Iron in PDB 7s5k: M. Xanthus Ferritin-Like Protein Encb

The structure of M. Xanthus Ferritin-Like Protein Encb, PDB code: 7s5k was solved by E.Eren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.44 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.49, 44.37, 127.96, 90, 114.08, 90
R / Rfree (%)	20.5 / 25.5

The structure of M. Xanthus Ferritin-Like Protein Encb also contains other interesting chemical elements:

Calcium

(Ca)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the M. Xanthus Ferritin-Like Protein Encb (pdb code 7s5k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the M. Xanthus Ferritin-Like Protein Encb, PDB code: 7s5k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:77.6 occ:1.00 OE2 B:GLU58 2.6 33.6 1.0 OE2 A:GLU58 2.7 35.2 1.0 ND1 A:HIS61 2.7 34.4 1.0 OH B:TYR35 2.8 30.1 1.0 OE1 A:GLU58 3.3 31.6 1.0 CD A:GLU58 3.3 35.8 1.0 CE1 A:HIS61 3.4 37.2 1.0 CD B:GLU58 3.5 35.7 1.0 CZ B:TYR35 3.7 28.2 1.0 CA A:CA102 3.7 28.4 0.3 CE2 B:TYR35 3.8 24.0 1.0 CG A:HIS61 3.8 34.5 1.0 OE1 B:GLU58 3.9 31.7 1.0 CG A:GLU28 4.1 23.7 1.0 FE B:FE202 4.2 80.9 1.0 CB A:HIS61 4.3 27.3 1.0 OE1 A:GLU28 4.4 28.8 1.0 CG2 B:THR31 4.4 28.0 1.0 O B:HOH311 4.6 36.3 1.0 NE2 A:HIS61 4.6 38.3 1.0 CG B:GLU58 4.6 29.7 1.0 CD A:GLU28 4.7 30.1 1.0 CG A:GLU58 4.8 27.7 1.0 CD2 A:HIS61 4.9 36.8 1.0 CB B:GLU58 4.9 28.0 1.0 CA B:CA203 5.0 68.7 1.0

Iron binding site 2 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:119.0 occ:1.00 OE2 A:GLU64 2.5 44.6 1.0 OE1 B:GLU57 2.6 57.6 1.0 OE2 B:GLU57 2.9 47.3 1.0 CD B:GLU57 3.0 43.4 1.0 NE2 B:HIS53 3.3 40.7 1.0 CE1 B:HIS53 3.4 37.2 1.0 CD A:GLU64 3.5 42.7 1.0 OE1 A:GLU64 3.7 39.9 1.0 CG A:GLU60 4.0 32.0 1.0 OE2 A:GLU60 4.2 32.3 1.0 CG B:GLU57 4.4 35.1 1.0 CD A:GLU60 4.6 35.9 1.0 CD2 B:HIS53 4.6 34.6 1.0 ND1 B:HIS53 4.7 37.9 1.0 CG A:GLU64 4.9 32.9 1.0 CD2 A:HIS61 4.9 36.8 1.0

Iron binding site 3 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:80.9 occ:1.00 OH A:TYR35 2.6 30.1 1.0 OE1 A:GLU58 2.7 31.6 1.0 ND1 B:HIS61 2.7 40.1 1.0 OE1 B:GLU58 2.8 31.7 1.0 OE2 B:GLU58 3.4 33.6 1.0 CD B:GLU58 3.4 35.7 1.0 CE1 B:HIS61 3.4 42.4 1.0 CZ A:TYR35 3.5 30.5 1.0 CE2 A:TYR35 3.5 30.2 1.0 CD A:GLU58 3.7 35.8 1.0 CG B:HIS61 3.9 39.1 1.0 CG B:GLU28 3.9 26.1 1.0 OE2 B:GLU28 4.0 33.6 1.0 CA B:CA203 4.0 68.7 1.0 OE2 A:GLU58 4.2 35.2 1.0 FE A:FE101 4.2 77.6 1.0 CB B:HIS61 4.3 31.5 1.0 O A:HOH305 4.4 37.0 1.0 CG2 A:THR31 4.4 27.4 1.0 CD B:GLU28 4.4 34.9 1.0 NE2 B:HIS61 4.6 40.1 1.0 CE1 A:TYR35 4.8 29.1 1.0 CG A:GLU58 4.8 27.7 1.0 CG B:GLU58 4.8 29.7 1.0 CD2 A:TYR35 4.9 28.0 1.0 CD2 B:HIS61 4.9 40.6 1.0

Iron binding site 4 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:95.2 occ:1.00 OE2 F:GLU58 2.5 48.5 1.0 OE1 E:GLU58 2.7 48.9 1.0 OH F:TYR35 2.7 32.1 1.0 CD F:GLU58 3.4 44.6 1.0 CD E:GLU58 3.4 49.5 1.0 OE2 E:GLU58 3.5 51.7 1.0 CE2 F:TYR35 3.5 39.8 1.0 CZ F:TYR35 3.6 38.3 1.0 ND1 E:HIS61 3.7 56.3 1.0 CA E:CA203 3.8 37.7 0.4 OE1 F:GLU58 3.8 48.3 1.0 FE F:FE201 4.1 106.2 1.0 CG E:GLU28 4.2 34.2 1.0 O F:HOH301 4.2 35.6 1.0 CG2 F:THR31 4.2 33.3 1.0 OE2 E:GLU28 4.3 43.3 1.0 CE1 E:HIS61 4.3 59.0 1.0 CG E:HIS61 4.4 51.8 1.0 CG F:GLU58 4.5 38.4 1.0 CA F:CA202 4.6 35.7 0.4 FE E:FE202 4.6 169.4 1.0 CD E:GLU28 4.7 39.0 1.0 CB E:HIS61 4.7 45.4 1.0 CG E:GLU58 4.8 42.1 1.0 CB F:GLU58 4.8 33.7 1.0 CD2 F:TYR35 4.8 38.4 1.0 CE1 F:TYR35 4.9 39.2 1.0

Iron binding site 5 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe202 b:169.4 occ:1.00 CE1 F:HIS61 2.4 54.7 1.0 OE2 E:GLU58 2.5 51.7 1.0 ND1 E:HIS61 2.8 56.3 1.0 CE1 E:HIS61 3.0 59.0 1.0 N E:GLU58 3.1 37.3 1.0 C E:GLU57 3.2 40.5 1.0 ND1 F:HIS61 3.2 52.9 1.0 CA E:GLU58 3.3 39.7 1.0 O E:GLU57 3.4 42.5 1.0 NE2 F:HIS61 3.5 52.2 1.0 CD E:GLU58 3.6 49.5 1.0 CB E:GLU57 3.6 39.9 1.0 CB E:GLU58 3.8 35.6 1.0 FE F:FE201 3.9 106.2 1.0 CA E:GLU57 4.0 40.9 1.0 CG E:HIS61 4.1 51.8 1.0 O E:LEU54 4.1 28.3 1.0 NE2 E:HIS61 4.2 61.4 1.0 CG E:GLU58 4.2 42.1 1.0 O F:HOH304 4.3 55.4 1.0 OE1 E:GLU58 4.5 48.9 1.0 CG F:HIS61 4.5 43.5 1.0 OE2 F:GLU58 4.6 48.5 1.0 FE E:FE201 4.6 95.2 1.0 CD2 F:HIS61 4.6 46.3 1.0 C E:GLU58 4.7 39.6 1.0 CD2 E:HIS61 4.8 56.6 1.0 CB E:HIS61 4.8 45.4 1.0 N E:GLU57 4.9 32.5 1.0 CG E:GLU57 5.0 49.2 1.0

Iron binding site 6 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:106.2 occ:1.00 OE2 E:GLU58 2.5 51.7 1.0 OE1 F:GLU58 2.7 48.3 1.0 OH E:TYR35 2.7 28.9 1.0 CD E:GLU58 3.3 49.5 1.0 OE2 F:GLU58 3.4 48.5 1.0 CD F:GLU58 3.4 44.6 1.0 ND1 F:HIS61 3.5 52.9 1.0 CA F:CA202 3.5 35.7 0.4 CE2 E:TYR35 3.6 32.6 1.0 CZ E:TYR35 3.6 31.6 1.0 OE1 E:GLU58 3.6 48.9 1.0 FE E:FE202 3.9 169.4 1.0 FE E:FE201 4.1 95.2 1.0 CG2 E:THR31 4.1 32.3 1.0 CE1 F:HIS61 4.1 54.7 1.0 CG F:GLU28 4.2 32.4 1.0 OE2 F:GLU28 4.4 43.5 1.0 CG F:HIS61 4.5 43.5 1.0 CG E:GLU58 4.5 42.1 1.0 CD F:GLU28 4.7 39.6 1.0 CB F:HIS61 4.8 41.1 1.0 CG F:GLU58 4.8 38.4 1.0 CA E:CA203 4.8 37.7 0.4 CD2 E:TYR35 4.9 30.8 1.0 CE1 E:TYR35 4.9 34.2 1.0 CB E:GLU58 4.9 35.6 1.0

Iron binding site 7 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


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 Encb within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe201 b:42.1 occ:0.35 OH H:TYR35 2.6 37.5 1.0 OE2 G:GLU58 2.7 48.3 1.0 OE2 H:GLU58 2.8 42.7 1.0 ND1 G:HIS61 3.1 48.0 1.0 OE1 G:GLU58 3.4 44.8 1.0 CD G:GLU58 3.4 42.7 1.0 CZ H:TYR35 3.5 31.1 1.0 CE2 H:TYR35 3.6 33.6 1.0 CD H:GLU58 3.7 40.8 1.0 CE1 G:HIS61 3.8 52.6 1.0 CA G:CA203 3.8 37.4 0.3 CG G:GLU28 3.9 33.9 1.0 FE H:FE102 4.1 104.9 1.0 OE1 H:GLU58 4.1 43.4 1.0 OE2 G:GLU28 4.1 40.9 1.0 CG G:HIS61 4.2 45.1 1.0 O H:HOH206 4.2 38.3 1.0 CG2 H:THR31 4.3 34.9 1.0 CD G:GLU28 4.4 37.6 1.0 CB G:HIS61 4.5 40.8 1.0 CA H:CA103 4.7 81.7 1.0 CG G:GLU58 4.8 36.6 1.0 CG H:GLU58 4.8 36.1 1.0 CE1 H:TYR35 4.8 34.5 1.0 CD2 H:TYR35 4.9 32.7 1.0

Iron binding site 8 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe202 b:100.3 occ:1.00 OE2 G:GLU57 2.7 58.9 1.0 OE2 H:GLU64 2.8 44.6 1.0 NE2 G:HIS53 3.1 43.5 1.0 CE1 G:HIS53 3.3 41.7 1.0 CD G:GLU57 3.3 46.7 1.0 OE1 G:GLU57 3.5 52.0 1.0 CD H:GLU64 3.8 40.5 1.0 OE1 H:GLU64 4.0 43.0 1.0 CD2 G:HIS53 4.5 35.8 1.0 CG H:GLU60 4.5 34.4 1.0 CG G:GLU57 4.6 43.3 1.0 ND1 G:HIS53 4.6 41.8 1.0 OE2 H:GLU60 4.6 37.7 1.0 FE H:FE101 5.0 107.6 1.0

Iron binding site 9 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe101 b:107.6 occ:1.00 NE2 H:HIS61 3.1 42.3 1.0 OE2 G:GLU57 3.3 58.9 1.0 O H:GLU57 3.4 34.6 1.0 CB H:GLU57 3.5 38.5 1.0 CD2 H:HIS61 3.6 39.6 1.0 CE1 H:HIS61 3.7 46.7 1.0 CD G:GLU57 3.9 46.7 1.0 CA H:GLU57 3.9 35.7 1.0 C H:GLU57 3.9 32.1 1.0 CG H:GLU57 4.0 44.5 1.0 NE2 G:HIS61 4.1 53.4 1.0 CD H:GLU57 4.2 48.5 1.0 CB H:GLU60 4.3 29.5 1.0 OE1 G:GLU57 4.3 52.0 1.0 CG H:HIS61 4.4 39.5 1.0 ND1 H:HIS61 4.4 44.0 1.0 CG H:GLU60 4.5 34.4 1.0 CE1 G:HIS61 4.5 52.6 1.0 OE2 H:GLU57 4.6 57.1 1.0 OE1 H:GLU57 4.6 55.5 1.0 CB G:GLU57 4.6 37.1 1.0 CG G:GLU57 4.8 43.3 1.0 FE G:FE202 5.0 100.3 1.0

Iron binding site 10 out of 16 in the M. Xanthus Ferritin-Like Protein Encb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of M. Xanthus Ferritin-Like Protein Encb within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe102 b:104.9 occ:1.00 OE1 H:GLU58 2.6 43.4 1.0 OE1 G:GLU58 2.7 44.8 1.0 OH G:TYR35 2.9 39.5 1.0 ND1 H:HIS61 3.1 44.0 1.0 OE2 H:GLU58 3.3 42.7 1.0 CD H:GLU58 3.3 40.8 1.0 CD G:GLU58 3.5 42.7 1.0 CA H:CA103 3.5 81.7 1.0 CE1 H:HIS61 3.7 46.7 1.0 CZ G:TYR35 3.8 35.6 1.0 CE2 G:TYR35 3.8 31.0 1.0 OE2 G:GLU58 3.8 48.3 1.0 FE G:FE201 4.1 42.1 0.3 CG H:GLU28 4.1 31.4 1.0 CG H:HIS61 4.1 39.5 1.0 CG2 G:THR31 4.2 33.5 1.0 OE2 H:GLU28 4.3 37.2 1.0 CB H:HIS61 4.5 34.3 1.0 CD H:GLU28 4.7 38.7 1.0 CG G:GLU58 4.7 36.6 1.0 CG H:GLU58 4.7 36.1 1.0 NE2 H:HIS61 4.9 42.3 1.0 CA G:CA203 4.9 37.4 0.3 CB G:GLU58 5.0 29.7 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