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Sodium in PDB 7k3v: Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector

Enzymatic activity of Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector

All present enzymatic activity of Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector:
1.16.3.1;

Other elements in 7k3v:

The structure of Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector also contains other interesting chemical elements:

Zinc (Zn) 254 atoms

Sodium Binding Sites:

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;

Binding sites:

The binding sites of Sodium atom in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector (pdb code 7k3v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 80 binding sites of Sodium where determined in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector, PDB code: 7k3v:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 80 in 7k3v

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Sodium binding site 1 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:6.0
occ:1.00
 O A:HOH381 2.2 6.0 1.0
O A:CYS90 2.5 8.0 1.0
OG A:SER36 2.5 3.0 1.0
ZN A:ZN205 2.9 5.0 1.0
CB A:SER36 3.3 4.0 1.0
C A:CYS90 3.5 9.0 1.0
CB A:PRO88 3.6 6.0 1.0
CG A:PRO88 3.7 4.0 1.0
O S:HOH385 3.7 7.0 1.0
CA A:ASP91 3.8 18.0 1.0
CD A:PRO88 3.8 5.0 1.0
OD1 A:ASP91 3.8 18.0 1.0
CD1 S:LEU82 3.8 3.0 1.0
N A:ASP91 3.9 8.0 1.0
O A:HOH361 4.1 10.0 1.0
CB S:LEU82 4.3 5.0 1.0
CG S:LEU82 4.4 6.0 1.0
O A:PRO88 4.5 7.0 1.0
N A:PRO88 4.5 5.0 1.0
CA A:PRO88 4.5 9.0 1.0
CG A:ASP91 4.6 34.0 1.0
CB A:ASP91 4.6 14.0 1.0
C A:PRO88 4.6 6.0 1.0
NE1 A:TRP93 4.6 5.0 1.0
CA A:SER36 4.6 8.0 1.0
CA A:CYS90 4.7 19.0 1.0
N A:CYS90 4.7 8.0 1.0
C A:ASP91 4.8 10.0 1.0
CZ2 A:TRP93 4.8 8.0 1.0
O A:ASP91 4.9 5.0 1.0

Sodium binding site 2 out of 80 in 7k3v

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Sodium binding site 2 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:4.0
occ:1.00
 OD1 A:ASN109 2.4 14.0 1.0
O A:HIS105 2.7 4.0 1.0
O A:HOH401 3.0 9.0 1.0
CG A:ASN109 3.2 16.0 1.0
CD2 A:HIS105 3.3 16.0 1.0
NE2 A:HIS105 3.4 15.0 1.0
N A:ASN109 3.5 5.0 1.0
CB A:LYS108 3.5 4.0 1.0
CG A:HIS105 3.5 10.0 1.0
C A:HIS105 3.6 5.0 1.0
CE1 A:HIS105 3.7 9.0 1.0
ND1 A:HIS105 3.7 16.0 1.0
CA A:HIS105 3.8 8.0 1.0
ND2 A:ASN109 3.9 19.0 1.0
C A:LYS108 3.9 8.0 1.0
CA A:ASN109 4.1 8.0 1.0
CB A:ASN109 4.2 6.0 1.0
CA A:LYS108 4.2 9.0 1.0
CB A:HIS105 4.2 4.0 1.0
O A:LYS108 4.7 6.0 1.0
CG A:LYS108 4.7 5.0 1.0
N A:LYS108 4.7 4.0 1.0
O A:HOH372 4.8 8.0 1.0
N A:LEU106 4.9 4.0 1.0
CD A:LYS108 4.9 9.0 1.0
O A:HOH399 4.9 5.0 1.0
O A:LEU104 4.9 4.0 1.0

Sodium binding site 3 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 3 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na214

b:7.0
occ:1.00
 OE1 A:GLN112 1.9 10.0 1.0
CD A:GLN112 2.9 11.0 1.0
NE2 T:GLN10 3.0 7.0 1.0
CG A:GLN112 3.4 7.0 1.0
CG T:GLN10 3.6 5.0 1.0
CD T:GLN10 3.8 9.0 1.0
CB A:GLN112 3.8 4.0 1.0
NE2 A:GLN112 4.0 15.0 1.0
O T:HOH364 4.3 9.0 1.0
CA A:GLN112 4.6 9.0 1.0
OE1 T:GLN10 5.0 4.0 1.0

Sodium binding site 4 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 4 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:6.0
occ:1.00
 O B:HOH381 2.2 6.0 1.0
O B:CYS90 2.5 8.0 1.0
OG B:SER36 2.5 3.0 1.0
ZN B:ZN205 2.9 5.0 1.0
CB B:SER36 3.3 4.0 1.0
C B:CYS90 3.5 9.0 1.0
CB B:PRO88 3.6 6.0 1.0
CG B:PRO88 3.7 4.0 1.0
O P:HOH384 3.7 7.0 1.0
CA B:ASP91 3.8 18.0 1.0
CD B:PRO88 3.8 5.0 1.0
OD1 B:ASP91 3.8 18.0 1.0
CD1 P:LEU82 3.8 3.0 1.0
N B:ASP91 3.9 8.0 1.0
O B:HOH361 4.1 10.0 1.0
CB P:LEU82 4.3 5.0 1.0
CG P:LEU82 4.4 6.0 1.0
O B:PRO88 4.5 7.0 1.0
N B:PRO88 4.5 5.0 1.0
CA B:PRO88 4.5 9.0 1.0
CG B:ASP91 4.6 34.0 1.0
CB B:ASP91 4.6 14.0 1.0
C B:PRO88 4.6 6.0 1.0
NE1 B:TRP93 4.6 5.0 1.0
CA B:SER36 4.6 8.0 1.0
CA B:CYS90 4.7 19.0 1.0
N B:CYS90 4.7 8.0 1.0
C B:ASP91 4.8 10.0 1.0
CZ2 B:TRP93 4.8 8.0 1.0
O B:ASP91 4.9 5.0 1.0

Sodium binding site 5 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 5 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na210

b:4.0
occ:1.00
 OD1 B:ASN109 2.4 14.0 1.0
O B:HIS105 2.7 4.0 1.0
O B:HOH401 3.0 9.0 1.0
CG B:ASN109 3.2 16.0 1.0
CD2 B:HIS105 3.3 16.0 1.0
NE2 B:HIS105 3.4 15.0 1.0
N B:ASN109 3.5 5.0 1.0
CB B:LYS108 3.5 4.0 1.0
CG B:HIS105 3.5 10.0 1.0
C B:HIS105 3.6 5.0 1.0
CE1 B:HIS105 3.7 9.0 1.0
ND1 B:HIS105 3.7 16.0 1.0
CA B:HIS105 3.8 8.0 1.0
ND2 B:ASN109 3.9 19.0 1.0
C B:LYS108 3.9 8.0 1.0
CA B:ASN109 4.1 8.0 1.0
CB B:ASN109 4.2 6.0 1.0
CA B:LYS108 4.2 9.0 1.0
CB B:HIS105 4.2 4.0 1.0
O B:LYS108 4.7 6.0 1.0
CG B:LYS108 4.7 5.0 1.0
N B:LYS108 4.7 4.0 1.0
O B:HOH372 4.8 8.0 1.0
N B:LEU106 4.9 4.0 1.0
CD B:LYS108 4.9 9.0 1.0
O B:HOH399 4.9 5.0 1.0
O B:LEU104 4.9 4.0 1.0

Sodium binding site 6 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 6 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na214

b:7.0
occ:1.00
 OE1 B:GLN112 1.9 10.0 1.0
CD B:GLN112 2.9 11.0 1.0
NE2 M:GLN10 3.0 7.0 1.0
CG B:GLN112 3.4 7.0 1.0
CG M:GLN10 3.6 5.0 1.0
CD M:GLN10 3.8 9.0 1.0
CB B:GLN112 3.8 4.0 1.0
NE2 B:GLN112 4.0 15.0 1.0
O M:HOH363 4.3 9.0 1.0
CA B:GLN112 4.6 9.0 1.0
OE1 M:GLN10 5.0 4.0 1.0

Sodium binding site 7 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 7 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na206

b:6.0
occ:1.00
 O C:HOH382 2.2 6.0 1.0
O C:CYS90 2.5 8.0 1.0
OG C:SER36 2.5 3.0 1.0
ZN C:ZN205 2.9 5.0 1.0
CB C:SER36 3.3 4.0 1.0
C C:CYS90 3.5 9.0 1.0
CB C:PRO88 3.6 6.0 1.0
CG C:PRO88 3.7 4.0 1.0
O U:HOH384 3.7 7.0 1.0
CA C:ASP91 3.8 18.0 1.0
CD C:PRO88 3.8 5.0 1.0
OD1 C:ASP91 3.8 18.0 1.0
CD1 U:LEU82 3.8 3.0 1.0
N C:ASP91 3.9 8.0 1.0
O C:HOH362 4.1 10.0 1.0
CB U:LEU82 4.3 5.0 1.0
CG U:LEU82 4.4 6.0 1.0
O C:PRO88 4.5 7.0 1.0
N C:PRO88 4.5 5.0 1.0
CA C:PRO88 4.5 9.0 1.0
CG C:ASP91 4.6 34.0 1.0
CB C:ASP91 4.6 14.0 1.0
C C:PRO88 4.6 6.0 1.0
NE1 C:TRP93 4.6 5.0 1.0
CA C:SER36 4.6 8.0 1.0
CA C:CYS90 4.7 19.0 1.0
N C:CYS90 4.7 8.0 1.0
C C:ASP91 4.8 10.0 1.0
CZ2 C:TRP93 4.8 8.0 1.0
O C:ASP91 4.9 5.0 1.0

Sodium binding site 8 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 8 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na210

b:4.0
occ:1.00
 OD1 C:ASN109 2.4 14.0 1.0
O C:HIS105 2.7 4.0 1.0
O C:HOH402 3.0 9.0 1.0
CG C:ASN109 3.2 16.0 1.0
CD2 C:HIS105 3.3 16.0 1.0
NE2 C:HIS105 3.4 15.0 1.0
N C:ASN109 3.5 5.0 1.0
CB C:LYS108 3.5 4.0 1.0
CG C:HIS105 3.5 10.0 1.0
C C:HIS105 3.6 5.0 1.0
CE1 C:HIS105 3.7 9.0 1.0
ND1 C:HIS105 3.7 16.0 1.0
CA C:HIS105 3.8 8.0 1.0
ND2 C:ASN109 3.9 19.0 1.0
C C:LYS108 3.9 8.0 1.0
CA C:ASN109 4.1 8.0 1.0
CB C:ASN109 4.2 6.0 1.0
CA C:LYS108 4.2 9.0 1.0
CB C:HIS105 4.2 4.0 1.0
O C:LYS108 4.7 6.0 1.0
CG C:LYS108 4.7 5.0 1.0
N C:LYS108 4.7 4.0 1.0
O C:HOH373 4.8 8.0 1.0
N C:LEU106 4.9 4.0 1.0
CD C:LYS108 4.9 9.0 1.0
O C:HOH400 4.9 5.0 1.0
O C:LEU104 4.9 4.0 1.0

Sodium binding site 9 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 9 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na214

b:7.0
occ:1.00
 OE1 C:GLN112 1.9 10.0 1.0
CD C:GLN112 2.9 11.0 1.0
NE2 V:GLN10 3.0 7.0 1.0
CG C:GLN112 3.4 7.0 1.0
CG V:GLN10 3.6 5.0 1.0
CD V:GLN10 3.8 9.0 1.0
CB C:GLN112 3.8 4.0 1.0
NE2 C:GLN112 4.0 15.0 1.0
O V:HOH363 4.3 9.0 1.0
CA C:GLN112 4.6 9.0 1.0
OE1 V:GLN10 5.0 4.0 1.0

Sodium binding site 10 out of 80 in 7k3v

Go back to Sodium Binding Sites List in 7k3v
Sodium binding site 10 out of 80 in the Apoferritin Structure at 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 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 1.34 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with K3 Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na206

b:6.0
occ:1.00
 O D:HOH381 2.2 6.0 1.0
O D:CYS90 2.5 8.0 1.0
OG D:SER36 2.5 3.0 1.0
ZN D:ZN205 2.9 5.0 1.0
CB D:SER36 3.3 4.0 1.0
C D:CYS90 3.5 9.0 1.0
CB D:PRO88 3.6 6.0 1.0
CG D:PRO88 3.7 4.0 1.0
O F:HOH384 3.7 7.0 1.0
CA D:ASP91 3.8 18.0 1.0
CD D:PRO88 3.8 5.0 1.0
OD1 D:ASP91 3.8 18.0 1.0
CD1 F:LEU82 3.8 3.0 1.0
N D:ASP91 3.9 8.0 1.0
O D:HOH361 4.1 10.0 1.0
CB F:LEU82 4.3 5.0 1.0
CG F:LEU82 4.4 6.0 1.0
O D:PRO88 4.5 7.0 1.0
N D:PRO88 4.5 5.0 1.0
CA D:PRO88 4.5 9.0 1.0
CG D:ASP91 4.6 34.0 1.0
CB D:ASP91 4.6 14.0 1.0
C D:PRO88 4.6 6.0 1.0
NE1 D:TRP93 4.6 5.0 1.0
CA D:SER36 4.6 8.0 1.0
CA D:CYS90 4.7 19.0 1.0
N D:CYS90 4.7 8.0 1.0
C D:ASP91 4.8 10.0 1.0
CZ2 D:TRP93 4.8 8.0 1.0
O D:ASP91 4.9 5.0 1.0

Reference:

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
Page generated: Tue Oct 8 17:07:00 2024

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