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Sodium in PDB 8cpt: Human Apoferritin After 488 Nm Laser Exposure

Other elements in 8cpt:

The structure of Human Apoferritin After 488 Nm Laser Exposure 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 After 488 Nm Laser Exposure (pdb code 8cpt). 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 After 488 Nm Laser Exposure, PDB code: 8cpt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 8cpt

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Sodium binding site 1 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na201

b:2.7
occ:1.00
 OE1 1:GLU27 2.3 1.6 1.0
OE1 1:GLU62 2.4 1.7 1.0
ND1 1:HIS65 2.4 1.6 1.0
O 1:HOH309 2.4 2.2 1.0
O 1:HOH304 2.4 2.2 1.0
CD 1:GLU62 2.9 1.7 1.0
OE2 1:GLU62 3.0 1.7 1.0
CD 1:GLU27 3.2 1.6 1.0
CE1 1:HIS65 3.3 1.6 1.0
CG 1:HIS65 3.4 1.6 1.0
OE2 1:GLU27 3.5 1.6 1.0
CB 1:HIS65 3.7 1.6 1.0
OE1 1:GLN141 3.9 1.8 1.0
O 1:HOH328 4.0 2.0 1.0
CG 1:GLU62 4.3 1.7 1.0
CA 1:GLU62 4.4 1.7 1.0
NE2 1:HIS65 4.4 1.6 1.0
CG1 1:VAL110 4.5 1.9 1.0
CD2 1:HIS65 4.5 1.6 1.0
CG 1:GLU27 4.6 1.6 1.0
CB 1:GLU62 4.7 1.7 1.0
CD 1:GLN141 4.7 1.8 1.0
O 1:HOH311 4.9 2.3 1.0
CB 1:GLU27 4.9 1.6 1.0

Sodium binding site 2 out of 24 in 8cpt

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Sodium binding site 2 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na201

b:2.7
occ:1.00
 OE1 2:GLU27 2.3 1.6 1.0
OE1 2:GLU62 2.4 1.6 1.0
ND1 2:HIS65 2.4 1.6 1.0
O 2:HOH309 2.4 2.3 1.0
O 2:HOH304 2.4 2.3 1.0
CD 2:GLU62 2.9 1.6 1.0
OE2 2:GLU62 3.0 1.6 1.0
CD 2:GLU27 3.2 1.6 1.0
CE1 2:HIS65 3.3 1.6 1.0
CG 2:HIS65 3.4 1.6 1.0
OE2 2:GLU27 3.5 1.6 1.0
CB 2:HIS65 3.7 1.6 1.0
OE1 2:GLN141 3.9 1.8 1.0
O 2:HOH328 4.0 2.0 1.0
CG 2:GLU62 4.3 1.6 1.0
CA 2:GLU62 4.4 1.6 1.0
NE2 2:HIS65 4.4 1.6 1.0
CG1 2:VAL110 4.5 1.8 1.0
CD2 2:HIS65 4.5 1.6 1.0
CG 2:GLU27 4.6 1.6 1.0
CB 2:GLU62 4.7 1.6 1.0
CD 2:GLN141 4.7 1.8 1.0
O 2:HOH310 4.9 2.3 1.0
CB 2:GLU27 4.9 1.6 1.0

Sodium binding site 3 out of 24 in 8cpt

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Sodium binding site 3 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Na201

b:2.8
occ:1.00
 OE1 4:GLU27 2.3 1.6 1.0
OE1 4:GLU62 2.4 1.7 1.0
ND1 4:HIS65 2.4 1.7 1.0
O 4:HOH310 2.4 2.4 1.0
O 4:HOH304 2.4 2.3 1.0
CD 4:GLU62 2.9 1.7 1.0
OE2 4:GLU62 3.0 1.7 1.0
CD 4:GLU27 3.2 1.6 1.0
CE1 4:HIS65 3.3 1.7 1.0
CG 4:HIS65 3.4 1.7 1.0
OE2 4:GLU27 3.5 1.6 1.0
CB 4:HIS65 3.7 1.7 1.0
OE1 4:GLN141 3.9 1.8 1.0
O 4:HOH327 4.0 2.1 1.0
CG 4:GLU62 4.3 1.7 1.0
CA 4:GLU62 4.4 1.7 1.0
NE2 4:HIS65 4.4 1.7 1.0
CG1 4:VAL110 4.5 1.9 1.0
CD2 4:HIS65 4.5 1.7 1.0
CG 4:GLU27 4.6 1.6 1.0
CB 4:GLU62 4.7 1.7 1.0
CD 4:GLN141 4.7 1.8 1.0
O 4:HOH309 4.9 2.4 1.0
CB 4:GLU27 4.9 1.6 1.0

Sodium binding site 4 out of 24 in 8cpt

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Sodium binding site 4 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Na201

b:2.8
occ:1.00
 OE1 6:GLU27 2.3 1.6 1.0
OE1 6:GLU62 2.4 1.6 1.0
ND1 6:HIS65 2.4 1.6 1.0
O 6:HOH309 2.4 2.2 1.0
O 6:HOH304 2.4 2.2 1.0
CD 6:GLU62 2.9 1.6 1.0
OE2 6:GLU62 3.0 1.6 1.0
CD 6:GLU27 3.2 1.6 1.0
CE1 6:HIS65 3.3 1.6 1.0
CG 6:HIS65 3.4 1.6 1.0
OE2 6:GLU27 3.5 1.6 1.0
CB 6:HIS65 3.7 1.6 1.0
OE1 6:GLN141 3.8 1.7 1.0
O 6:HOH340 4.0 2.0 1.0
CG 6:GLU62 4.3 1.6 1.0
NE2 6:HIS65 4.4 1.6 1.0
CA 6:GLU62 4.4 1.6 1.0
CG1 6:VAL110 4.5 1.8 1.0
CD2 6:HIS65 4.5 1.6 1.0
CG 6:GLU27 4.6 1.6 1.0
CB 6:GLU62 4.7 1.6 1.0
CD 6:GLN141 4.7 1.7 1.0
O 6:HOH312 4.9 2.2 1.0
CB 6:GLU27 4.9 1.6 1.0

Sodium binding site 5 out of 24 in 8cpt

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Sodium binding site 5 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:2.9
occ:1.00
 OE1 A:GLU27 2.3 1.6 1.0
OE1 A:GLU62 2.4 1.7 1.0
ND1 A:HIS65 2.4 1.7 1.0
O A:HOH609 2.4 2.4 1.0
O A:HOH604 2.4 2.3 1.0
CD A:GLU62 2.9 1.7 1.0
OE2 A:GLU62 2.9 1.7 1.0
CD A:GLU27 3.2 1.6 1.0
CE1 A:HIS65 3.3 1.7 1.0
CG A:HIS65 3.4 1.7 1.0
OE2 A:GLU27 3.5 1.6 1.0
CB A:HIS65 3.7 1.7 1.0
OE1 A:GLN141 3.9 1.8 1.0
O A:HOH628 4.0 2.1 1.0
CG A:GLU62 4.3 1.7 1.0
CA A:GLU62 4.4 1.7 1.0
NE2 A:HIS65 4.4 1.7 1.0
CG1 A:VAL110 4.5 1.9 1.0
CD2 A:HIS65 4.5 1.7 1.0
CG A:GLU27 4.6 1.6 1.0
CB A:GLU62 4.7 1.7 1.0
CD A:GLN141 4.7 1.8 1.0
O A:HOH611 4.9 2.4 1.0
CB A:GLU27 4.9 1.6 1.0

Sodium binding site 6 out of 24 in 8cpt

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Sodium binding site 6 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na500

b:2.8
occ:1.00
 OE1 B:GLU27 2.3 1.6 1.0
OE1 B:GLU62 2.4 1.7 1.0
ND1 B:HIS65 2.4 1.7 1.0
O B:HOH609 2.4 2.3 1.0
O B:HOH604 2.4 2.3 1.0
OE2 B:GLU62 2.9 1.7 1.0
CD B:GLU62 2.9 1.7 1.0
CD B:GLU27 3.2 1.6 1.0
CE1 B:HIS65 3.3 1.7 1.0
CG B:HIS65 3.4 1.7 1.0
OE2 B:GLU27 3.5 1.6 1.0
CB B:HIS65 3.7 1.7 1.0
OE1 B:GLN141 3.9 1.8 1.0
O B:HOH630 4.0 2.1 1.0
CG B:GLU62 4.3 1.7 1.0
NE2 B:HIS65 4.4 1.7 1.0
CA B:GLU62 4.5 1.7 1.0
CG1 B:VAL110 4.5 1.8 1.0
CD2 B:HIS65 4.5 1.7 1.0
CG B:GLU27 4.6 1.6 1.0
CD B:GLN141 4.7 1.8 1.0
CB B:GLU62 4.7 1.7 1.0
O B:HOH612 4.9 2.3 1.0
CB B:GLU27 4.9 1.6 1.0

Sodium binding site 7 out of 24 in 8cpt

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Sodium binding site 7 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na500

b:2.8
occ:1.00
 OE1 E:GLU27 2.3 1.6 1.0
OE1 E:GLU62 2.4 1.7 1.0
ND1 E:HIS65 2.4 1.6 1.0
O E:HOH609 2.4 2.4 1.0
O E:HOH604 2.4 2.3 1.0
CD E:GLU62 2.9 1.7 1.0
OE2 E:GLU62 3.0 1.7 1.0
CD E:GLU27 3.2 1.6 1.0
CE1 E:HIS65 3.3 1.6 1.0
CG E:HIS65 3.4 1.6 1.0
OE2 E:GLU27 3.5 1.6 1.0
CB E:HIS65 3.7 1.6 1.0
OE1 E:GLN141 3.9 1.8 1.0
O E:HOH627 4.0 2.1 1.0
CG E:GLU62 4.3 1.7 1.0
CA E:GLU62 4.4 1.7 1.0
NE2 E:HIS65 4.4 1.6 1.0
CG1 E:VAL110 4.5 1.9 1.0
CD2 E:HIS65 4.5 1.6 1.0
CG E:GLU27 4.6 1.6 1.0
CB E:GLU62 4.7 1.7 1.0
CD E:GLN141 4.7 1.8 1.0
O E:HOH611 4.9 2.5 1.0
CB E:GLU27 4.9 1.6 1.0

Sodium binding site 8 out of 24 in 8cpt

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Sodium binding site 8 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na500

b:2.9
occ:1.00
 OE1 F:GLU27 2.3 1.6 1.0
OE1 F:GLU62 2.4 1.6 1.0
ND1 F:HIS65 2.4 1.6 1.0
O F:HOH610 2.4 2.3 1.0
O F:HOH604 2.4 2.3 1.0
CD F:GLU62 2.9 1.6 1.0
OE2 F:GLU62 3.0 1.6 1.0
CD F:GLU27 3.2 1.6 1.0
CE1 F:HIS65 3.3 1.6 1.0
CG F:HIS65 3.4 1.6 1.0
OE2 F:GLU27 3.5 1.6 1.0
CB F:HIS65 3.7 1.6 1.0
OE1 F:GLN141 3.9 1.8 1.0
O F:HOH627 4.0 2.1 1.0
CG F:GLU62 4.3 1.6 1.0
CA F:GLU62 4.4 1.6 1.0
NE2 F:HIS65 4.4 1.6 1.0
CG1 F:VAL110 4.5 1.9 1.0
CD2 F:HIS65 4.5 1.6 1.0
CG F:GLU27 4.6 1.6 1.0
CB F:GLU62 4.7 1.6 1.0
CD F:GLN141 4.7 1.8 1.0
O F:HOH609 4.9 2.4 1.0
CB F:GLU27 4.9 1.6 1.0

Sodium binding site 9 out of 24 in 8cpt

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Sodium binding site 9 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:2.7
occ:1.00
 OE1 G:GLU27 2.3 1.6 1.0
OE1 G:GLU62 2.4 1.6 1.0
ND1 G:HIS65 2.4 1.6 1.0
O G:HOH309 2.4 2.3 1.0
O G:HOH304 2.4 2.3 1.0
CD G:GLU62 3.0 1.6 1.0
OE2 G:GLU62 3.0 1.6 1.0
CD G:GLU27 3.2 1.6 1.0
CE1 G:HIS65 3.3 1.6 1.0
CG G:HIS65 3.4 1.6 1.0
OE2 G:GLU27 3.5 1.6 1.0
CB G:HIS65 3.7 1.6 1.0
OE1 G:GLN141 3.8 1.7 1.0
O G:HOH338 4.0 2.0 1.0
CG G:GLU62 4.3 1.6 1.0
NE2 G:HIS65 4.4 1.6 1.0
CA G:GLU62 4.4 1.6 1.0
CG1 G:VAL110 4.5 1.8 1.0
CD2 G:HIS65 4.5 1.6 1.0
CG G:GLU27 4.6 1.6 1.0
CB G:GLU62 4.7 1.6 1.0
CD G:GLN141 4.7 1.7 1.0
O G:HOH311 4.9 2.4 1.0
CB G:GLU27 4.9 1.6 1.0

Sodium binding site 10 out of 24 in 8cpt

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Sodium binding site 10 out of 24 in the Human Apoferritin After 488 Nm Laser Exposure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Human Apoferritin After 488 Nm Laser Exposure within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:2.8
occ:1.00
 OE1 H:GLU27 2.3 1.6 1.0
OE1 H:GLU62 2.4 1.6 1.0
ND1 H:HIS65 2.4 1.6 1.0
O H:HOH310 2.4 2.2 1.0
O H:HOH304 2.4 2.3 1.0
CD H:GLU62 2.9 1.6 1.0
OE2 H:GLU62 3.0 1.6 1.0
CD H:GLU27 3.2 1.6 1.0
CE1 H:HIS65 3.3 1.6 1.0
CG H:HIS65 3.4 1.6 1.0
OE2 H:GLU27 3.5 1.6 1.0
CB H:HIS65 3.7 1.6 1.0
OE1 H:GLN141 3.9 1.8 1.0
O H:HOH326 4.0 2.0 1.0
CG H:GLU62 4.3 1.6 1.0
CA H:GLU62 4.4 1.6 1.0
NE2 H:HIS65 4.4 1.6 1.0
CG1 H:VAL110 4.5 1.9 1.0
CD2 H:HIS65 4.5 1.6 1.0
CG H:GLU27 4.6 1.6 1.0
CB H:GLU62 4.7 1.6 1.0
CD H:GLN141 4.7 1.8 1.0
O H:HOH309 4.9 2.3 1.0
CB H:GLU27 4.9 1.6 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 13:28:25 2025

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