Iron in PDB 7s8t: M. Xanthus Ferritin-Like Protein Encc

The structure of M. Xanthus Ferritin-Like Protein Encc, PDB code: 7s8t was solved by E.Eren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.703, 47.797, 135.33, 90, 90.13, 90
R / Rfree (%)	32.5 / 34

The binding sites of Iron atom in the M. Xanthus Ferritin-Like Protein Encc (pdb code 7s8t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the M. Xanthus Ferritin-Like Protein Encc, PDB code: 7s8t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:57.5 occ:0.50 OE2 J:GLU68 2.3 52.0 1.0 OE2 A:GLU38 2.4 52.3 1.0 CD J:GLU68 3.0 53.3 1.0 CD A:GLU38 3.0 52.0 1.0 OE1 J:GLU68 3.0 54.3 1.0 OE1 A:GLU38 3.0 52.6 1.0 OE2 A:GLU68 3.4 52.9 1.0 CG A:GLU68 3.6 52.6 1.0 CD A:GLU68 3.7 52.5 1.0 OH J:TYR45 4.2 53.3 1.0 O J:HOH303 4.2 53.0 1.0 CB J:ALA41 4.2 54.9 1.0 CB A:ALA41 4.3 51.7 1.0 FE J:FE201 4.3 55.5 0.5 CG A:GLU38 4.3 51.6 1.0 CA A:GLU38 4.4 52.1 1.0 CG J:GLU68 4.4 53.3 1.0 OE1 A:GLU68 4.6 52.8 1.0 ND1 A:HIS71 4.6 55.0 1.0 CB A:GLU68 4.7 53.4 1.0 O A:ALA37 4.8 52.6 1.0 CE2 J:TYR45 4.8 53.4 1.0 N A:GLU38 4.9 52.0 1.0 CB A:GLU38 4.9 51.8 1.0 CZ J:TYR45 5.0 53.7 1.0

Iron binding site 2 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:66.0 occ:0.50 OE1 E:GLU38 2.6 53.0 1.0 OE2 F:GLU68 2.6 52.6 1.0 FE F:FE201 2.7 58.6 0.5 OE2 E:GLU38 2.8 51.9 1.0 CD E:GLU38 3.0 51.8 1.0 ND1 E:HIS71 3.4 52.7 1.0 CD F:GLU68 3.4 52.2 1.0 CG F:GLU68 3.5 51.7 1.0 OE2 E:GLU68 3.5 51.5 1.0 CG E:GLU68 3.9 53.6 1.0 CD E:GLU68 4.0 52.4 1.0 CE1 E:HIS71 4.1 52.0 1.0 CG E:HIS71 4.3 52.8 1.0 CB E:GLU68 4.3 54.1 1.0 CG1 F:VAL64 4.5 53.6 1.0 CA E:GLU68 4.5 53.3 1.0 CG E:GLU38 4.5 51.7 1.0 CB E:HIS71 4.5 51.6 1.0 OE1 F:GLU68 4.6 52.8 1.0 ND1 F:HIS71 4.8 52.1 1.0 CB F:GLU68 4.8 51.9 1.0 CA E:GLU38 4.9 52.7 1.0 CE2 F:TYR45 5.0 51.6 1.0 OE1 E:GLU68 5.0 53.5 1.0

Iron binding site 3 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:58.6 occ:0.50 OE2 E:GLU68 2.2 51.5 1.0 OE2 F:GLU38 2.5 50.9 1.0 FE E:FE201 2.7 66.0 0.5 CD F:GLU38 3.1 50.8 1.0 OE1 F:GLU38 3.2 51.7 1.0 OE2 F:GLU68 3.3 52.6 1.0 CD E:GLU68 3.3 52.4 1.0 ND1 F:HIS71 3.7 52.1 1.0 CG F:GLU68 3.8 51.7 1.0 CD F:GLU68 3.8 52.2 1.0 CG E:GLU68 3.8 53.6 1.0 OH E:TYR45 4.4 52.1 1.0 CB F:GLU68 4.4 51.9 1.0 OE1 E:GLU68 4.4 53.5 1.0 CB E:ALA41 4.4 52.1 1.0 CE2 E:TYR45 4.5 51.5 1.0 CG F:GLU38 4.5 50.7 1.0 CE1 F:HIS71 4.6 52.2 1.0 CA F:GLU68 4.6 52.5 1.0 CG F:HIS71 4.7 50.7 1.0 CB F:ALA41 4.7 50.8 1.0 CB F:HIS71 4.7 50.9 1.0 OE1 F:GLU68 4.8 52.8 1.0 CZ E:TYR45 5.0 50.7 1.0 OE1 E:GLU38 5.0 53.0 1.0

Iron binding site 4 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:54.1 occ:0.50 OE1 H:GLU38 2.6 51.9 1.0 ND1 H:HIS71 2.6 51.1 1.0 OE2 C:GLU68 2.7 50.5 1.0 OE1 H:GLU68 2.9 52.4 1.0 OE2 H:GLU38 3.0 49.8 1.0 CG C:GLU68 3.0 51.0 1.0 CE1 H:HIS71 3.2 51.2 1.0 CD H:GLU38 3.2 51.1 1.0 CD C:GLU68 3.3 51.5 1.0 CD H:GLU68 3.5 51.7 1.0 CG H:HIS71 3.6 51.0 1.0 OE2 H:GLU68 3.7 50.7 1.0 CG1 C:VAL64 3.8 52.8 1.0 CB H:HIS71 4.1 51.0 1.0 NE2 H:HIS71 4.2 51.9 1.0 CB C:GLU68 4.4 50.2 1.0 CD2 H:HIS71 4.4 51.9 1.0 OE1 C:GLU68 4.5 52.4 1.0 CE2 C:TYR45 4.6 50.9 1.0 O C:VAL64 4.6 52.6 1.0 CG H:GLU38 4.7 51.6 1.0 CA H:GLU68 4.7 51.5 1.0 CG H:GLU68 4.7 52.1 1.0 ND1 C:HIS71 4.7 51.9 1.0 CA C:GLU68 4.8 51.0 1.0 CE1 C:HIS71 4.8 51.7 1.0 CB H:GLU68 5.0 51.2 1.0 OH C:TYR45 5.0 52.4 1.0 N C:GLU68 5.0 51.3 1.0

Iron binding site 5 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:59.5 occ:0.50 CD I:GLU68 2.3 55.4 1.0 OE1 I:GLU68 2.4 55.4 1.0 OE2 I:GLU68 2.5 55.4 1.0 OE1 G:GLU38 2.7 53.8 1.0 CG I:GLU68 3.2 57.2 1.0 CD2 G:HIS71 3.5 56.0 1.0 OH I:TYR45 3.5 54.5 1.0 CE2 I:TYR45 3.6 55.5 1.0 FE I:FE202 3.6 59.6 0.5 CG G:HIS71 3.7 55.0 1.0 CG1 I:VAL64 3.9 56.7 1.0 CD G:GLU38 3.9 53.1 1.0 NE2 G:HIS71 4.0 55.9 1.0 CZ I:TYR45 4.0 54.2 1.0 OE2 G:GLU68 4.1 53.0 1.0 CB G:HIS71 4.1 53.3 1.0 ND1 G:HIS71 4.3 55.0 1.0 CE1 G:HIS71 4.4 55.8 1.0 CG G:GLU38 4.5 53.3 1.0 CB I:GLU68 4.6 58.3 1.0 CD2 I:TYR45 4.7 56.4 1.0 CG G:GLU68 4.7 55.7 1.0 CD G:GLU68 4.7 55.1 1.0 O I:VAL64 4.7 60.5 1.0 CB I:ALA41 4.7 55.5 1.0 OE2 G:GLU38 4.9 53.2 1.0 CA G:GLU68 4.9 54.7 1.0

Iron binding site 6 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:59.6 occ:0.50 OE1 I:GLU68 2.4 55.4 1.0 OE2 G:GLU68 2.4 53.0 1.0 OE2 I:GLU38 2.5 54.6 1.0 CG G:GLU68 2.8 55.7 1.0 CD G:GLU68 3.0 55.1 1.0 CD2 I:HIS71 3.1 55.6 1.0 CD I:GLU38 3.3 55.4 1.0 NE2 I:HIS71 3.4 54.8 1.0 CD I:GLU68 3.4 55.4 1.0 CG I:HIS71 3.5 55.4 1.0 OE1 I:GLU38 3.5 56.5 1.0 FE I:FE201 3.6 59.5 0.5 CG1 G:VAL64 3.7 55.2 1.0 CE1 I:HIS71 3.8 55.3 1.0 OE2 I:GLU68 3.8 55.4 1.0 ND1 I:HIS71 3.9 55.3 1.0 CB G:GLU68 4.1 54.4 1.0 CB I:HIS71 4.2 55.5 1.0 CE2 G:TYR45 4.2 54.0 1.0 OE1 G:GLU68 4.2 57.0 1.0 O G:VAL64 4.3 54.8 1.0 CA G:GLU68 4.4 54.7 1.0 OE1 G:GLU38 4.5 53.8 1.0 N G:GLU68 4.6 54.6 1.0 OH G:TYR45 4.6 54.7 1.0 CD2 G:HIS71 4.6 56.0 1.0 CG I:GLU68 4.7 57.2 1.0 CG I:GLU38 4.8 55.8 1.0 NE2 G:HIS71 4.9 55.9 1.0 CZ G:TYR45 4.9 54.3 1.0 CA I:GLU68 5.0 58.1 1.0

Iron binding site 7 out of 7 in the M. Xanthus Ferritin-Like Protein Encc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of M. Xanthus Ferritin-Like Protein Encc within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe201 b:55.5 occ:0.50 OE1 J:GLU38 2.2 54.5 1.0 OE2 A:GLU68 2.7 52.9 1.0 CD2 J:HIS71 2.8 55.0 1.0 CD J:GLU38 2.9 53.4 1.0 OE2 J:GLU38 2.9 53.5 1.0 CG J:HIS71 3.0 53.5 1.0 CG A:GLU68 3.3 52.6 1.0 NE2 J:HIS71 3.3 54.9 1.0 CD A:GLU68 3.3 52.5 1.0 OE1 J:GLU68 3.3 54.3 1.0 CD J:GLU68 3.4 53.3 1.0 ND1 J:HIS71 3.6 53.9 1.0 OE2 J:GLU68 3.6 52.0 1.0 CG1 A:VAL64 3.6 53.6 1.0 CB J:HIS71 3.7 52.9 1.0 CE1 J:HIS71 3.7 54.0 1.0 O J:HOH303 4.2 53.0 1.0 CG J:GLU68 4.2 53.3 1.0 CG J:GLU38 4.3 53.2 1.0 FE A:FE201 4.3 57.5 0.5 CA J:GLU68 4.3 53.8 1.0 OE1 A:GLU68 4.4 52.8 1.0 CB J:GLU68 4.5 53.4 1.0 OH A:TYR45 4.6 53.3 1.0 CE2 A:TYR45 4.6 53.1 1.0 O A:VAL64 4.7 61.5 1.0 CB A:GLU68 4.7 53.4 1.0 ND1 A:HIS71 4.9 55.0 1.0 CE1 A:HIS71 4.9 54.5 1.0

E.Eren, B.Wang, D.C.Winkler, N.R.Watts, A.C.Steven, P.T.Wingfield. Structural Characterization of the Myxococcus Xanthus Encapsulin and Ferritin-Like Cargo System Gives Insight Into Its Iron Storage Mechanism. Structure V. 30 551 2022.
ISSN: ISSN 0969-2126
PubMed: 35150605
DOI: 10.1016/J.STR.2022.01.008