Sodium in PDB 6z9e: 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;

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 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 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 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 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 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 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 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 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 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 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

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.