Sodium in PDB 8j5a: Single-Particle Cryo-Em Structure of Mouse Apoferritin at 1.19 Angstrom Resolution (Dataset A)

The binding sites of Sodium atom in the Single-Particle Cryo-Em Structure of Mouse Apoferritin at 1.19 Angstrom Resolution (Dataset A) (pdb code 8j5a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Single-Particle Cryo-Em Structure of Mouse Apoferritin at 1.19 Angstrom Resolution (Dataset A), PDB code: 8j5a:

Sodium binding site 1 out of 1 in the Single-Particle Cryo-Em Structure of Mouse Apoferritin at 1.19 Angstrom Resolution (Dataset A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Single-Particle Cryo-Em Structure of Mouse Apoferritin at 1.19 Angstrom Resolution (Dataset A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:27.7 occ:1.00 OE1 A:GLU27 1.9 27.2 1.0 OE1 A:GLU62 2.0 34.4 1.0 ND1 A:HIS65 2.2 26.4 1.0 O A:HOH332 2.2 39.5 0.5 O A:HOH321 2.3 35.6 1.0 CD A:GLU27 2.9 22.4 1.0 CD A:GLU62 2.9 27.0 1.0 CE1 A:HIS65 3.1 28.1 1.0 CG A:HIS65 3.2 21.3 1.0 OE2 A:GLU62 3.2 37.7 1.0 OE2 A:GLU27 3.3 26.8 1.0 HG11 A:VAL110 3.3 23.1 1.0 CB A:HIS65 3.4 16.7 1.0 OE1 A:GLN141 4.0 36.2 1.0 O A:HOH388 4.1 38.7 1.0 O A:HOH306 4.1 46.5 1.0 HB3 A:GLU27 4.1 18.8 1.0 HA A:GLU27 4.2 16.2 1.0 CG A:GLU27 4.2 16.8 1.0 CG A:GLU62 4.2 19.7 1.0 CA A:GLU62 4.2 14.4 1.0 NE2 A:HIS65 4.3 29.6 1.0 CG1 A:VAL110 4.3 19.2 1.0 CD2 A:HIS65 4.3 22.4 1.0 CB A:GLU62 4.4 15.2 1.0 HE2 A:TYR137 4.5 22.4 1.0 HG12 A:VAL110 4.5 23.1 1.0 HD2 A:TYR137 4.5 22.4 1.0 CB A:GLU27 4.6 13.8 1.0 HG3 A:GLU27 4.6 21.7 1.0 HG21 A:VAL110 4.7 22.6 1.0 HB3 A:ALA30 4.7 19.7 1.0 HG13 A:VAL110 4.7 23.1 1.0 O A:GLU62 4.7 17.7 1.0 CD A:GLN141 4.9 25.3 1.0 CA A:GLU27 4.9 12.1 1.0 CA A:HIS65 4.9 14.8 1.0 HG2 A:GLU27 4.9 21.7 1.0 HD11 A:LEU114 4.9 22.7 1.0

S.Maki-Yonekura, K.Kawakami, K.Takaba, T.Hamaguchi, K.Yonekura. Measurement of Charges and Chemical Bonding in A Cryo-Em Structure. Commun Chem V. 6 98 2023.
ISSN: ESSN 2399-3669
PubMed: 37258702
DOI: 10.1038/S42004-023-00900-X