Sodium in PDB 6z9f: 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;

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 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 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 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 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 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 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 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 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 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 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

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.