6 1.0 CB B:LYS108 3.8 1.9 1.0 ND2 B:ASN109 3.8 6.8 0.5 CB B:HIS105 4.0 2.3 1.0 CB B:ASN109 4.2 1.7 0.5 C B:LYS108 4.2 0.7 1.0 CB B:ASN109 4.2 6.8 0.5 CA B:ASN109 4.2 0.8 1.0 CA B:LYS108 4.5 0.6 1.0 N B:LEU106 4.7 0.0 1.0 N B:LYS108 4.9 0.0 1.0 CG B:LYS108 4.9 1.4 1.0 O B:LYS108 4.9 7.6 1.0 N B:HIS105 5.0 0.2 1.0 O B:LEU104 5.0 5.5 1.0

Sodium binding site 8 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na212 b:28.5 occ:1.00 O M:HOH325 2.6 12.2 1.0 O B:HOH364 2.8 18.0 1.0 CG B:LEU104 3.9 0.0 1.0 CD B:LYS108 4.0 6.0 1.0 CA B:HIS105 4.0 0.0 1.0 CD2 B:LEU104 4.0 0.9 1.0 N B:HIS105 4.1 0.2 1.0 CB B:HIS105 4.3 2.3 1.0 O B:HOH400 4.4 19.4 1.0 C B:LEU104 4.4 0.0 1.0 CD2 B:HIS105 4.5 12.4 1.0 O B:LEU104 4.6 5.5 1.0 CB B:LEU104 4.6 0.0 1.0 O M:GLN7 4.8 6.1 1.0 CG B:HIS105 4.8 8.4 1.0 CG B:LYS108 4.9 1.4 1.0 O B:GLU101 4.9 1.7 1.0 NZ B:LYS108 5.0 12.3 1.0

Sodium binding site 9 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na215 b:31.7 occ:1.00 O B:HOH335 2.5 15.9 1.0 O B:HOH410 2.6 20.1 1.0 CD1 B:LEU26 3.4 2.2 1.0 CD2 B:TYR29 3.8 0.0 1.0 CG B:TYR29 4.0 0.0 1.0 CB B:TYR29 4.2 0.0 1.0 CE2 B:TYR29 4.3 1.6 1.0 O B:HOH376 4.3 7.6 1.0 CA B:LEU26 4.5 0.2 1.0 CD1 B:TYR29 4.6 0.0 1.0 CG B:LEU26 4.6 0.0 1.0 O B:HOH336 4.7 13.8 1.0 OD1 B:ASN25 4.7 7.0 1.0 O B:HOH409 4.7 24.3 1.0 CB B:LEU26 4.8 0.0 1.0 CZ B:TYR29 4.9 0.4 1.0

Sodium binding site 10 out of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na216 b:31.0 occ:1.00 OE1 B:GLN112 2.2 23.0 1.0 NE2 M:GLN10 2.8 2.2 1.0 CD B:GLN112 3.2 13.8 1.0 CG B:GLN112 3.6 6.5 1.0 CD M:GLN10 3.8 2.8 1.0 CG M:GLN10 3.8 0.0 1.0 CB B:GLN112 3.8 3.2 1.0 NE2 B:GLN112 4.3 19.7 1.0 CA B:GLN112 4.8 0.0 1.0 O M:HOH308 4.9 23.3 1.0 OE1 M:GLN10 4.9 3.8 1.0 O B:LYS108 4.9 7.6 1.0

D.Hrebik, M.Gondova, L.Valentova, T.Fuzik, A.Pridal, J.Novacek, P.Plevka. Polyelectrolyte Coating of Cryo-Em Grids Improves Lateral Distribution and Prevents Aggregation of Macromolecules. Acta Crystallogr D Struct V. 78 1337 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36322417
DOI: 10.1107/S2059798322009299