Iron 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:

Magnesium

(Mg)

4 atoms

The binding sites of Iron 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 Iron atom.
In total 6 binding sites of Iron where determined in the Unitary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos)-M1 (Mg Formate Condition), PDB code: 8pp5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 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 Iron with other atoms in the Fe 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:Fe201 b:41.4 occ:1.00 HD1 A:HIS65 1.4 31.4 0.0 OE1 A:GLU62 2.0 30.7 1.0 OE1 A:GLU27 2.1 27.4 1.0 O A:HOH317 2.2 34.1 1.0 ND1 A:HIS65 2.2 31.7 1.0 O A:HOH305 2.2 27.6 1.0 CD A:GLU62 3.0 30.8 1.0 CD A:GLU27 3.1 25.8 1.0 CE1 A:HIS65 3.2 34.1 1.0 CG A:HIS65 3.3 28.8 1.0 HE1 A:HIS65 3.3 33.1 1.0 OE2 A:GLU62 3.3 34.0 1.0 HG13 A:VAL110 3.4 24.7 1.0 OE2 A:GLU27 3.4 27.6 1.0 HB2 A:HIS65 3.4 24.8 1.0 HB3 A:HIS65 3.4 24.8 1.0 CB A:HIS65 3.6 24.1 1.0 HA A:GLU62 3.7 22.7 1.0 OE1 A:GLN141 4.0 34.6 1.0 O A:HOH390 4.0 34.2 1.0 HA A:GLU27 4.3 21.7 1.0 CG1 A:VAL110 4.3 25.1 1.0 NE2 A:HIS65 4.3 32.3 1.0 CG A:GLU62 4.3 24.8 1.0 CD2 A:HIS65 4.4 30.4 1.0 HB3 A:GLU27 4.4 21.3 1.0 CG A:GLU27 4.4 21.7 1.0 HG12 A:VAL110 4.4 24.6 1.0 HB3 A:GLU62 4.5 23.3 1.0 HG21 A:VAL110 4.5 25.6 1.0 CA A:GLU62 4.5 23.5 1.0 HE2 A:TYR137 4.6 24.8 1.0 HD2 A:TYR137 4.6 25.4 1.0 CB A:GLU62 4.7 22.6 1.0 HG11 A:VAL110 4.8 24.6 1.0 HB3 A:ALA30 4.8 24.6 1.0 CB A:GLU27 4.8 20.7 1.0 HG3 A:GLU27 4.8 22.3 1.0 HG3 A:GLU62 4.9 25.5 1.0 HG2 A:GLU62 4.9 25.5 1.0 CD A:GLN141 4.9 33.1 1.0 HD11 A:LEU114 5.0 24.3 1.0

Iron binding site 2 out of 6 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 Iron with other atoms in the Fe 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:Fe201 b:42.8 occ:1.00 HD1 B:HIS65 1.4 26.9 0.0 OE1 B:GLU62 2.1 33.9 1.0 OE1 B:GLU27 2.1 29.0 1.0 O B:HOH317 2.2 34.5 1.0 ND1 B:HIS65 2.2 26.9 1.0 O B:HOH307 2.3 24.3 1.0 CD B:GLU62 3.0 28.1 1.0 CE1 B:HIS65 3.1 31.2 1.0 CD B:GLU27 3.1 26.4 1.0 HE1 B:HIS65 3.2 29.7 1.0 OE2 B:GLU62 3.3 35.8 1.0 HG13 B:VAL110 3.3 25.6 1.0 CG B:HIS65 3.3 28.5 1.0 OE2 B:GLU27 3.4 28.5 1.0 HB2 B:HIS65 3.5 24.9 1.0 HB3 B:HIS65 3.6 24.9 1.0 HA B:GLU62 3.7 23.7 1.0 CB B:HIS65 3.7 24.2 1.0 OE1 B:GLN141 4.0 34.8 1.0 O B:HOH368 4.0 38.8 1.0 CG1 B:VAL110 4.2 26.4 1.0 NE2 B:HIS65 4.2 29.1 1.0 HB3 B:GLU27 4.2 22.7 1.0 HA B:GLU27 4.3 22.2 1.0 HG12 B:VAL110 4.3 25.6 1.0 O B:HOH302 4.3 52.1 1.0 CG B:GLU62 4.4 22.8 1.0 CD2 B:HIS65 4.4 26.6 1.0 CG B:GLU27 4.4 25.9 1.0 HB3 B:GLU62 4.5 23.1 1.0 HG21 B:VAL110 4.5 25.2 1.0 CA B:GLU62 4.6 23.8 1.0 HD2 B:TYR137 4.6 21.4 1.0 HE2 B:TYR137 4.6 21.3 1.0 HG11 B:VAL110 4.7 25.6 1.0 CB B:GLU27 4.7 21.8 1.0 CB B:GLU62 4.7 22.9 1.0 HB3 B:ALA30 4.7 26.1 1.0 HG3 B:GLU27 4.8 25.0 1.0 OE1 B:GLU107 4.9 44.6 1.0 HG3 B:GLU62 4.9 24.0 1.0 CD B:GLN141 4.9 28.0 1.0 HG2 B:GLU62 4.9 23.9 1.0

Iron binding site 3 out of 6 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 Iron with other atoms in the Fe 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:Fe201 b:43.5 occ:1.00 HD1 C:HIS65 1.5 32.4 0.0 OE1 C:GLU62 2.1 32.6 1.0 OE1 C:GLU27 2.1 28.1 1.0 O C:HOH325 2.1 38.3 1.0 O C:HOH318 2.2 27.1 1.0 ND1 C:HIS65 2.4 32.6 1.0 CD C:GLU62 3.0 29.0 1.0 CD C:GLU27 3.0 27.2 1.0 OE2 C:GLU27 3.3 26.7 1.0 OE2 C:GLU62 3.3 32.4 1.0 CE1 C:HIS65 3.3 39.6 1.0 HB2 C:HIS65 3.4 27.2 1.0 CG C:HIS65 3.4 31.4 1.0 HE1 C:HIS65 3.4 36.9 1.0 HG13 C:VAL110 3.5 29.4 1.0 HB3 C:HIS65 3.5 27.1 1.0 CB C:HIS65 3.6 26.7 1.0 HA C:GLU62 3.7 23.5 1.0 OE1 C:GLN141 3.9 35.3 1.0 O C:HOH382 4.0 42.5 1.0 HA C:GLU27 4.3 22.3 1.0 HB3 C:GLU27 4.3 23.5 1.0 CG1 C:VAL110 4.4 29.6 1.0 CG C:GLU27 4.4 23.4 1.0 CG C:GLU62 4.4 25.4 1.0 HG12 C:VAL110 4.4 29.4 1.0 NE2 C:HIS65 4.5 35.8 1.0 CD2 C:HIS65 4.5 31.4 1.0 HE2 C:TYR137 4.5 24.4 1.0 HB3 C:GLU62 4.5 24.7 1.0 HD2 C:TYR137 4.6 24.7 1.0 CA C:GLU62 4.6 23.7 1.0 HB3 C:ALA30 4.7 24.4 1.0 HG21 C:VAL110 4.7 27.5 1.0 CB C:GLU62 4.7 24.9 1.0 HG3 C:GLU27 4.7 24.4 1.0 CB C:GLU27 4.8 23.9 1.0 HG11 C:VAL110 4.9 29.4 1.0 O C:HOH401 4.9 42.9 1.0 HG3 C:GLU62 4.9 26.1 1.0 OE1 C:GLU107 4.9 39.5 1.0 CD C:GLN141 4.9 28.8 1.0 HG2 C:GLU62 4.9 26.1 1.0

Iron binding site 4 out of 6 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 Iron with other atoms in the Fe 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 D:Fe201 b:47.9 occ:1.00 HD1 D:HIS65 1.3 33.8 0.0 OE1 D:GLU62 2.0 35.8 1.0 OE1 D:GLU27 2.1 29.8 1.0 ND1 D:HIS65 2.2 34.3 1.0 O D:HOH307 2.2 27.3 1.0 O D:HOH313 2.2 32.1 1.0 CD D:GLU62 3.0 32.4 1.0 CE1 D:HIS65 3.1 34.4 1.0 CD D:GLU27 3.1 25.6 1.0 HE1 D:HIS65 3.2 34.2 1.0 OE2 D:GLU62 3.2 37.8 1.0 CG D:HIS65 3.2 32.6 1.0 HG13 D:VAL110 3.3 29.1 1.0 OE2 D:GLU27 3.4 28.0 1.0 HB2 D:HIS65 3.4 27.0 1.0 HB3 D:HIS65 3.4 26.9 1.0 CB D:HIS65 3.6 25.9 1.0 HA D:GLU62 3.7 24.4 1.0 O D:HOH381 3.9 38.9 1.0 OE1 D:GLN141 4.1 33.5 1.0 CG1 D:VAL110 4.2 30.6 1.0 NE2 D:HIS65 4.2 33.7 1.0 HG12 D:VAL110 4.3 29.1 1.0 HB3 D:GLU27 4.3 24.5 1.0 HA D:GLU27 4.3 23.8 1.0 CG D:GLU62 4.3 26.1 1.0 CD2 D:HIS65 4.3 32.8 1.0 CG D:GLU27 4.4 25.3 1.0 HD2 D:TYR137 4.5 24.1 1.0 HE2 D:TYR137 4.6 24.0 1.0 HG11 D:VAL110 4.6 29.1 1.0 HG21 D:VAL110 4.6 26.2 1.0 CA D:GLU62 4.6 24.6 1.0 HB3 D:GLU62 4.6 23.9 1.0 CB D:GLU27 4.7 24.4 1.0 CB D:GLU62 4.8 22.7 1.0 HB3 D:ALA30 4.8 22.6 1.0 HG3 D:GLU27 4.8 25.2 1.0 HG3 D:GLU62 4.8 26.6 1.0 HG2 D:GLU62 4.9 26.6 1.0 O D:HOH389 4.9 45.6 1.0 HD11 D:LEU114 4.9 24.3 1.0 CD D:GLN141 5.0 30.7 1.0 HE2 D:HIS65 5.0 33.0 0.0

Iron binding site 5 out of 6 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 Iron with other atoms in the Fe binding site number 5 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 E:Fe201 b:44.9 occ:1.00 HD1 E:HIS65 1.3 28.0 0.0 OE1 E:GLU62 2.0 29.6 1.0 OE1 E:GLU27 2.1 26.1 1.0 O E:HOH365 2.1 39.7 1.0 ND1 E:HIS65 2.2 28.3 1.0 O E:HOH333 2.3 29.9 1.0 CD E:GLU62 3.0 28.9 1.0 CD E:GLU27 3.1 24.6 1.0 CE1 E:HIS65 3.1 34.7 1.0 HE1 E:HIS65 3.2 33.4 1.0 CG E:HIS65 3.2 31.5 1.0 HB2 E:HIS65 3.3 26.4 1.0 OE2 E:GLU27 3.4 28.3 1.0 HG13 E:VAL110 3.4 28.7 1.0 OE2 E:GLU62 3.4 37.9 1.0 HB3 E:HIS65 3.4 26.4 1.0 CB E:HIS65 3.6 26.2 1.0 HA E:GLU62 3.6 23.2 1.0 OE1 E:GLN141 4.1 40.4 1.0 O E:HOH309 4.1 35.3 1.0 NE2 E:HIS65 4.2 36.3 1.0 HA E:GLU27 4.3 23.1 1.0 CG1 E:VAL110 4.3 29.1 1.0 HB3 E:GLU27 4.3 22.6 1.0 HG12 E:VAL110 4.3 28.7 1.0 CG E:GLU62 4.3 25.1 1.0 CD2 E:HIS65 4.3 31.2 1.0 CG E:GLU27 4.4 21.1 1.0 HB3 E:GLU62 4.4 23.4 1.0 HD2 E:TYR137 4.5 25.2 1.0 CA E:GLU62 4.5 23.5 1.0 HE2 E:TYR137 4.6 24.1 1.0 CB E:GLU62 4.7 22.7 1.0 HB3 E:ALA30 4.7 23.5 1.0 HG3 E:GLU27 4.7 22.3 1.0 CB E:GLU27 4.7 22.6 1.0 HG21 E:VAL110 4.7 29.3 1.0 HG11 E:VAL110 4.8 28.7 1.0 HG2 E:GLU62 4.9 25.3 1.0 O E:HOH391 4.9 48.3 1.0 HG3 E:GLU62 4.9 25.4 1.0 CD E:GLN141 5.0 28.9 1.0

Iron binding site 6 out of 6 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 Iron with other atoms in the Fe binding site number 6 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 F:Fe201 b:47.4 occ:1.00 HD1 F:HIS65 1.4 29.8 0.0 OE1 F:GLU27 2.1 27.6 1.0 OE1 F:GLU62 2.1 30.1 1.0 O F:HOH315 2.2 31.1 1.0 O F:HOH305 2.2 28.9 1.0 ND1 F:HIS65 2.2 29.7 1.0 CD F:GLU27 3.0 27.6 1.0 CD F:GLU62 3.1 28.5 1.0 CE1 F:HIS65 3.1 32.0 1.0 CG F:HIS65 3.2 27.9 1.0 HE1 F:HIS65 3.3 31.0 1.0 HB2 F:HIS65 3.3 27.0 1.0 OE2 F:GLU27 3.3 27.2 1.0 OE2 F:GLU62 3.4 36.7 1.0 HB3 F:HIS65 3.4 27.0 1.0 HG13 F:VAL110 3.4 29.6 1.0 CB F:HIS65 3.5 27.6 1.0 HA F:GLU62 3.7 23.8 1.0 O F:HOH371 4.1 37.5 1.0 OE1 F:GLN141 4.1 35.4 1.0 HA F:GLU27 4.2 23.2 1.0 CG1 F:VAL110 4.3 30.5 1.0 NE2 F:HIS65 4.3 30.4 1.0 HB3 F:GLU27 4.3 24.0 1.0 CG F:GLU27 4.3 25.9 1.0 HG12 F:VAL110 4.3 29.6 1.0 CD2 F:HIS65 4.4 30.9 1.0 CG F:GLU62 4.4 25.8 1.0 HD2 F:TYR137 4.5 24.8 1.0 HB3 F:GLU62 4.5 23.6 1.0 HE2 F:TYR137 4.5 23.5 1.0 CA F:GLU62 4.6 23.9 1.0 HG11 F:VAL110 4.7 29.6 1.0 CB F:GLU27 4.7 23.3 1.0 HG3 F:GLU27 4.7 25.6 1.0 HB3 F:ALA30 4.7 24.1 1.0 CB F:GLU62 4.7 22.5 1.0 HG21 F:VAL110 4.7 27.4 1.0 HG3 F:GLU62 4.9 25.6 1.0 HG2 F:GLU62 4.9 25.5 1.0 HG2 F:GLU27 5.0 25.6 1.0 CA F:GLU27 5.0 24.1 1.0

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