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Sodium in PDB 8cps: Human Apoferritin

Other elements in 8cps:

The structure of Human Apoferritin also contains other interesting chemical elements:

Magnesium (Mg) 14 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the Human Apoferritin (pdb code 8cps). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the Human Apoferritin, PDB code: 8cps:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 8cps

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Sodium binding site 1 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na201

b:6.3
occ:1.00
 O 1:HOH305 2.4 5.8 1.0
OE1 1:GLU27 2.4 4.6 1.0
OE1 1:GLU62 2.4 4.7 1.0
O 1:HOH303 2.4 5.8 1.0
ND1 1:HIS65 2.5 4.7 1.0
OE2 1:GLU62 2.8 4.7 1.0
CD 1:GLU62 2.9 4.7 1.0
CD 1:GLU27 3.3 4.6 1.0
CE1 1:HIS65 3.3 4.7 1.0
OE2 1:GLU27 3.4 4.6 1.0
CG 1:HIS65 3.5 4.7 1.0
OE1 1:GLN141 3.7 5.4 1.0
CB 1:HIS65 3.9 4.7 1.0
CG1 1:VAL110 4.1 5.2 1.0
CG 1:GLU62 4.4 4.7 1.0
CD 1:GLN141 4.4 5.4 1.0
NE2 1:HIS65 4.5 4.7 1.0
CD2 1:HIS65 4.6 4.7 1.0
CA 1:GLU62 4.6 4.7 1.0
OE1 1:GLU107 4.7 5.2 1.0
CG 1:GLU27 4.7 4.6 1.0
NE2 1:GLN141 4.8 5.4 1.0
CB 1:GLU62 4.8 4.7 1.0

Sodium binding site 2 out of 24 in 8cps

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Sodium binding site 2 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na502

b:6.5
occ:1.00
 OE1 2:GLU27 2.4 4.6 1.0
O 2:HOH604 2.4 5.8 1.0
O 2:HOH603 2.4 6.0 1.0
OE1 2:GLU62 2.4 4.7 1.0
ND1 2:HIS65 2.5 4.7 1.0
OE2 2:GLU62 2.8 4.7 1.0
CD 2:GLU62 2.9 4.7 1.0
CD 2:GLU27 3.3 4.6 1.0
CE1 2:HIS65 3.3 4.7 1.0
OE2 2:GLU27 3.4 4.6 1.0
CG 2:HIS65 3.5 4.7 1.0
OE1 2:GLN141 3.7 5.4 1.0
CB 2:HIS65 3.9 4.7 1.0
CG1 2:VAL110 4.1 5.2 1.0
CG 2:GLU62 4.4 4.7 1.0
CD 2:GLN141 4.4 5.4 1.0
NE2 2:HIS65 4.5 4.7 1.0
CD2 2:HIS65 4.6 4.7 1.0
CA 2:GLU62 4.7 4.7 1.0
CG 2:GLU27 4.7 4.6 1.0
OE2 2:GLU107 4.7 5.3 1.0
NE2 2:GLN141 4.8 5.4 1.0
CB 2:GLU62 4.9 4.7 1.0

Sodium binding site 3 out of 24 in 8cps

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Sodium binding site 3 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Na201

b:6.4
occ:1.00
 O 4:HOH304 2.4 5.8 1.0
OE1 4:GLU27 2.4 4.5 1.0
OE1 4:GLU62 2.4 4.7 1.0
O 4:HOH302 2.4 5.9 1.0
ND1 4:HIS65 2.5 4.7 1.0
OE2 4:GLU62 2.9 4.7 1.0
CD 4:GLU62 2.9 4.7 1.0
CD 4:GLU27 3.3 4.5 1.0
CE1 4:HIS65 3.3 4.7 1.0
OE2 4:GLU27 3.4 4.5 1.0
CG 4:HIS65 3.5 4.7 1.0
OE1 4:GLN141 3.7 5.4 1.0
CB 4:HIS65 3.9 4.7 1.0
CG1 4:VAL110 4.1 5.2 1.0
CG 4:GLU62 4.4 4.7 1.0
CD 4:GLN141 4.4 5.4 1.0
NE2 4:HIS65 4.5 4.7 1.0
CD2 4:HIS65 4.6 4.7 1.0
CA 4:GLU62 4.6 4.7 1.0
OE1 4:GLU107 4.7 5.2 1.0
CG 4:GLU27 4.7 4.5 1.0
NE2 4:GLN141 4.8 5.4 1.0
CB 4:GLU62 4.8 4.7 1.0

Sodium binding site 4 out of 24 in 8cps

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Sodium binding site 4 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Na201

b:6.5
occ:1.00
 O 6:HOH304 2.4 5.8 1.0
OE1 6:GLU27 2.4 4.6 1.0
OE1 6:GLU62 2.4 4.7 1.0
O 6:HOH302 2.4 6.0 1.0
ND1 6:HIS65 2.5 4.7 1.0
OE2 6:GLU62 2.9 4.7 1.0
CD 6:GLU62 2.9 4.7 1.0
CD 6:GLU27 3.3 4.6 1.0
CE1 6:HIS65 3.3 4.7 1.0
OE2 6:GLU27 3.4 4.6 1.0
CG 6:HIS65 3.5 4.7 1.0
OE1 6:GLN141 3.7 5.4 1.0
CB 6:HIS65 3.9 4.7 1.0
CG1 6:VAL110 4.1 5.2 1.0
CG 6:GLU62 4.4 4.7 1.0
CD 6:GLN141 4.4 5.4 1.0
NE2 6:HIS65 4.5 4.7 1.0
CD2 6:HIS65 4.6 4.7 1.0
CA 6:GLU62 4.6 4.7 1.0
OE1 6:GLU107 4.7 5.3 1.0
CG 6:GLU27 4.7 4.6 1.0
CB 6:GLU62 4.8 4.7 1.0
NE2 6:GLN141 4.9 5.4 1.0

Sodium binding site 5 out of 24 in 8cps

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Sodium binding site 5 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:6.5
occ:1.00
 O A:HOH605 2.4 5.8 1.0
OE1 A:GLU27 2.4 4.6 1.0
OE1 A:GLU62 2.4 4.7 1.0
O A:HOH603 2.4 5.8 1.0
ND1 A:HIS65 2.5 4.7 1.0
OE2 A:GLU62 2.8 4.7 1.0
CD A:GLU62 2.9 4.7 1.0
CD A:GLU27 3.3 4.6 1.0
CE1 A:HIS65 3.3 4.7 1.0
OE2 A:GLU27 3.4 4.6 1.0
CG A:HIS65 3.5 4.7 1.0
OE1 A:GLN141 3.7 5.5 1.0
CB A:HIS65 3.9 4.7 1.0
CG1 A:VAL110 4.1 5.2 1.0
CG A:GLU62 4.4 4.7 1.0
CD A:GLN141 4.4 5.5 1.0
NE2 A:HIS65 4.5 4.7 1.0
CD2 A:HIS65 4.6 4.7 1.0
CA A:GLU62 4.6 4.7 1.0
OE1 A:GLU107 4.7 5.3 1.0
CG A:GLU27 4.7 4.6 1.0
NE2 A:GLN141 4.8 5.5 1.0
CB A:GLU62 4.8 4.7 1.0

Sodium binding site 6 out of 24 in 8cps

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Sodium binding site 6 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na500

b:6.3
occ:1.00
 O B:HOH605 2.4 5.7 1.0
OE1 B:GLU27 2.4 4.6 1.0
OE1 B:GLU62 2.4 4.7 1.0
O B:HOH603 2.4 5.8 1.0
ND1 B:HIS65 2.5 4.7 1.0
OE2 B:GLU62 2.8 4.7 1.0
CD B:GLU62 2.9 4.7 1.0
CD B:GLU27 3.3 4.6 1.0
CE1 B:HIS65 3.3 4.7 1.0
OE2 B:GLU27 3.4 4.6 1.0
CG B:HIS65 3.5 4.7 1.0
OE1 B:GLN141 3.7 5.3 1.0
CB B:HIS65 3.9 4.7 1.0
CG1 B:VAL110 4.1 5.1 1.0
CG B:GLU62 4.4 4.7 1.0
CD B:GLN141 4.4 5.3 1.0
NE2 B:HIS65 4.5 4.7 1.0
CD2 B:HIS65 4.6 4.7 1.0
CA B:GLU62 4.6 4.7 1.0
OE1 B:GLU107 4.7 5.2 1.0
CG B:GLU27 4.7 4.6 1.0
NE2 B:GLN141 4.8 5.3 1.0
CB B:GLU62 4.8 4.7 1.0

Sodium binding site 7 out of 24 in 8cps

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Sodium binding site 7 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na500

b:6.5
occ:1.00
 OE1 E:GLU27 2.4 4.6 1.0
O E:HOH605 2.4 5.8 1.0
O E:HOH603 2.4 6.0 1.0
OE1 E:GLU62 2.4 4.8 1.0
ND1 E:HIS65 2.5 4.8 1.0
OE2 E:GLU62 2.8 4.8 1.0
CD E:GLU62 2.9 4.8 1.0
CD E:GLU27 3.3 4.6 1.0
CE1 E:HIS65 3.3 4.8 1.0
OE2 E:GLU27 3.4 4.6 1.0
CG E:HIS65 3.5 4.8 1.0
OE1 E:GLN141 3.7 5.4 1.0
CB E:HIS65 3.9 4.8 1.0
CG1 E:VAL110 4.1 5.1 1.0
CG E:GLU62 4.4 4.8 1.0
CD E:GLN141 4.4 5.4 1.0
NE2 E:HIS65 4.5 4.8 1.0
CD2 E:HIS65 4.6 4.8 1.0
OE1 E:GLU107 4.6 5.3 1.0
CA E:GLU62 4.7 4.8 1.0
CG E:GLU27 4.7 4.6 1.0
NE2 E:GLN141 4.8 5.4 1.0
CB E:GLU62 4.9 4.8 1.0

Sodium binding site 8 out of 24 in 8cps

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Sodium binding site 8 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na500

b:6.5
occ:1.00
 O F:HOH604 2.4 5.8 1.0
OE1 F:GLU27 2.4 4.7 1.0
OE1 F:GLU62 2.4 4.9 1.0
O F:HOH602 2.4 6.0 1.0
ND1 F:HIS65 2.5 4.8 1.0
OE2 F:GLU62 2.8 4.9 1.0
CD F:GLU62 2.9 4.9 1.0
CD F:GLU27 3.3 4.7 1.0
CE1 F:HIS65 3.3 4.8 1.0
OE2 F:GLU27 3.4 4.7 1.0
CG F:HIS65 3.5 4.8 1.0
OE1 F:GLN141 3.7 5.5 1.0
CB F:HIS65 3.9 4.8 1.0
CG1 F:VAL110 4.1 5.3 1.0
CG F:GLU62 4.4 4.9 1.0
CD F:GLN141 4.4 5.5 1.0
NE2 F:HIS65 4.5 4.8 1.0
CD2 F:HIS65 4.6 4.8 1.0
CA F:GLU62 4.6 4.9 1.0
OE1 F:GLU107 4.7 5.4 1.0
CG F:GLU27 4.7 4.7 1.0
NE2 F:GLN141 4.8 5.5 1.0
CB F:GLU62 4.8 4.9 1.0

Sodium binding site 9 out of 24 in 8cps

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Sodium binding site 9 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:6.4
occ:1.00
 O G:HOH304 2.4 5.8 1.0
OE1 G:GLU27 2.4 4.5 1.0
OE1 G:GLU62 2.4 4.7 1.0
O G:HOH302 2.4 5.9 1.0
ND1 G:HIS65 2.5 4.6 1.0
OE2 G:GLU62 2.9 4.7 1.0
CD G:GLU62 2.9 4.7 1.0
CD G:GLU27 3.3 4.5 1.0
CE1 G:HIS65 3.3 4.6 1.0
OE2 G:GLU27 3.4 4.5 1.0
CG G:HIS65 3.5 4.6 1.0
OE1 G:GLN141 3.6 5.3 1.0
CB G:HIS65 3.9 4.6 1.0
CG1 G:VAL110 4.1 5.1 1.0
CG G:GLU62 4.4 4.7 1.0
CD G:GLN141 4.4 5.3 1.0
NE2 G:HIS65 4.5 4.6 1.0
CD2 G:HIS65 4.6 4.6 1.0
CA G:GLU62 4.6 4.7 1.0
OE1 G:GLU107 4.7 5.2 1.0
CG G:GLU27 4.7 4.5 1.0
CB G:GLU62 4.8 4.7 1.0
NE2 G:GLN141 4.9 5.3 1.0

Sodium binding site 10 out of 24 in 8cps

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Sodium binding site 10 out of 24 in the Human Apoferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Human Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:6.5
occ:1.00
 O H:HOH304 2.4 5.7 1.0
OE1 H:GLU27 2.4 4.6 1.0
OE1 H:GLU62 2.4 4.8 1.0
O H:HOH302 2.4 6.1 1.0
ND1 H:HIS65 2.5 4.7 1.0
OE2 H:GLU62 2.8 4.8 1.0
CD H:GLU62 2.9 4.8 1.0
CD H:GLU27 3.3 4.6 1.0
CE1 H:HIS65 3.3 4.7 1.0
OE2 H:GLU27 3.4 4.6 1.0
CG H:HIS65 3.5 4.7 1.0
OE1 H:GLN141 3.7 5.4 1.0
CB H:HIS65 3.9 4.7 1.0
CG1 H:VAL110 4.1 5.1 1.0
CG H:GLU62 4.4 4.8 1.0
CD H:GLN141 4.4 5.4 1.0
NE2 H:HIS65 4.5 4.7 1.0
CD2 H:HIS65 4.6 4.7 1.0
CA H:GLU62 4.6 4.8 1.0
OE2 H:GLU107 4.7 5.3 1.0
CG H:GLU27 4.7 4.6 1.0
NE2 H:GLN141 4.8 5.4 1.0
CB H:GLU62 4.8 4.8 1.0

Reference:

M.G.F.Last, W.E.M.Noteborn, L.M.Voortman, T.H.Sharp. Super-Resolution Fluorescence Imaging of Cryosamples Does Not Damage Protein Structure To Be Published.
Page generated: Mon Aug 18 13:28:24 2025

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