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Sodium in PDB 6z9e: 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope

Enzymatic activity of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope

All present enzymatic activity of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope:
1.16.3.1;

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Sodium atom in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope (pdb code 6z9e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 32 binding sites of Sodium where determined in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope, PDB code: 6z9e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 32 in 6z9e

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Sodium binding site 1 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na201

b:39.0
occ:1.00
 OE1 1:GLU27 2.0 39.1 1.0
O 1:HOH317 2.1 39.7 1.0
OE1 1:GLU62 2.2 39.1 1.0
ND1 1:HIS65 2.5 34.0 1.0
CD 1:GLU62 2.9 35.9 1.0
OE2 1:GLU62 3.0 54.6 1.0
CD 1:GLU27 3.0 32.6 1.0
OE2 1:GLU27 3.3 36.5 1.0
CE1 1:HIS65 3.5 43.1 1.0
CG 1:HIS65 3.5 30.2 1.0
CB 1:HIS65 3.7 22.2 1.0
OE1 1:GLN141 3.8 36.8 1.0
O 1:HOH312 4.0 45.4 1.0
O 1:HOH334 4.2 43.9 1.0
CG 1:GLU62 4.3 25.7 1.0
CG1 1:VAL110 4.3 24.9 1.0
CG 1:GLU27 4.3 30.7 1.0
CA 1:GLU62 4.5 17.4 1.0
NE2 1:HIS65 4.6 43.3 1.0
CD2 1:HIS65 4.7 36.8 1.0
CB 1:GLU62 4.7 20.8 1.0
CD 1:GLN141 4.7 26.2 1.0
CB 1:GLU27 4.8 20.8 1.0

Sodium binding site 2 out of 32 in 6z9e

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Sodium binding site 2 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na202

b:50.1
occ:1.00
 OE2 1:GLU134 2.5 42.3 1.0
OE2 Y:GLU134 2.5 42.5 1.0
OE2 E:GLU134 2.6 42.8 1.0
O E:HOH426 2.8 35.5 1.0
OD2 Y:ASP131 2.9 40.8 1.0
OD2 1:ASP131 2.9 41.0 1.0
OD2 E:ASP131 2.9 41.0 1.0
O Y:HOH452 3.2 43.8 1.0
O E:HOH455 3.2 44.1 1.0
O 1:HOH354 3.2 44.1 1.0
CD 1:GLU134 3.8 39.4 1.0
CD Y:GLU134 3.8 39.6 1.0
CD E:GLU134 3.8 39.8 1.0
CG Y:ASP131 4.1 34.5 1.0
CG 1:ASP131 4.1 35.2 1.0
CG E:ASP131 4.1 34.7 1.0
OE1 1:GLU134 4.5 40.6 1.0
OE1 Y:GLU134 4.5 40.4 1.0
OE1 E:GLU134 4.5 40.5 1.0
CB 1:GLU134 4.7 28.0 1.0
CB Y:GLU134 4.8 28.0 1.0
CB E:GLU134 4.8 28.1 1.0
CB Y:ASP131 4.8 23.5 1.0
CB 1:ASP131 4.8 23.5 1.0
CB E:ASP131 4.8 23.5 1.0
CG 1:GLU134 4.9 33.4 1.0
CG Y:GLU134 4.9 33.2 1.0
CG E:GLU134 4.9 33.5 1.0
CA Y:ASP131 5.0 19.5 1.0
CA 1:ASP131 5.0 19.5 1.0
CA E:ASP131 5.0 19.5 1.0

Sodium binding site 3 out of 32 in 6z9e

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Sodium binding site 3 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:39.0
occ:1.00
 OE1 A:GLU27 2.0 38.5 1.0
O A:HOH321 2.1 39.6 1.0
OE1 A:GLU62 2.2 39.8 1.0
ND1 A:HIS65 2.5 34.0 1.0
CD A:GLU62 2.9 36.0 1.0
OE2 A:GLU62 3.0 53.5 1.0
CD A:GLU27 3.0 32.7 1.0
OE2 A:GLU27 3.3 37.0 1.0
CE1 A:HIS65 3.5 42.8 1.0
CG A:HIS65 3.5 30.1 1.0
CB A:HIS65 3.7 22.5 1.0
OE1 A:GLN141 3.8 36.0 1.0
O A:HOH316 4.0 45.3 1.0
O A:HOH342 4.2 44.0 1.0
CG A:GLU62 4.3 25.8 1.0
CG1 A:VAL110 4.3 24.7 1.0
CG A:GLU27 4.3 30.8 1.0
CA A:GLU62 4.5 17.7 1.0
NE2 A:HIS65 4.6 42.5 1.0
CD2 A:HIS65 4.6 36.0 1.0
CB A:GLU62 4.7 20.9 1.0
CD A:GLN141 4.7 26.0 1.0
CB A:GLU27 4.8 20.5 1.0

Sodium binding site 4 out of 32 in 6z9e

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Sodium binding site 4 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:49.9
occ:1.00
 OE2 F:GLU134 2.5 42.4 1.0
OE2 e:GLU134 2.5 42.7 1.0
OE2 A:GLU134 2.6 42.2 1.0
O A:HOH327 2.8 35.4 1.0
OD2 A:ASP131 2.9 40.9 1.0
OD2 e:ASP131 2.9 40.9 1.0
OD2 F:ASP131 2.9 41.0 1.0
O e:HOH452 3.2 43.9 1.0
O A:HOH362 3.2 44.0 1.0
O F:HOH448 3.2 43.8 1.0
CD F:GLU134 3.8 39.5 1.0
CD e:GLU134 3.8 39.7 1.0
CD A:GLU134 3.8 39.3 1.0
CG A:ASP131 4.1 34.9 1.0
CG e:ASP131 4.1 35.0 1.0
CG F:ASP131 4.1 35.0 1.0
OE1 F:GLU134 4.5 40.5 1.0
OE1 e:GLU134 4.5 40.5 1.0
OE1 A:GLU134 4.5 40.7 1.0
CB F:GLU134 4.8 28.1 1.0
CB e:GLU134 4.8 28.1 1.0
CB A:GLU134 4.8 27.6 1.0
CB e:ASP131 4.8 23.4 1.0
CB F:ASP131 4.8 23.4 1.0
CB A:ASP131 4.8 23.1 1.0
CG F:GLU134 4.9 33.5 1.0
CG e:GLU134 4.9 33.5 1.0
CG A:GLU134 4.9 33.6 1.0
CA F:ASP131 5.0 19.5 1.0
CA e:ASP131 5.0 19.5 1.0
CA A:ASP131 5.0 19.1 1.0

Sodium binding site 5 out of 32 in 6z9e

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Sodium binding site 5 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na201

b:39.0
occ:1.00
 OE1 K:GLU27 2.0 39.1 1.0
O K:HOH416 2.1 39.6 1.0
OE1 K:GLU62 2.2 38.6 1.0
ND1 K:HIS65 2.5 34.1 1.0
CD K:GLU62 2.9 35.9 1.0
OE2 K:GLU62 3.0 53.2 1.0
CD K:GLU27 3.0 32.7 1.0
OE2 K:GLU27 3.3 36.6 1.0
CE1 K:HIS65 3.5 42.9 1.0
CG K:HIS65 3.5 30.4 1.0
CB K:HIS65 3.7 22.2 1.0
OE1 K:GLN141 3.8 36.8 1.0
O K:HOH413 4.0 45.4 1.0
O K:HOH432 4.2 43.8 1.0
CG K:GLU62 4.3 25.9 1.0
CG1 K:VAL110 4.3 24.9 1.0
CG K:GLU27 4.3 30.6 1.0
CA K:GLU62 4.5 17.4 1.0
NE2 K:HIS65 4.6 43.1 1.0
CD2 K:HIS65 4.7 36.6 1.0
CB K:GLU62 4.7 20.8 1.0
CD K:GLN141 4.7 26.2 1.0
CB K:GLU27 4.8 20.7 1.0

Sodium binding site 6 out of 32 in 6z9e

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Sodium binding site 6 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na202

b:49.9
occ:1.00
 OE2 X:GLU134 2.5 42.4 1.0
OE2 K:GLU134 2.5 42.5 1.0
OE2 H:GLU134 2.5 42.7 1.0
O H:HOH324 2.8 35.5 1.0
OD2 K:ASP131 2.9 40.8 1.0
OD2 X:ASP131 2.9 41.0 1.0
OD2 H:ASP131 2.9 41.0 1.0
O K:HOH453 3.2 43.9 1.0
O H:HOH354 3.2 43.9 1.0
O X:HOH454 3.2 44.0 1.0
CD X:GLU134 3.8 39.6 1.0
CD K:GLU134 3.8 39.7 1.0
CD H:GLU134 3.8 39.7 1.0
CG K:ASP131 4.1 34.6 1.0
CG X:ASP131 4.1 35.2 1.0
CG H:ASP131 4.1 34.8 1.0
OE1 X:GLU134 4.5 40.6 1.0
OE1 K:GLU134 4.5 40.4 1.0
OE1 H:GLU134 4.5 40.5 1.0
CB X:GLU134 4.7 28.1 1.0
CB K:GLU134 4.8 28.0 1.0
CB H:GLU134 4.8 28.1 1.0
CB K:ASP131 4.8 23.5 1.0
CB X:ASP131 4.8 23.5 1.0
CB H:ASP131 4.8 23.5 1.0
CG X:GLU134 4.9 33.4 1.0
CG K:GLU134 4.9 33.2 1.0
CG H:GLU134 4.9 33.4 1.0
CA K:ASP131 5.0 19.5 1.0
CA X:ASP131 5.0 19.5 1.0
CA H:ASP131 5.0 19.5 1.0

Sodium binding site 7 out of 32 in 6z9e

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Sodium binding site 7 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na201

b:39.0
occ:1.00
 OE1 a:GLU27 2.0 39.1 1.0
O a:HOH416 2.1 39.6 1.0
OE1 a:GLU62 2.2 38.6 1.0
ND1 a:HIS65 2.5 34.1 1.0
CD a:GLU62 2.9 36.0 1.0
OE2 a:GLU62 3.0 53.1 1.0
CD a:GLU27 3.0 32.7 1.0
OE2 a:GLU27 3.3 36.5 1.0
CE1 a:HIS65 3.5 43.0 1.0
CG a:HIS65 3.5 30.4 1.0
CB a:HIS65 3.7 22.2 1.0
OE1 a:GLN141 3.8 36.7 1.0
O a:HOH412 4.0 45.3 1.0
O a:HOH434 4.2 43.8 1.0
CG a:GLU62 4.3 25.9 1.0
CG1 a:VAL110 4.3 24.9 1.0
CG a:GLU27 4.3 30.6 1.0
CA a:GLU62 4.5 17.4 1.0
NE2 a:HIS65 4.6 43.2 1.0
CD2 a:HIS65 4.6 36.7 1.0
CB a:GLU62 4.7 20.8 1.0
CD a:GLN141 4.7 26.3 1.0
CB a:GLU27 4.8 20.8 1.0

Sodium binding site 8 out of 32 in 6z9e

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Sodium binding site 8 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na202

b:53.5
occ:1.00
 OE2 Q:GLU134 2.5 42.5 1.0
OE2 a:GLU134 2.5 42.5 1.0
OE2 M:GLU134 2.5 42.5 1.0
O a:HOH426 2.9 35.5 1.0
OD2 a:ASP131 2.9 40.8 1.0
OD2 Q:ASP131 2.9 40.8 1.0
OD2 M:ASP131 2.9 40.7 1.0
O Q:HOH453 3.2 43.7 1.0
O M:HOH353 3.2 43.9 1.0
O a:HOH455 3.2 43.7 1.0
CD Q:GLU134 3.8 39.4 1.0
CD a:GLU134 3.8 39.5 1.0
CD M:GLU134 3.8 39.5 1.0
CG a:ASP131 4.1 34.5 1.0
CG Q:ASP131 4.1 34.9 1.0
CG M:ASP131 4.1 34.5 1.0
OE1 Q:GLU134 4.5 40.4 1.0
OE1 a:GLU134 4.5 40.4 1.0
OE1 M:GLU134 4.5 40.4 1.0
CB Q:GLU134 4.8 28.0 1.0
CB a:GLU134 4.8 28.1 1.0
CB M:GLU134 4.8 28.1 1.0
CB a:ASP131 4.8 23.5 1.0
CB Q:ASP131 4.8 23.5 1.0
CB M:ASP131 4.8 23.5 1.0
CG Q:GLU134 4.9 33.3 1.0
CG a:GLU134 4.9 33.2 1.0
CG M:GLU134 4.9 33.5 1.0
CA a:ASP131 5.0 19.5 1.0
CA Q:ASP131 5.0 19.4 1.0
CA M:ASP131 5.0 19.5 1.0

Sodium binding site 9 out of 32 in 6z9e

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Sodium binding site 9 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:39.0
occ:1.00
 OE1 B:GLU27 2.0 39.0 1.0
O B:HOH316 2.1 39.7 1.0
OE1 B:GLU62 2.2 38.8 1.0
ND1 B:HIS65 2.5 34.2 1.0
CD B:GLU62 2.9 36.2 1.0
OE2 B:GLU62 3.0 54.9 1.0
CD B:GLU27 3.0 32.8 1.0
OE2 B:GLU27 3.3 36.6 1.0
CE1 B:HIS65 3.5 43.1 1.0
CG B:HIS65 3.5 30.7 1.0
CB B:HIS65 3.7 22.1 1.0
OE1 B:GLN141 3.8 37.0 1.0
O B:HOH312 4.0 45.4 1.0
O B:HOH334 4.2 43.9 1.0
CG B:GLU62 4.3 25.7 1.0
CG1 B:VAL110 4.3 24.9 1.0
CG B:GLU27 4.3 30.7 1.0
CA B:GLU62 4.5 17.4 1.0
NE2 B:HIS65 4.6 43.3 1.0
CD2 B:HIS65 4.7 36.8 1.0
CB B:GLU62 4.7 20.8 1.0
CD B:GLN141 4.7 26.2 1.0
CB B:GLU27 4.8 20.7 1.0

Sodium binding site 10 out of 32 in 6z9e

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Sodium binding site 10 out of 32 in the 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.55 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:50.0
occ:1.00
 OE2 O:GLU134 2.5 42.2 1.0
OE2 B:GLU134 2.5 42.5 1.0
OE2 P:GLU134 2.5 42.8 1.0
O B:HOH326 2.8 35.6 1.0
OD2 B:ASP131 2.9 40.7 1.0
OD2 O:ASP131 2.9 41.0 1.0
OD2 P:ASP131 2.9 41.0 1.0
O B:HOH355 3.2 44.0 1.0
O P:HOH453 3.2 44.0 1.0
O O:HOH453 3.2 44.0 1.0
CD O:GLU134 3.8 39.3 1.0
CD B:GLU134 3.8 39.6 1.0
CD P:GLU134 3.8 39.9 1.0
CG B:ASP131 4.1 34.6 1.0
CG O:ASP131 4.1 34.6 1.0
CG P:ASP131 4.1 35.1 1.0
OE1 O:GLU134 4.5 40.4 1.0
OE1 B:GLU134 4.5 40.4 1.0
OE1 P:GLU134 4.5 40.6 1.0
CB O:GLU134 4.7 28.0 1.0
CB B:GLU134 4.8 28.1 1.0
CB P:GLU134 4.8 28.1 1.0
CB B:ASP131 4.8 23.5 1.0
CB O:ASP131 4.8 23.5 1.0
CB P:ASP131 4.8 23.5 1.0
CG O:GLU134 4.9 33.2 1.0
CG B:GLU134 4.9 33.4 1.0
CG P:GLU134 4.9 33.4 1.0
CA B:ASP131 5.0 19.5 1.0
CA O:ASP131 5.0 19.5 1.0
CA P:ASP131 5.0 19.5 1.0

Reference:

K.M.Yip, N.Fischer, E.Paknia, A.Chari, H.Stark. 1.55A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope To Be Published.
Page generated: Mon Aug 18 08:42:47 2025

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