Sodium in PDB 7k3w: Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector

All present enzymatic activity of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector:
1.16.3.1;

The structure of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector 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 Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector (pdb code 7k3w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 112 binding sites of Sodium where determined in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector, PDB code: 7k3w:
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 Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:6.0 occ:1.00 O F:HOH343 2.5 8.0 1.0 O S:HOH319 2.7 8.0 1.0 NE2 A:GLN7 3.9 3.0 1.0 CD A:GLN7 4.0 8.0 1.0 CB S:ASP45 4.0 4.0 1.0 OE1 A:GLN7 4.3 4.0 1.0 ZN S:ZN202 4.3 7.0 1.0 CB A:GLN7 4.4 5.0 1.0 O F:HOH327 4.4 10.0 1.0 CG A:GLN7 4.4 5.0 1.0 NH1 F:ARG156 4.4 10.0 0.5 OG1 F:THR153 4.5 5.0 1.0 OD2 S:ASP44 4.5 7.0 1.0 CA S:ASP45 4.7 12.0 1.0 N A:GLN7 4.8 3.0 1.0

Sodium binding site 2 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:4.0 occ:1.00 OD1 A:ASN109 2.4 15.0 0.5 O A:HIS105 2.9 3.0 1.0 CD2 A:HIS105 3.3 24.0 1.0 CG A:ASN109 3.3 16.0 0.5 NE2 A:HIS105 3.4 6.0 1.0 CG A:HIS105 3.6 5.0 1.0 N A:ASN109 3.6 5.0 1.0 C A:HIS105 3.7 4.0 1.0 CB A:LYS108 3.7 4.0 1.0 CE1 A:HIS105 3.8 9.0 1.0 ND1 A:HIS105 3.8 15.0 1.0 CA A:HIS105 3.9 11.0 1.0 ND2 A:ASN109 3.9 14.0 0.5 C A:LYS108 4.1 6.0 1.0 CA A:ASN109 4.2 10.0 1.0 CB A:ASN109 4.2 4.0 0.5 CB A:ASN109 4.2 4.0 0.5 CB A:HIS105 4.3 4.0 1.0 CA A:LYS108 4.4 9.0 1.0 O A:LYS108 4.8 4.0 1.0 N A:LYS108 4.9 3.0 1.0 CG A:LYS108 4.9 3.0 1.0 NA A:NA212 4.9 8.0 1.0 N A:LEU106 4.9 4.0 1.0

Sodium binding site 3 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:8.0 occ:1.00 O T:HOH371 2.5 7.0 1.0 O A:HOH360 2.8 8.0 1.0 CA A:HIS105 3.7 11.0 1.0 N A:HIS105 3.8 4.0 1.0 CG A:LEU104 3.8 6.0 1.0 CD A:LYS108 3.9 7.0 1.0 CD2 A:LEU104 4.1 6.0 1.0 CB A:HIS105 4.1 4.0 1.0 C A:LEU104 4.2 6.0 1.0 O A:LEU104 4.3 3.0 1.0 CD2 A:HIS105 4.4 24.0 1.0 O A:HOH398 4.5 8.0 1.0 CB A:LEU104 4.5 5.0 1.0 CG A:HIS105 4.6 5.0 1.0 CG A:LYS108 4.7 3.0 1.0 O A:GLU101 4.8 6.0 1.0 O T:GLN7 4.9 7.0 1.0 NA A:NA209 4.9 4.0 1.0 CD1 A:LEU104 4.9 3.0 1.0

Sodium binding site 4 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:7.0 occ:1.00 O A:HOH410 2.2 10.0 1.0 O A:HOH337 2.9 5.0 1.0 CD1 A:TYR29 3.6 6.0 1.0 CG A:TYR29 3.7 7.0 1.0 CD1 A:LEU26 3.8 8.0 1.0 CE1 A:TYR29 3.9 5.0 1.0 O A:HOH369 4.0 4.0 1.0 CB A:TYR29 4.1 4.0 1.0 CD2 A:TYR29 4.2 6.0 1.0 O A:HOH408 4.2 7.0 1.0 CZ A:TYR29 4.4 6.0 1.0 CE2 A:TYR29 4.5 3.0 1.0 OD1 A:ASN25 4.8 5.0 1.0 CA A:LEU26 5.0 11.0 1.0

Sodium binding site 5 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:7.0 occ:1.00 OE1 A:GLN112 1.9 19.0 1.0 CD A:GLN112 3.0 11.0 1.0 NE2 T:GLN10 3.2 5.0 1.0 CG A:GLN112 3.7 5.0 1.0 CG T:GLN10 3.8 7.0 1.0 CD T:GLN10 4.0 6.0 1.0 NE2 A:GLN112 4.0 13.0 1.0 CB A:GLN112 4.1 3.0 1.0 O T:HOH366 4.4 9.0 1.0

Sodium binding site 6 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:6.0 occ:1.00 O S:HOH343 2.5 8.0 1.0 O P:HOH318 2.7 8.0 1.0 NE2 B:GLN7 3.9 3.0 1.0 CD B:GLN7 4.0 8.0 1.0 CB P:ASP45 4.0 4.0 1.0 OE1 B:GLN7 4.3 4.0 1.0 ZN P:ZN202 4.3 7.0 1.0 CB B:GLN7 4.4 5.0 1.0 O S:HOH327 4.4 10.0 1.0 CG B:GLN7 4.4 5.0 1.0 NH1 S:ARG156 4.4 10.0 0.5 OG1 S:THR153 4.5 5.0 1.0 OD2 P:ASP44 4.5 7.0 1.0 CA P:ASP45 4.7 12.0 1.0 N B:GLN7 4.8 3.0 1.0

Sodium binding site 7 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:4.0 occ:1.00 OD1 B:ASN109 2.4 15.0 0.5 O B:HIS105 2.9 3.0 1.0 CD2 B:HIS105 3.3 24.0 1.0 CG B:ASN109 3.3 16.0 0.5 NE2 B:HIS105 3.4 6.0 1.0 CG B:HIS105 3.6 5.0 1.0 N B:ASN109 3.6 5.0 1.0 C B:HIS105 3.7 4.0 1.0 CB B:LYS108 3.7 4.0 1.0 CE1 B:HIS105 3.8 9.0 1.0 ND1 B:HIS105 3.8 15.0 1.0 CA B:HIS105 3.9 11.0 1.0 ND2 B:ASN109 3.9 14.0 0.5 C B:LYS108 4.1 6.0 1.0 CA B:ASN109 4.2 10.0 1.0 CB B:ASN109 4.2 4.0 0.5 CB B:ASN109 4.2 4.0 0.5 CB B:HIS105 4.3 4.0 1.0 CA B:LYS108 4.4 9.0 1.0 O B:LYS108 4.8 4.0 1.0 N B:LYS108 4.9 3.0 1.0 CG B:LYS108 4.9 3.0 1.0 NA B:NA212 4.9 8.0 1.0 N B:LEU106 4.9 4.0 1.0

Sodium binding site 8 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ B:Na212 b:8.0 occ:1.00 O M:HOH371 2.5 7.0 1.0 O B:HOH360 2.8 8.0 1.0 CA B:HIS105 3.7 11.0 1.0 N B:HIS105 3.8 4.0 1.0 CG B:LEU104 3.8 6.0 1.0 CD B:LYS108 3.9 7.0 1.0 CD2 B:LEU104 4.1 6.0 1.0 CB B:HIS105 4.1 4.0 1.0 C B:LEU104 4.2 6.0 1.0 O B:LEU104 4.3 3.0 1.0 CD2 B:HIS105 4.4 24.0 1.0 O B:HOH398 4.5 8.0 1.0 CB B:LEU104 4.5 5.0 1.0 CG B:HIS105 4.6 5.0 1.0 CG B:LYS108 4.7 3.0 1.0 O B:GLU101 4.8 6.0 1.0 O M:GLN7 4.9 7.0 1.0 NA B:NA209 4.9 4.0 1.0 CD1 B:LEU104 4.9 3.0 1.0

Sodium binding site 9 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ B:Na215 b:7.0 occ:1.00 O B:HOH410 2.2 10.0 1.0 O B:HOH337 2.9 5.0 1.0 CD1 B:TYR29 3.6 6.0 1.0 CG B:TYR29 3.7 7.0 1.0 CD1 B:LEU26 3.8 8.0 1.0 CE1 B:TYR29 3.9 5.0 1.0 O B:HOH369 4.0 4.0 1.0 CB B:TYR29 4.1 4.0 1.0 CD2 B:TYR29 4.2 6.0 1.0 O B:HOH408 4.2 7.0 1.0 CZ B:TYR29 4.4 6.0 1.0 CE2 B:TYR29 4.5 3.0 1.0 OD1 B:ASN25 4.8 5.0 1.0 CA B:LEU26 5.0 11.0 1.0

Sodium binding site 10 out of 112 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ B:Na216 b:7.0 occ:1.00 OE1 B:GLN112 1.9 19.0 1.0 CD B:GLN112 3.0 11.0 1.0 NE2 M:GLN10 3.2 5.0 1.0 CG B:GLN112 3.7 5.0 1.0 CG M:GLN10 3.8 7.0 1.0 CD M:GLN10 4.0 6.0 1.0 NE2 B:GLN112 4.0 13.0 1.0 CB B:GLN112 4.1 3.0 1.0 O M:HOH366 4.4 9.0 1.0

K.Zhang, G.D.Pintilie, S.Li, M.F.Schmid, W.Chiu. Resolving Individual Atoms of Protein Complex By Cryo-Electron Microscopy. Cell Res. 2020.
ISSN: ISSN 1001-0602
PubMed: 33139928
DOI: 10.1038/S41422-020-00432-2