Magnesium in PDB 8pp5: Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition)

The structure of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition), PDB code: 8pp5 was solved by L.Lang, T.Beck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.09 / 2.00
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	126.898, 126.898, 187.468, 90, 90, 90
R / Rfree (%)	16 / 19.3

The structure of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) (pdb code 8pp5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition), PDB code: 8pp5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:32.5 occ:1.00 O D:HOH327 2.1 29.2 1.0 O B:HOH425 2.1 33.2 1.0 O B:HOH312 2.1 30.5 1.0 O A:HOH307 2.1 31.1 1.0 O A:HOH419 2.1 29.4 1.0 O D:HOH424 2.2 30.1 1.0 OE2 B:GLU134 3.8 29.9 1.0 OE2 D:GLU134 3.8 28.9 1.0 OE2 A:GLU134 3.9 29.0 1.0 O B:HOH449 4.1 33.8 1.0 O B:HOH315 4.2 30.6 1.0 O A:HOH450 4.3 29.5 1.0 O A:HOH327 4.3 30.5 1.0 OE1 D:GLU134 4.3 33.9 1.0 O D:HOH447 4.3 27.1 1.0 O D:HOH319 4.3 32.4 1.0 OE1 A:GLU134 4.3 31.6 1.0 OE1 B:GLU134 4.4 35.4 1.0 CD D:GLU134 4.5 32.8 1.0 CD A:GLU134 4.5 27.9 1.0 HB3 D:CYS130 4.5 25.7 1.0 CD B:GLU134 4.6 28.1 1.0 HB3 B:CYS130 4.6 24.8 1.0 HB3 A:CYS130 4.6 26.0 1.0 HE1 D:HIS118 4.7 23.5 1.0 HE1 B:HIS118 4.7 23.9 1.0 HE2 B:HIS118 4.8 22.3 0.0 HE1 A:HIS118 4.8 24.0 1.0 HE2 D:HIS118 4.8 23.3 0.0 HE2 A:HIS118 4.9 23.0 0.0

Magnesium binding site 2 out of 4 in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:63.3 occ:1.00 OD1 B:ASP131 3.4 26.6 1.0 OE1 B:GLU134 3.5 35.4 1.0 OD1 D:ASP131 3.5 34.0 1.0 OD1 A:ASP131 3.6 34.5 1.0 OE1 A:GLU134 3.6 31.6 1.0 OE1 D:GLU134 3.8 33.9 1.0 HA B:ASP131 4.1 24.4 1.0 HG1 B:THR135 4.2 24.6 0.0 HB2 B:GLU134 4.2 24.9 1.0 HG1 D:THR135 4.3 26.3 0.0 HG1 A:THR135 4.3 25.2 0.0 HA D:ASP131 4.3 25.5 1.0 HB2 A:GLU134 4.3 26.4 1.0 HB3 A:GLU134 4.4 26.4 1.0 HA A:ASP131 4.4 24.0 1.0 CG B:ASP131 4.5 32.4 1.0 HB2 B:ASP131 4.5 27.3 1.0 HB2 D:GLU134 4.5 27.1 1.0 OG1 B:THR135 4.6 24.6 1.0 CD B:GLU134 4.6 28.1 1.0 HB3 B:GLU134 4.6 24.9 1.0 CG D:ASP131 4.6 33.0 1.0 CD A:GLU134 4.6 27.9 1.0 HB3 D:GLU134 4.7 27.1 1.0 HB2 D:ASP131 4.7 28.5 1.0 CG A:ASP131 4.7 32.4 1.0 OG1 A:THR135 4.7 25.2 1.0 OG1 D:THR135 4.8 26.1 1.0 CB A:GLU134 4.8 25.8 1.0 CB B:ASP131 4.8 26.6 1.0 CD D:GLU134 4.8 32.8 1.0 CB B:GLU134 4.9 25.0 1.0 HB2 A:ASP131 4.9 27.0 1.0 CA B:ASP131 4.9 24.4 1.0

Magnesium binding site 3 out of 4 in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:52.1 occ:1.00 O E:HOH308 1.7 48.0 1.0 O F:HOH323 1.8 47.0 1.0 O C:HOH301 1.9 41.3 1.0 O E:HOH341 2.0 40.9 1.0 O E:HOH328 2.1 46.6 1.0 O F:HOH316 2.3 38.5 1.0 OD1 E:ASP131 3.3 36.1 1.0 OD1 C:ASP131 3.5 33.9 1.0 OD1 F:ASP131 3.6 31.5 1.0 HG1 F:THR135 3.8 26.8 0.0 HG1 E:THR135 3.9 27.0 0.0 HG1 C:THR135 4.0 27.3 0.0 OE1 E:GLU134 4.1 34.4 1.0 OE1 C:GLU134 4.1 36.8 1.0 OE1 F:GLU134 4.1 36.1 1.0 OG1 F:THR135 4.3 26.9 1.0 OG1 E:THR135 4.3 26.8 1.0 HA F:ASP131 4.4 27.2 1.0 HA C:ASP131 4.5 25.3 1.0 HB2 F:GLU134 4.5 26.8 1.0 OG1 C:THR135 4.5 27.1 1.0 HB2 E:GLU134 4.5 28.0 1.0 CG E:ASP131 4.5 33.7 1.0 HA E:ASP131 4.5 27.3 1.0 HB2 C:GLU134 4.5 27.1 1.0 HB3 F:GLU134 4.6 26.8 1.0 CG C:ASP131 4.6 37.0 1.0 O C:HOH381 4.6 46.9 1.0 HB3 E:GLU134 4.7 28.0 1.0 CG F:ASP131 4.7 33.5 1.0 HB2 F:ASP131 4.7 29.7 1.0 HB3 C:GLU134 4.8 27.1 1.0 HB2 C:ASP131 4.8 28.9 1.0 HB2 E:ASP131 5.0 29.1 1.0

Magnesium binding site 4 out of 4 in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:28.2 occ:1.00 O F:HOH415 2.1 29.9 1.0 O E:HOH368 2.1 31.4 1.0 O E:HOH422 2.1 27.6 1.0 O C:HOH308 2.1 24.9 1.0 O C:HOH427 2.2 31.0 1.0 O F:HOH317 2.2 29.5 1.0 OE2 F:GLU134 3.8 34.5 1.0 OE2 C:GLU134 3.9 31.6 1.0 OE2 E:GLU134 4.0 32.3 1.0 O F:HOH444 4.1 29.3 1.0 OE1 F:GLU134 4.2 36.1 1.0 O C:HOH450 4.2 34.8 1.0 O F:HOH329 4.2 34.3 1.0 O E:HOH453 4.3 30.0 1.0 OE1 C:GLU134 4.3 36.8 1.0 OE1 E:GLU134 4.3 34.4 1.0 O E:HOH340 4.3 31.5 1.0 O C:HOH306 4.4 34.5 1.0 CD F:GLU134 4.4 29.6 1.0 HB3 F:CYS130 4.5 26.8 1.0 CD C:GLU134 4.5 29.5 1.0 CD E:GLU134 4.6 30.4 1.0 HB3 C:CYS130 4.6 25.0 1.0 HB3 E:CYS130 4.6 27.0 1.0 HE1 F:HIS118 4.7 26.8 1.0 HE2 F:HIS118 4.7 26.0 0.0 HE1 E:HIS118 4.8 25.2 1.0 HE1 C:HIS118 4.8 23.8 1.0 HE2 E:HIS118 4.9 23.4 0.0 HE2 C:HIS118 4.9 22.1 0.0

L.Lang, H.Bohler, H.Wagler, T.Beck. Assembly Requirements For the Construction of Large-Scale Binary Protein Structures. Biomacromolecules 2023.
ISSN: ESSN 1526-4602
PubMed: 38059469
DOI: 10.1021/ACS.BIOMAC.3C00891