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Sodium in PDB 6z9f: 1.56 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope

Enzymatic activity of 1.56 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope

All present enzymatic activity of 1.56 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 1.56 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope (pdb code 6z9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 32 binding sites of Sodium where determined in the 1.56 A Structure of Human Apoferritin Obtained From Data Subset of Titan Mono-Bcor Microscope, PDB code: 6z9f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 32 in 6z9f

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Sodium binding site 1 out of 32 in the 1.56 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 1.56 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:72.4
occ:1.00
 O A:HOH313 2.0 58.1 1.0
OE1 A:GLU27 2.3 62.8 1.0
OE1 A:GLU62 2.4 59.5 1.0
ND1 A:HIS65 2.5 50.7 1.0
CD A:GLU62 3.0 48.0 1.0
OE2 A:GLU62 3.0 76.5 1.0
CD A:GLU27 3.2 52.2 1.0
CE1 A:HIS65 3.4 66.3 1.0
OE2 A:GLU27 3.4 49.9 1.0
OE1 A:GLN141 3.4 54.7 1.0
O A:HOH322 3.6 49.1 1.0
CG A:HIS65 3.6 40.0 1.0
O A:HOH327 3.8 55.4 1.0
CB A:HIS65 3.9 32.4 1.0
CG1 A:VAL110 4.1 36.3 1.0
CD A:GLN141 4.3 40.8 1.0
CG A:GLU62 4.4 36.9 1.0
NE2 A:HIS65 4.6 54.9 1.0
CG A:GLU27 4.6 39.9 1.0
CD2 A:HIS65 4.7 51.5 1.0
OE1 A:GLU107 4.7 63.9 1.0
CA A:GLU62 4.8 28.4 1.0
NE2 A:GLN141 4.8 42.7 1.0
CB A:GLU62 4.9 30.7 1.0

Sodium binding site 2 out of 32 in 6z9f

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Sodium binding site 2 out of 32 in the 1.56 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 1.56 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:64.2
occ:1.00
 O e:HOH404 2.2 55.8 1.0
OE2 e:GLU134 2.7 43.8 1.0
OE2 A:GLU134 2.7 43.8 1.0
OE2 F:GLU134 2.7 43.8 1.0
OD2 A:ASP131 2.9 59.7 1.0
OD2 F:ASP131 2.9 59.7 1.0
OD2 e:ASP131 2.9 59.7 1.0
O e:HOH437 3.1 56.6 1.0
O A:HOH333 3.1 56.6 1.0
O F:HOH435 3.1 56.7 1.0
CD e:GLU134 3.9 52.0 1.0
CD A:GLU134 3.9 52.0 1.0
CD F:GLU134 3.9 51.9 1.0
CG A:ASP131 4.1 45.2 1.0
CG F:ASP131 4.1 45.3 1.0
CG e:ASP131 4.1 45.2 1.0
OE1 e:GLU134 4.7 56.8 1.0
OE1 A:GLU134 4.7 56.8 1.0
OE1 F:GLU134 4.7 56.7 1.0
CB e:GLU134 4.7 37.9 1.0
CB A:GLU134 4.7 37.9 1.0
CB F:GLU134 4.7 37.9 1.0
CB A:ASP131 4.8 36.2 1.0
CB F:ASP131 4.8 36.2 1.0
CB e:ASP131 4.8 36.2 1.0
CG e:GLU134 5.0 47.0 1.0
CG A:GLU134 5.0 47.0 1.0
CG F:GLU134 5.0 47.0 1.0

Sodium binding site 3 out of 32 in 6z9f

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Sodium binding site 3 out of 32 in the 1.56 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 1.56 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:72.6
occ:1.00
 O 1:HOH316 2.0 58.1 1.0
OE1 1:GLU27 2.3 62.5 1.0
OE1 1:GLU62 2.4 59.2 1.0
ND1 1:HIS65 2.6 51.0 1.0
CD 1:GLU62 3.0 47.7 1.0
OE2 1:GLU62 3.0 76.3 1.0
CD 1:GLU27 3.2 52.3 1.0
CE1 1:HIS65 3.4 66.2 1.0
OE1 1:GLN141 3.4 54.8 1.0
OE2 1:GLU27 3.4 49.7 1.0
O 1:HOH329 3.6 49.5 1.0
CG 1:HIS65 3.6 39.9 1.0
O 1:HOH325 3.8 55.5 1.0
CB 1:HIS65 3.9 32.3 1.0
CG1 1:VAL110 4.1 36.4 1.0
CD 1:GLN141 4.3 40.8 1.0
CG 1:GLU62 4.4 36.9 1.0
CG 1:GLU27 4.6 40.0 1.0
NE2 1:HIS65 4.6 55.1 1.0
CD2 1:HIS65 4.7 51.8 1.0
OE1 1:GLU107 4.7 64.4 1.0
O 1:HOH415 4.7 59.1 1.0
CA 1:GLU62 4.8 28.3 1.0
NE2 1:GLN141 4.8 42.7 1.0
CB 1:GLU62 4.9 30.8 1.0

Sodium binding site 4 out of 32 in 6z9f

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Sodium binding site 4 out of 32 in the 1.56 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 1.56 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:64.3
occ:1.00
 O Y:HOH403 2.2 55.6 1.0
OE2 Y:GLU134 2.7 43.8 1.0
OE2 1:GLU134 2.7 43.9 1.0
OE2 E:GLU134 2.7 43.8 1.0
OD2 E:ASP131 2.9 59.8 1.0
OD2 1:ASP131 2.9 60.0 1.0
OD2 Y:ASP131 2.9 59.6 1.0
O 1:HOH337 3.1 56.6 1.0
O Y:HOH436 3.1 56.6 1.0
O E:HOH436 3.1 56.8 1.0
CD Y:GLU134 3.9 51.9 1.0
CD E:GLU134 3.9 51.8 1.0
CD 1:GLU134 3.9 51.9 1.0
CG E:ASP131 4.1 45.2 1.0
CG 1:ASP131 4.1 45.2 1.0
CG Y:ASP131 4.1 45.3 1.0
OE1 Y:GLU134 4.7 56.7 1.0
OE1 E:GLU134 4.7 56.7 1.0
OE1 1:GLU134 4.7 56.9 1.0
CB E:GLU134 4.7 38.0 1.0
CB Y:GLU134 4.7 37.9 1.0
CB 1:GLU134 4.7 37.9 1.0
CB E:ASP131 4.8 36.2 1.0
CB 1:ASP131 4.8 36.2 1.0
CB Y:ASP131 4.8 36.2 1.0
CG Y:GLU134 5.0 47.0 1.0
CG 1:GLU134 5.0 46.9 1.0
CG E:GLU134 5.0 47.0 1.0

Sodium binding site 5 out of 32 in 6z9f

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Sodium binding site 5 out of 32 in the 1.56 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 1.56 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:Na300

b:72.6
occ:1.00
 O K:HOH416 2.0 58.1 1.0
OE1 K:GLU27 2.3 62.8 1.0
OE1 K:GLU62 2.4 59.1 1.0
ND1 K:HIS65 2.5 50.9 1.0
CD K:GLU62 3.0 47.7 1.0
OE2 K:GLU62 3.0 76.5 1.0
CD K:GLU27 3.2 52.3 1.0
CE1 K:HIS65 3.4 66.2 1.0
OE1 K:GLN141 3.4 54.7 1.0
OE2 K:GLU27 3.4 49.7 1.0
O K:HOH426 3.6 49.1 1.0
CG K:HIS65 3.6 40.0 1.0
O K:HOH429 3.8 55.2 1.0
CB K:HIS65 3.9 32.3 1.0
CG1 K:VAL110 4.1 36.4 1.0
CD K:GLN141 4.3 40.9 1.0
CG K:GLU62 4.4 37.0 1.0
NE2 K:HIS65 4.6 54.9 1.0
CG K:GLU27 4.6 39.8 1.0
CD2 K:HIS65 4.7 51.5 1.0
OE1 K:GLU107 4.7 64.5 1.0
CA K:GLU62 4.8 28.3 1.0
NE2 K:GLN141 4.8 42.6 1.0
CB K:GLU62 4.9 30.7 1.0

Sodium binding site 6 out of 32 in 6z9f

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Sodium binding site 6 out of 32 in the 1.56 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 1.56 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:Na300

b:72.5
occ:1.00
 O a:HOH415 2.0 58.2 1.0
OE1 a:GLU27 2.3 62.8 1.0
OE1 a:GLU62 2.4 59.1 1.0
ND1 a:HIS65 2.5 50.8 1.0
CD a:GLU62 3.0 47.7 1.0
OE2 a:GLU62 3.0 76.7 1.0
CD a:GLU27 3.2 52.3 1.0
CE1 a:HIS65 3.4 66.3 1.0
OE1 a:GLN141 3.4 54.7 1.0
OE2 a:GLU27 3.4 49.8 1.0
O a:HOH428 3.6 49.1 1.0
CG a:HIS65 3.6 40.0 1.0
O a:HOH424 3.8 55.5 1.0
CB a:HIS65 3.9 32.3 1.0
CG1 a:VAL110 4.1 36.4 1.0
CD a:GLN141 4.3 40.8 1.0
CG a:GLU62 4.5 37.0 1.0
NE2 a:HIS65 4.6 54.9 1.0
CG a:GLU27 4.6 39.9 1.0
CD2 a:HIS65 4.7 51.4 1.0
OE1 a:GLU107 4.7 64.5 1.0
CA a:GLU62 4.8 28.3 1.0
NE2 a:GLN141 4.8 42.6 1.0
CB a:GLU62 4.9 30.8 1.0

Sodium binding site 7 out of 32 in 6z9f

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Sodium binding site 7 out of 32 in the 1.56 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 1.56 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:72.4
occ:1.00
 O B:HOH315 2.0 58.1 1.0
OE1 B:GLU27 2.3 62.7 1.0
OE1 B:GLU62 2.4 59.2 1.0
ND1 B:HIS65 2.5 50.8 1.0
CD B:GLU62 3.0 47.6 1.0
OE2 B:GLU62 3.0 77.9 1.0
CD B:GLU27 3.2 52.5 1.0
CE1 B:HIS65 3.4 66.3 1.0
OE1 B:GLN141 3.4 54.8 1.0
OE2 B:GLU27 3.4 49.7 1.0
O B:HOH327 3.6 49.2 1.0
CG B:HIS65 3.6 40.0 1.0
O B:HOH323 3.8 56.1 1.0
CB B:HIS65 3.9 32.3 1.0
CG1 B:VAL110 4.1 36.4 1.0
CD B:GLN141 4.3 40.8 1.0
CG B:GLU62 4.4 36.9 1.0
NE2 B:HIS65 4.6 55.1 1.0
CG B:GLU27 4.6 39.9 1.0
CD2 B:HIS65 4.7 51.6 1.0
OE1 B:GLU107 4.7 64.9 1.0
CA B:GLU62 4.8 28.3 1.0
NE2 B:GLN141 4.8 42.6 1.0
CB B:GLU62 4.9 30.7 1.0

Sodium binding site 8 out of 32 in 6z9f

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Sodium binding site 8 out of 32 in the 1.56 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 1.56 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:64.3
occ:1.00
 O O:HOH403 2.2 55.5 1.0
OE2 O:GLU134 2.7 43.8 1.0
OE2 B:GLU134 2.7 43.8 1.0
OE2 P:GLU134 2.7 43.9 1.0
OD2 B:ASP131 2.9 59.7 1.0
OD2 O:ASP131 2.9 59.7 1.0
OD2 P:ASP131 2.9 59.9 1.0
O P:HOH436 3.1 56.5 1.0
O O:HOH436 3.1 56.6 1.0
O B:HOH337 3.1 56.8 1.0
CD O:GLU134 3.9 52.0 1.0
CD B:GLU134 3.9 51.8 1.0
CD P:GLU134 4.0 51.9 1.0
CG B:ASP131 4.1 45.2 1.0
CG O:ASP131 4.1 45.3 1.0
CG P:ASP131 4.1 45.2 1.0
OE1 O:GLU134 4.7 56.7 1.0
OE1 B:GLU134 4.7 56.7 1.0
OE1 P:GLU134 4.7 56.8 1.0
CB O:GLU134 4.7 37.9 1.0
CB B:GLU134 4.7 38.0 1.0
CB P:GLU134 4.7 37.9 1.0
CB B:ASP131 4.8 36.2 1.0
CB O:ASP131 4.8 36.2 1.0
CB P:ASP131 4.8 36.2 1.0
CG O:GLU134 5.0 47.0 1.0
CG B:GLU134 5.0 46.9 1.0
CG P:GLU134 5.0 47.0 1.0

Sodium binding site 9 out of 32 in 6z9f

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Sodium binding site 9 out of 32 in the 1.56 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 1.56 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
E:Na300

b:72.3
occ:1.00
 O E:HOH415 2.0 58.1 1.0
OE1 E:GLU27 2.3 62.6 1.0
OE1 E:GLU62 2.4 59.4 1.0
ND1 E:HIS65 2.6 51.0 1.0
CD E:GLU62 3.0 47.7 1.0
OE2 E:GLU62 3.0 77.8 1.0
CD E:GLU27 3.2 52.5 1.0
CE1 E:HIS65 3.4 66.0 1.0
OE1 E:GLN141 3.4 54.7 1.0
OE2 E:GLU27 3.4 49.7 1.0
O E:HOH429 3.6 49.6 1.0
CG E:HIS65 3.6 40.0 1.0
O E:HOH422 3.8 55.9 1.0
CB E:HIS65 3.9 32.3 1.0
CG1 E:VAL110 4.1 36.4 1.0
CD E:GLN141 4.3 40.8 1.0
CG E:GLU62 4.4 36.9 1.0
CG E:GLU27 4.6 39.9 1.0
NE2 E:HIS65 4.6 55.1 1.0
CD2 E:HIS65 4.7 51.7 1.0
OE1 E:GLU107 4.7 64.9 1.0
O E:HOH513 4.8 59.1 1.0
CA E:GLU62 4.8 28.3 1.0
NE2 E:GLN141 4.8 42.7 1.0
CB E:GLU62 4.9 30.7 1.0

Sodium binding site 10 out of 32 in 6z9f

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Sodium binding site 10 out of 32 in the 1.56 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 1.56 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
e:Na300

b:72.5
occ:1.00
 O e:HOH416 2.0 58.1 1.0
OE1 e:GLU27 2.3 62.8 1.0
OE1 e:GLU62 2.4 59.4 1.0
ND1 e:HIS65 2.5 50.7 1.0
CD e:GLU62 3.0 48.0 1.0
OE2 e:GLU62 3.0 76.4 1.0
CD e:GLU27 3.2 52.3 1.0
CE1 e:HIS65 3.4 66.2 1.0
OE2 e:GLU27 3.4 49.7 1.0
OE1 e:GLN141 3.4 54.7 1.0
O e:HOH425 3.6 49.2 1.0
CG e:HIS65 3.6 39.9 1.0
O e:HOH430 3.8 55.3 1.0
CB e:HIS65 3.9 32.3 1.0
CG1 e:VAL110 4.1 36.3 1.0
CD e:GLN141 4.3 40.9 1.0
CG e:GLU62 4.5 36.9 1.0
CG e:GLU27 4.6 39.9 1.0
NE2 e:HIS65 4.6 55.0 1.0
CD2 e:HIS65 4.7 51.4 1.0
OE1 e:GLU107 4.7 63.8 1.0
CA e:GLU62 4.8 28.3 1.0
NE2 e:GLN141 4.8 42.7 1.0
CB e:GLU62 4.9 30.7 1.0

Reference:

K.M.Yip, N.Fischer, E.Paknia, A.Chari, H.Stark. 1.25 A Structure of Human Apoferritin Obtained From Titan Mono-Bcor Microscope To Be Published.
Page generated: Tue Oct 8 15:25:15 2024

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