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Sodium in PDB 7vd8: 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope

Enzymatic activity of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope

All present enzymatic activity of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope:
1.16.3.1;

Other elements in 7vd8:

The structure of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope 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 - 75;

Binding sites:

The binding sites of Sodium atom in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope (pdb code 7vd8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope, PDB code: 7vd8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 7vd8

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Sodium binding site 1 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:9.6
occ:1.00
O A:CYS90 2.5 14.4 1.0
OG A:SER36 2.9 2.9 1.0
CB A:PRO88 3.0 4.4 1.0
O A:HOH305 3.0 9.9 1.0
ZN A:ZN205 3.1 13.4 1.0
O S:HOH380 3.2 9.8 1.0
CG A:PRO88 3.2 2.9 1.0
C A:CYS90 3.5 14.1 1.0
CD A:PRO88 3.5 2.7 1.0
CB A:SER36 3.6 0.3 1.0
O A:PRO88 3.9 10.0 1.0
CA A:ASP91 3.9 17.0 1.0
CA A:PRO88 4.0 6.3 1.0
N A:ASP91 4.0 16.0 1.0
O S:HOH388 4.0 0.0 1.0
C A:PRO88 4.1 8.2 1.0
N A:PRO88 4.1 4.2 1.0
CD1 S:LEU82 4.3 1.5 1.0
OD2 A:ASP91 4.3 37.8 1.0
N A:CYS90 4.5 16.1 1.0
CZ2 A:TRP93 4.5 3.8 1.0
CB S:LEU82 4.5 1.2 1.0
CG A:ASP91 4.5 28.0 1.0
CA A:CYS90 4.6 16.0 1.0
CB A:ASP91 4.6 21.5 1.0
CG S:LEU82 4.8 2.3 1.0
NE1 A:TRP93 4.9 3.1 1.0
N A:ASP89 4.9 15.1 1.0
C A:ASP91 5.0 16.4 1.0

Sodium binding site 2 out of 75 in 7vd8

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Sodium binding site 2 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:4.3
occ:1.00
OD1 A:ASN109 2.4 13.3 1.0
O A:HIS105 2.7 2.7 1.0
CB A:LYS108 3.0 1.3 1.0
N A:ASN109 3.3 2.3 1.0
CG A:ASN109 3.4 10.6 1.0
C A:HIS105 3.6 2.2 1.0
C A:LYS108 3.6 1.6 1.0
CD2 A:HIS105 3.8 11.0 1.0
CA A:HIS105 3.8 2.6 1.0
CA A:LYS108 3.8 1.8 1.0
CG A:HIS105 3.8 9.4 1.0
NE2 A:HIS105 4.0 12.7 1.0
CA A:ASN109 4.0 2.6 1.0
ND1 A:HIS105 4.1 12.7 1.0
CE1 A:HIS105 4.1 13.9 1.0
CG A:LYS108 4.2 2.7 1.0
CB A:ASN109 4.2 3.2 1.0
ND2 A:ASN109 4.3 19.5 1.0
CD A:LYS108 4.3 2.9 1.0
N A:LYS108 4.3 1.7 1.0
CB A:HIS105 4.4 4.0 1.0
O A:LYS108 4.4 2.5 1.0
O A:HOH396 4.5 3.0 1.0
O A:LEU104 4.8 1.5 1.0
N A:LEU106 4.9 1.7 1.0

Sodium binding site 3 out of 75 in 7vd8

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Sodium binding site 3 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na215

b:19.0
occ:1.00
NE2 A:GLN10 2.6 1.8 1.0
NE2 F:GLN112 3.3 10.7 1.0
CD A:GLN10 3.5 3.0 1.0
CG A:GLN10 3.6 2.1 1.0
CG F:GLN112 3.8 5.3 1.0
CB F:GLN112 3.9 2.7 1.0
CD F:GLN112 4.0 9.1 1.0
OE1 A:GLN10 4.7 5.2 1.0
O A:HOH311 4.8 0.3 1.0
O F:LYS108 4.8 2.4 1.0
CA F:GLN112 4.9 2.9 1.0
CB A:GLN10 5.0 2.5 1.0

Sodium binding site 4 out of 75 in 7vd8

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Sodium binding site 4 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:12.9
occ:1.00
O B:CYS90 2.5 14.2 1.0
OG B:SER36 2.9 2.9 1.0
CB B:PRO88 3.0 4.3 1.0
O P:HOH380 3.1 13.7 1.0
ZN B:ZN205 3.1 19.7 1.0
CG B:PRO88 3.2 2.8 1.0
C B:CYS90 3.5 14.2 1.0
CD B:PRO88 3.5 2.4 1.0
CB B:SER36 3.6 0.3 1.0
O B:PRO88 3.9 10.2 1.0
CA B:ASP91 3.9 17.7 1.0
CA B:PRO88 4.0 6.2 1.0
N B:ASP91 4.0 16.2 1.0
O P:HOH385 4.0 0.0 1.0
C B:PRO88 4.1 8.0 1.0
N B:PRO88 4.1 4.0 1.0
O B:HOH304 4.2 13.8 1.0
CD1 P:LEU82 4.3 1.5 1.0
OD2 B:ASP91 4.3 36.7 1.0
N B:CYS90 4.5 17.2 1.0
CZ2 B:TRP93 4.5 3.7 1.0
CB P:LEU82 4.5 1.1 1.0
CG B:ASP91 4.5 27.4 1.0
CA B:CYS90 4.6 17.3 1.0
CB B:ASP91 4.6 22.0 1.0
CG P:LEU82 4.7 2.4 1.0
NE1 B:TRP93 4.9 3.0 1.0
N B:ASP89 4.9 14.8 1.0
C B:ASP91 5.0 16.9 1.0

Sodium binding site 5 out of 75 in 7vd8

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Sodium binding site 5 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na210

b:5.1
occ:1.00
OD1 B:ASN109 2.4 13.5 1.0
O B:HIS105 2.7 2.5 1.0
CB B:LYS108 3.0 1.1 1.0
N B:ASN109 3.3 2.1 1.0
CG B:ASN109 3.4 9.9 1.0
C B:HIS105 3.6 2.0 1.0
C B:LYS108 3.6 1.4 1.0
CD2 B:HIS105 3.7 10.3 1.0
CA B:HIS105 3.8 2.4 1.0
CG B:HIS105 3.8 8.6 1.0
CA B:LYS108 3.8 1.6 1.0
NE2 B:HIS105 3.9 12.2 1.0
CA B:ASN109 4.0 2.1 1.0
ND1 B:HIS105 4.0 12.4 1.0
CE1 B:HIS105 4.1 13.4 1.0
CG B:LYS108 4.2 2.4 1.0
CB B:ASN109 4.2 2.9 1.0
ND2 B:ASN109 4.3 19.4 1.0
N B:LYS108 4.3 1.5 1.0
CD B:LYS108 4.3 2.7 1.0
CB B:HIS105 4.4 3.9 1.0
O B:LYS108 4.4 2.3 1.0
O B:HOH393 4.5 2.4 1.0
O B:LEU104 4.7 1.5 1.0
N B:LEU106 4.8 1.5 1.0

Sodium binding site 6 out of 75 in 7vd8

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Sodium binding site 6 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na216

b:38.9
occ:1.00
NE2 B:GLN10 2.6 2.0 1.0
NE2 S:GLN112 3.1 10.9 1.0
CD B:GLN10 3.6 3.5 1.0
CG B:GLN10 3.7 2.3 1.0
CG S:GLN112 3.7 6.0 1.0
CB S:GLN112 3.8 2.9 1.0
CD S:GLN112 3.8 9.6 1.0
OE1 B:GLN10 4.7 5.8 1.0
O B:HOH312 4.8 0.0 1.0
O S:LYS108 4.8 2.6 1.0
CA S:GLN112 4.8 2.9 1.0

Sodium binding site 7 out of 75 in 7vd8

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Sodium binding site 7 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na206

b:7.9
occ:1.00
O C:CYS90 2.5 15.4 1.0
OG C:SER36 2.9 2.8 1.0
O C:HOH304 3.0 8.6 1.0
CB C:PRO88 3.0 4.8 1.0
ZN C:ZN205 3.1 12.8 1.0
O U:HOH374 3.2 8.4 1.0
CG C:PRO88 3.2 3.1 1.0
C C:CYS90 3.4 15.8 1.0
CD C:PRO88 3.5 2.8 1.0
CB C:SER36 3.6 0.3 1.0
O C:PRO88 3.9 11.1 1.0
CA C:ASP91 3.9 20.3 1.0
CA C:PRO88 4.0 7.0 1.0
N C:ASP91 4.0 18.4 1.0
O U:HOH387 4.0 0.1 1.0
C C:PRO88 4.1 8.9 1.0
N C:PRO88 4.1 4.5 1.0
CD1 U:LEU82 4.3 1.5 1.0
OD2 C:ASP91 4.3 36.8 1.0
N C:CYS90 4.5 18.6 1.0
CB U:LEU82 4.5 1.2 1.0
CZ2 C:TRP93 4.5 4.2 1.0
CG C:ASP91 4.5 28.7 1.0
CA C:CYS90 4.6 18.3 1.0
CB C:ASP91 4.6 24.1 1.0
CG U:LEU82 4.7 2.3 1.0
NE1 C:TRP93 4.9 3.2 1.0
N C:ASP89 4.9 15.6 1.0
C C:ASP91 5.0 18.7 1.0

Sodium binding site 8 out of 75 in 7vd8

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Sodium binding site 8 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na210

b:5.2
occ:1.00
OD1 C:ASN109 2.4 13.1 1.0
O C:HIS105 2.7 2.6 1.0
CB C:LYS108 3.0 1.2 1.0
N C:ASN109 3.3 2.3 1.0
CG C:ASN109 3.4 9.7 1.0
C C:HIS105 3.6 2.2 1.0
C C:LYS108 3.6 1.6 1.0
ND1 C:HIS105 3.7 12.2 1.0
CA C:HIS105 3.8 2.5 1.0
CA C:LYS108 3.8 1.7 1.0
CG C:HIS105 3.8 8.9 1.0
CE1 C:HIS105 3.9 11.5 1.0
CA C:ASN109 4.0 2.4 1.0
CD2 C:HIS105 4.1 10.4 1.0
NE2 C:HIS105 4.1 14.4 1.0
CG C:LYS108 4.2 2.7 1.0
CB C:ASN109 4.2 3.0 1.0
ND2 C:ASN109 4.3 18.7 1.0
CD C:LYS108 4.3 2.8 1.0
N C:LYS108 4.3 1.6 1.0
CB C:HIS105 4.3 4.0 1.0
O C:LYS108 4.4 2.6 1.0
O C:HOH398 4.5 3.1 1.0
O C:LEU104 4.7 1.6 1.0
N C:LEU106 4.8 1.7 1.0

Sodium binding site 9 out of 75 in 7vd8

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Sodium binding site 9 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na215

b:12.6
occ:1.00
NE2 C:GLN10 2.6 1.9 1.0
NE2 P:GLN112 3.2 11.3 1.0
CD C:GLN10 3.6 3.2 1.0
CG C:GLN10 3.7 2.2 1.0
CG P:GLN112 3.7 5.8 1.0
CB P:GLN112 3.9 2.8 1.0
CD P:GLN112 3.9 9.7 1.0
OE1 C:GLN10 4.7 5.4 1.0
O C:HOH313 4.8 2.7 1.0
O P:LYS108 4.8 2.6 1.0
CA P:GLN112 4.9 2.8 1.0
CB C:GLN10 5.0 2.5 1.0

Sodium binding site 10 out of 75 in 7vd8

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Sodium binding site 10 out of 75 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na206

b:13.9
occ:1.00
O D:CYS90 2.5 14.4 1.0
OG D:SER36 2.9 2.6 1.0
CB D:PRO88 3.1 4.4 1.0
ZN D:ZN205 3.1 15.8 1.0
O F:HOH380 3.1 14.1 1.0
CG D:PRO88 3.2 3.0 1.0
CD D:PRO88 3.4 2.6 1.0
C D:CYS90 3.5 14.0 1.0
CB D:SER36 3.6 0.3 1.0
O D:PRO88 3.9 10.2 1.0
CA D:ASP91 3.9 17.8 1.0
CA D:PRO88 4.0 6.2 1.0
N D:ASP91 4.0 16.2 1.0
O F:HOH387 4.0 0.0 1.0
C D:PRO88 4.1 8.2 1.0
N D:PRO88 4.1 4.5 1.0
OD2 D:ASP91 4.2 36.4 1.0
O D:HOH305 4.2 14.2 1.0
CD1 F:LEU82 4.3 1.5 1.0
N D:CYS90 4.5 16.2 1.0
CZ2 D:TRP93 4.5 3.6 1.0
CB F:LEU82 4.5 1.2 1.0
CG D:ASP91 4.6 27.1 1.0
CA D:CYS90 4.6 15.9 1.0
CB D:ASP91 4.7 21.2 1.0
CG F:LEU82 4.7 2.4 1.0
NE1 D:TRP93 4.9 2.6 1.0
N D:ASP89 4.9 15.2 1.0
C D:ASP91 5.0 16.9 1.0

Reference:

H.Fan, B.Wang, Y.Zhang, Y.Zhu, B.Song, H.Xu, Y.Zhai, M.Qiao, F.Sun. A Cryo-Electron Microscopy Support Film Formed By 2D Crystals of Hydrophobin Hfbi. Nat Commun V. 12 7257 2021.
ISSN: ESSN 2041-1723
PubMed: 34907237
DOI: 10.1038/S41467-021-27596-8
Page generated: Thu Mar 31 04:39:24 2022

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