Magnesium in PDB 8pp2: Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition)

The structure of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition), PDB code: 8pp2 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)	49.06 / 2.00
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	126.802, 126.802, 175.598, 90, 90, 90
R / Rfree (%)	20.3 / 24.7

The structure of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

The binding sites of Magnesium atom in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) (pdb code 8pp2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition), PDB code: 8pp2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (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 Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:21.8 occ:1.00 O F:HOH389 2.0 28.6 1.0 O F:HOH316 2.0 28.4 1.0 O B:HOH364 2.1 22.5 1.0 O B:HOH323 2.2 26.5 1.0 OE2 F:GLU135 3.8 25.8 1.0 OE1 B:GLU135 4.0 25.5 1.0 O B:HOH324 4.2 28.7 1.0 O F:HOH401 4.2 28.1 1.0 O B:HOH370 4.2 30.4 1.0 OE1 F:GLU135 4.3 25.6 1.0 O F:HOH301 4.3 27.0 1.0 OE2 B:GLU135 4.3 27.6 1.0 HB3 F:CYS131 4.4 22.1 1.0 CD F:GLU135 4.5 24.6 1.0 HB3 B:CYS131 4.6 25.6 1.0 CD B:GLU135 4.6 26.9 1.0 HE1 F:HIS119 4.6 22.4 1.0 HE2 F:HIS119 4.6 22.6 0.0 HE2 B:HIS119 5.0 24.4 0.0 HB2 F:CYS131 5.0 22.0 1.0 HE1 B:HIS119 5.0 23.7 1.0 HG F:CYS131 5.0 24.6 0.0

Magnesium binding site 2 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (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 Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:26.3 occ:1.00 O C:HOH312 1.9 26.1 1.0 O C:HOH385 2.1 29.5 1.0 O E:HOH396 2.1 19.8 1.0 O E:HOH328 2.1 24.3 1.0 O D:HOH344 2.2 24.8 1.0 O D:HOH392 2.2 22.6 1.0 OE2 C:GLU135 3.8 24.4 1.0 OE2 E:GLU135 3.9 24.5 1.0 OE2 D:GLU135 3.9 22.9 1.0 O C:HOH396 4.1 30.7 1.0 O E:HOH405 4.2 24.4 1.0 O C:HOH352 4.2 22.8 1.0 O E:HOH349 4.2 26.0 1.0 O D:HOH405 4.3 28.4 1.0 OE1 C:GLU135 4.3 26.7 1.0 OE1 E:GLU135 4.3 24.3 1.0 OE1 D:GLU135 4.3 27.7 1.0 O D:HOH333 4.3 29.2 1.0 HB3 C:CYS131 4.4 20.9 1.0 CD C:GLU135 4.5 24.3 1.0 HB3 E:CYS131 4.5 22.0 1.0 CD E:GLU135 4.5 25.1 1.0 HB3 D:CYS131 4.5 21.6 1.0 CD D:GLU135 4.5 23.2 1.0 HE1 E:HIS119 4.6 23.1 1.0 HE2 C:HIS119 4.6 22.1 0.0 HE2 E:HIS119 4.7 21.9 0.0 HE1 C:HIS119 4.9 22.3 1.0 HE2 D:HIS119 4.9 22.5 0.0 HE1 D:HIS119 4.9 22.7 1.0

Magnesium binding site 3 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (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 Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:51.8 occ:1.00 O B:HOH302 1.8 42.5 1.0 OD1 F:ASP132 2.8 26.9 1.0 CG F:ASP132 3.9 23.2 1.0 HA F:ASP132 3.9 21.4 1.0 OD1 B:ASP132 3.9 28.0 1.0 OE1 F:GLU135 4.1 25.6 1.0 HB2 F:ASP132 4.1 21.9 1.0 OG1 F:THR136 4.4 25.2 1.0 HG1 F:THR136 4.4 25.2 0.0 CB F:ASP132 4.4 21.4 1.0 OE2 B:GLU135 4.4 27.6 1.0 HB2 F:GLU135 4.5 23.8 1.0 CA F:ASP132 4.6 21.7 1.0 HB3 F:GLU135 4.7 23.9 1.0 OD2 F:ASP132 4.9 25.4 1.0 HA B:ASP132 5.0 22.5 1.0 CD F:GLU135 5.0 24.6 1.0

Magnesium binding site 4 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (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 Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg202 b:33.5 occ:1.00 O G:HOH328 2.0 34.2 1.0 O J:HOH327 2.1 36.2 1.0 O J:HOH303 2.2 41.4 1.0 O G:HOH302 2.4 32.4 1.0 OE2 J:GLU135 3.9 39.4 1.0 O G:HOH306 4.0 74.1 1.0 OE2 G:GLU135 4.0 34.9 1.0 OE1 J:GLU135 4.2 40.8 1.0 OE1 G:GLU135 4.3 38.8 1.0 CD J:GLU135 4.5 41.2 1.0 HB3 J:CYS131 4.5 36.0 1.0 HB3 G:CYS131 4.6 38.1 1.0 CD G:GLU135 4.6 36.1 1.0 HE2 J:HIS119 4.6 40.6 0.0 HE1 G:HIS119 4.8 26.0 1.0 HE1 J:HIS119 4.8 39.6 1.0 HE2 G:HIS119 5.0 24.4 0.0

Magnesium binding site 5 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg202 b:62.1 occ:1.00 O J:HOH302 1.8 45.4 1.0 O G:HOH312 2.1 54.0 1.0 O G:HOH306 2.6 74.1 1.0 HB3 J:GLU135 3.4 34.2 1.0 OE1 J:GLU135 3.4 40.8 1.0 HB2 J:GLU135 3.6 34.2 1.0 OD1 J:ASP132 3.7 36.1 1.0 CB J:GLU135 4.0 33.0 1.0 HA J:ASP132 4.1 33.4 1.0 OD1 G:ASP132 4.1 35.6 1.0 CD J:GLU135 4.2 41.2 1.0 OG1 J:THR136 4.3 31.8 1.0 OE1 G:GLU135 4.5 38.8 1.0 CG J:GLU135 4.6 38.2 1.0 HG1 J:THR136 4.7 32.0 0.0 H J:THR136 4.8 32.4 1.0 CG J:ASP132 4.8 41.4 1.0 N J:THR136 4.9 32.0 1.0 HA J:THR136 4.9 33.2 1.0 O J:ASP132 5.0 32.9 1.0 CA J:ASP132 5.0 34.6 1.0

Magnesium binding site 6 out of 6 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Native(K86Q) Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg202 b:42.5 occ:1.00 O L:HOH310 2.1 40.6 1.0 O K:HOH326 2.2 48.2 1.0 O L:HOH302 2.3 43.5 1.0 O K:HOH302 2.3 33.6 1.0 OE1 L:GLU135 3.7 50.0 1.0 OE2 K:GLU135 3.9 42.9 1.0 OE2 L:GLU135 4.0 55.9 1.0 OE1 K:GLU135 4.2 45.8 1.0 CD L:GLU135 4.3 52.7 1.0 CD K:GLU135 4.5 44.8 1.0 HB3 K:CYS131 4.6 45.9 1.0 HB3 L:CYS131 4.8 46.5 1.0 HE2 K:HIS119 4.9 41.2 0.0 HE2 L:HIS119 4.9 59.4 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