Sodium in PDB 9jiu: Ferritin Mutant R63MEHIS

All present enzymatic activity of Ferritin Mutant R63MEHIS:
1.16.3.1;

The structure of Ferritin Mutant R63MEHIS, PDB code: 9jiu was solved by J.-C.Tsou, K.-F.Huang, T.-P.Ko, Y.-S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 2.28
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	219.169, 219.169, 147.906, 90, 90, 90
R / Rfree (%)	23.9 / 27.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the Ferritin Mutant R63MEHIS (pdb code 9jiu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Ferritin Mutant R63MEHIS, PDB code: 9jiu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:54.1 occ:1.00 OE1 H:GLU134 2.3 51.0 1.0 OE1 K:GLU134 2.5 50.1 1.0 OE1 A:GLU134 2.5 49.9 1.0 CD H:GLU134 3.3 50.6 1.0 CD A:GLU134 3.5 53.6 1.0 CD K:GLU134 3.5 47.9 1.0 OE2 H:GLU134 3.7 47.3 1.0 OE2 A:GLU134 3.8 58.5 1.0 OE2 K:GLU134 3.9 53.1 1.0 O H:HOH397 4.1 59.1 1.0 OD1 A:ASP131 4.3 42.8 1.0 OD1 H:ASP131 4.4 41.6 1.0 OD1 K:ASP131 4.5 45.0 1.0 O H:HOH303 4.6 53.6 1.0 CG H:GLU134 4.7 44.2 1.0 O H:HOH301 4.7 59.5 1.0 CG A:GLU134 4.8 42.4 1.0 CG K:GLU134 4.8 45.9 1.0 CA A:ASP131 4.9 37.7 1.0 CB H:GLU134 4.9 37.9 1.0 CB A:GLU134 4.9 33.0 1.0 CA H:ASP131 5.0 33.8 1.0 CB A:ASP131 5.0 40.1 1.0

Sodium binding site 2 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:63.0 occ:1.00 OE1 A:GLU27 2.1 52.4 1.0 ND1 A:HIS65 2.2 56.3 1.0 OE2 A:GLU62 2.3 50.9 1.0 CD A:GLU27 2.7 44.4 1.0 OE2 A:GLU27 2.8 29.8 1.0 CG A:HIS65 3.0 51.2 1.0 CB A:HIS65 3.2 43.1 1.0 CE1 A:HIS65 3.2 57.6 1.0 CD A:GLU62 3.4 53.3 1.0 OE1 A:GLN141 3.6 48.2 1.0 NA A:NA203 3.9 55.3 1.0 CG A:GLU62 3.9 46.6 1.0 CG1 A:VAL110 4.1 37.6 1.0 CG A:GLU27 4.1 40.8 1.0 CD2 A:HIS65 4.2 54.4 1.0 NE2 A:HIS65 4.3 59.4 1.0 CD A:GLN141 4.4 39.6 1.0 CD2 A:TYR137 4.4 32.9 1.0 OE1 A:GLU62 4.4 62.5 1.0 CA A:GLU62 4.5 40.6 1.0 CE2 A:TYR137 4.6 37.8 1.0 CB A:GLU27 4.7 39.7 1.0 CA A:HIS65 4.7 43.5 1.0 O A:GLU62 4.9 40.4 1.0 CB A:GLU62 4.9 39.6 1.0

Sodium binding site 3 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:55.3 occ:1.00 OE2 A:GLU62 2.5 50.9 1.0 O A:HOH313 2.7 52.5 1.0 OE1 A:GLU62 2.7 62.5 1.0 OE1 A:GLU107 2.8 48.6 1.0 OE1 A:GLN141 2.8 48.2 1.0 CD A:GLU62 2.9 53.3 1.0 OE2 A:GLU107 3.1 47.7 1.0 CD A:GLU107 3.3 43.8 1.0 CD A:GLN141 3.7 39.6 1.0 NA A:NA202 3.9 63.0 1.0 CE1 A:HIS65 3.9 57.6 1.0 NE2 A:GLN141 4.0 37.1 1.0 ND1 A:HIS65 4.1 56.3 1.0 CG A:GLU62 4.4 46.6 1.0 CB A:ALA144 4.6 28.8 1.0 CG A:GLU107 4.8 40.3 1.0

Sodium binding site 4 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:43.0 occ:1.00 OE1 L:GLU134 2.3 52.3 1.0 OE1 B:GLU134 2.5 50.6 1.0 O B:HOH346 2.8 67.7 1.0 CD L:GLU134 3.4 51.9 1.0 CD B:GLU134 3.5 49.1 1.0 OE2 B:GLU134 3.7 53.5 1.0 OE2 L:GLU134 3.8 44.8 1.0 OD1 L:ASP131 4.5 45.2 1.0 OD1 B:ASP131 4.6 36.4 1.0 CG L:GLU134 4.7 50.8 1.0 CG B:GLU134 4.8 43.4 1.0 CB L:GLU134 4.9 38.7 1.0 CA L:ASP131 5.0 40.4 1.0

Sodium binding site 5 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:55.8 occ:1.00 OE2 B:GLU62 2.2 52.5 1.0 OE1 B:GLU107 2.3 46.6 1.0 O B:HOH320 2.5 51.9 1.0 OE1 B:GLN141 2.5 39.4 1.0 CD B:GLU107 2.9 48.5 1.0 OE2 B:GLU107 2.9 44.7 1.0 CD B:GLU62 3.4 45.3 1.0 CD B:GLN141 3.4 30.5 1.0 NE2 B:GLN141 3.6 34.4 1.0 CE1 B:HIS65 4.2 61.2 1.0 OE1 B:GLU62 4.2 51.2 1.0 CB B:ALA144 4.2 27.4 1.0 CG B:GLU62 4.3 34.9 1.0 CG B:GLU107 4.3 44.0 1.0 ND1 B:HIS65 4.5 56.2 1.0 OE1 B:GLU61 4.7 84.6 1.0 CD B:GLU61 4.7 82.8 1.0 CG B:GLN141 4.8 43.5 1.0 OE2 B:GLU61 4.9 79.6 1.0 CB B:GLU107 5.0 41.3 1.0

Sodium binding site 6 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:55.3 occ:1.00 OE1 I:GLU134 2.4 48.1 1.0 OE1 C:GLU134 2.4 46.0 1.0 O C:HOH309 2.7 47.3 1.0 CD C:GLU134 3.3 48.3 1.0 CD I:GLU134 3.3 44.1 1.0 OE2 C:GLU134 3.4 51.2 1.0 OE2 I:GLU134 3.5 49.1 1.0 OD1 I:ASP131 4.6 51.9 1.0 CG I:GLU134 4.7 35.8 1.0 CG C:GLU134 4.7 37.9 1.0 OD1 C:ASP131 4.8 38.8 1.0 CA I:ASP131 5.0 33.5 1.0

Sodium binding site 7 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:58.2 occ:1.00 OE2 C:GLU62 2.3 51.1 1.0 OE1 C:GLU107 2.5 44.7 1.0 OE1 C:GLN141 2.6 41.2 1.0 O C:HOH301 2.6 55.6 1.0 OE2 C:GLU107 2.9 43.4 1.0 CD C:GLU107 3.0 39.1 1.0 CD C:GLN141 3.5 41.0 1.0 NA C:NA203 3.5 63.8 1.0 CD C:GLU62 3.5 53.9 1.0 NE2 C:GLN141 3.7 40.9 1.0 CE1 C:HIS65 4.0 53.2 1.0 ND1 C:HIS65 4.3 55.5 1.0 OE1 C:GLU62 4.3 54.4 1.0 CB C:ALA144 4.4 33.3 1.0 CG C:GLU107 4.5 37.3 1.0 CG C:GLU62 4.5 42.6 1.0 CG C:GLN141 4.9 35.6 1.0

Sodium binding site 8 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:63.8 occ:1.00 OE1 C:GLU27 2.2 56.9 1.0 ND1 C:HIS65 2.2 55.5 1.0 OE2 C:GLU62 2.5 51.1 1.0 OE1 C:GLU62 2.5 54.4 1.0 CD C:GLU62 2.7 53.9 1.0 CD C:GLU27 3.1 50.0 1.0 CE1 C:HIS65 3.1 53.2 1.0 CG C:HIS65 3.2 49.6 1.0 OE2 C:GLU27 3.4 42.4 1.0 NA C:NA202 3.5 58.2 1.0 CB C:HIS65 3.5 44.8 1.0 OE1 C:GLN141 3.5 41.2 1.0 CG C:GLU62 4.1 42.6 1.0 CA C:GLU62 4.2 41.1 1.0 CG1 C:VAL110 4.2 31.9 1.0 NE2 C:HIS65 4.3 51.2 1.0 CD2 C:HIS65 4.3 47.6 1.0 CD C:GLN141 4.5 41.0 1.0 CB C:GLU62 4.5 38.7 1.0 CG C:GLU27 4.5 42.0 1.0 CB C:GLU27 4.8 34.9 1.0 O C:GLU62 4.8 43.1 1.0 O C:GLU61 4.9 45.7 1.0 N C:GLU62 4.9 42.4 1.0 NE2 C:GLN141 5.0 40.9 1.0

Sodium binding site 9 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:48.0 occ:1.00 OE1 J:GLU134 2.3 52.3 1.0 OE1 D:GLU134 2.4 45.9 1.0 O E:HOH310 2.6 49.1 1.0 OE1 E:GLU134 2.7 51.2 1.0 O D:HOH304 2.8 51.6 1.0 CD J:GLU134 3.3 47.8 1.0 CD D:GLU134 3.3 46.1 1.0 O E:HOH319 3.3 51.3 1.0 OE2 D:GLU134 3.5 47.6 1.0 CD E:GLU134 3.5 48.9 1.0 OE2 E:GLU134 3.5 50.6 1.0 OE2 J:GLU134 3.6 42.0 1.0 OD1 J:ASP131 4.5 48.9 1.0 CG J:GLU134 4.6 42.5 1.0 CG D:GLU134 4.7 39.7 1.0 OD1 D:ASP131 4.8 36.7 1.0 OD1 E:ASP131 4.8 42.1 1.0 CA J:ASP131 4.8 35.4 1.0 CG E:GLU134 4.9 43.0 1.0 CB J:GLU134 4.9 38.4 1.0 CB J:ASP131 5.0 39.2 1.0

Sodium binding site 10 out of 18 in the Ferritin Mutant R63MEHIS


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Ferritin Mutant R63MEHIS within 5.0Å range: probe atom residue distance (Å) B Occ D:Na202 b:50.4 occ:1.00 OE2 D:GLU62 2.2 53.5 1.0 OE1 D:GLU107 2.2 42.2 1.0 O D:HOH316 2.4 47.8 1.0 OE1 D:GLN141 2.7 32.5 1.0 OE2 D:GLU107 2.7 41.0 1.0 CD D:GLU107 2.8 43.7 1.0 CD D:GLU62 3.4 43.6 1.0 CD D:GLN141 3.5 36.9 1.0 NE2 D:GLN141 3.7 32.4 1.0 OE1 D:GLU62 4.2 48.8 1.0 CE1 D:HIS65 4.2 59.3 1.0 CG D:GLU107 4.2 40.7 1.0 CB D:ALA144 4.3 34.5 1.0 CG D:GLU62 4.3 29.8 1.0 ND1 D:HIS65 4.5 54.7 1.0 CB D:GLU107 4.9 36.4 1.0 CG D:GLN141 4.9 38.6 1.0

J.C.Tsou, C.J.Tsou, C.H.Wang, A.A.Ko, Y.H.Wang, H.H.Liang, J.C.Sun, K.F.Huang, T.P.Ko, S.Y.Lin, Y.S.Wang. Site-Specific Histidine Aza-Michael Addition in Proteins Enabled By A Ferritin-Based Metalloenzyme. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 39499210
DOI: 10.1021/JACS.4C14446