Iron in PDB 7die: Crystal Structure of M. Penetrans Ferritin

All present enzymatic activity of Crystal Structure of M. Penetrans Ferritin:
1.16.3.2;

The structure of Crystal Structure of M. Penetrans Ferritin, PDB code: 7die was solved by W.M.Wang, Y.Zhang, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.86 / 1.90
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	151.334, 151.334, 125.213, 90, 90, 90
R / Rfree (%)	15.3 / 17.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of M. Penetrans Ferritin (pdb code 7die). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Crystal Structure of M. Penetrans Ferritin, PDB code: 7die:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:36.0 occ:0.68 OD2 A:ASP134 2.1 35.0 1.0 OD2 A:ASP55 2.3 31.1 0.6 NE2 A:HIS60 2.3 30.7 1.0 O A:HOH310 2.4 40.8 1.0 OD2 A:ASP138 2.4 29.3 1.0 OD1 A:ASP138 2.5 28.3 1.0 CG A:ASP138 2.8 32.1 1.0 FE A:FE202 2.8 91.6 0.9 CG A:ASP134 3.3 31.9 1.0 CE1 A:HIS60 3.3 29.1 1.0 CG A:ASP55 3.3 32.4 0.6 CD2 A:HIS60 3.3 29.5 1.0 OD1 A:ASP55 3.6 33.0 0.6 OD1 A:ASP134 3.8 32.1 1.0 O A:HOH362 4.0 34.4 1.0 O A:HOH311 4.3 46.1 1.0 CB A:ASP138 4.3 28.1 1.0 O A:HOH309 4.4 50.0 1.0 ND1 A:HIS60 4.4 29.4 1.0 CG A:HIS60 4.5 26.4 1.0 CB A:ASP134 4.5 26.8 1.0 CH2 A:TRP130 4.5 29.1 1.0 O A:ASP134 4.6 27.1 1.0 CB A:ASP55 4.7 28.6 0.6 CB A:ASP55 4.7 28.6 0.4 O A:HOH394 4.8 50.2 1.0 NZ A:LYS56 4.9 29.3 1.0

Iron binding site 2 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:91.6 occ:0.90 OD1 A:ASP138 2.6 28.3 1.0 O A:HOH394 2.6 50.2 1.0 FE A:FE201 2.8 36.0 0.7 O A:HOH311 2.8 46.1 1.0 O A:HOH309 2.9 50.0 1.0 O A:HOH310 3.3 40.8 1.0 OD2 A:ASP55 3.3 31.1 0.6 CG A:ASP138 3.7 32.1 1.0 CG A:ASP55 3.8 32.4 0.6 OD2 A:ASP134 3.9 35.0 1.0 OD1 A:ASP55 4.0 33.0 0.6 OD2 A:ASP55 4.1 31.7 0.4 OD1 A:ASP134 4.2 32.1 1.0 OD2 A:ASP138 4.2 29.3 1.0 CG A:ASP134 4.5 31.9 1.0 O A:HOH362 4.6 34.4 1.0 CB A:ASP55 4.7 28.6 0.6 CB A:ASP55 4.8 28.6 0.4 CG A:ASP55 4.8 31.5 0.4 CB A:GLU137 4.9 30.3 1.0 CA A:ASP138 4.9 25.8 1.0 CB A:ASP138 4.9 28.1 1.0 N A:ASP138 4.9 27.5 1.0

Iron binding site 3 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:62.5 occ:0.14 FE A:FE204 2.6 56.2 0.1 OD1 A:ASN153 3.6 41.7 0.3 O A:HOH395 3.9 45.1 1.0 ND2 A:ASN153 3.9 43.5 0.3 CG A:ASN153 4.2 39.4 0.3 O A:ASN153 4.9 38.1 0.7 O A:ASN153 4.9 38.1 0.3

Iron binding site 4 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:56.2 occ:0.15 FE A:FE203 2.6 62.5 0.1 O A:HOH395 2.7 45.1 1.0 FE A:FE205 3.0 32.2 0.2 OD1 A:ASN155 4.6 30.5 1.0 O A:ASN153 4.7 38.1 0.7 O A:ASN153 4.7 38.1 0.3 OD1 A:ASN153 4.8 41.7 0.3 ND2 A:ASN158 5.0 28.7 1.0

Iron binding site 5 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:32.2 occ:0.16 FE A:FE204 3.0 56.2 0.1 OD1 A:ASN158 3.3 31.7 1.0 O A:HOH395 3.8 45.1 1.0 ND2 A:ASN158 3.9 28.7 1.0 CG A:ASN158 4.0 34.5 1.0 OD1 A:ASN155 4.3 30.5 1.0

Iron binding site 6 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:36.8 occ:0.45 OD1 A:ASN161 3.0 37.5 1.0 OD1 A:ASN158 3.1 31.7 1.0 CA A:ASN158 3.5 29.5 1.0 CG A:ASN161 3.8 37.5 1.0 CB A:ASN161 3.8 34.1 1.0 CG A:ASN158 4.0 34.5 1.0 N A:ASN158 4.0 27.8 1.0 O A:ILE157 4.1 30.2 1.0 CB A:ASN158 4.2 27.7 1.0 C A:ILE157 4.3 30.6 1.0 CG2 A:ILE157 4.5 26.1 1.0 O A:ASN158 4.5 27.4 1.0 C A:ASN158 4.5 27.4 1.0 ND2 A:ASN161 5.0 42.5 1.0

Iron binding site 7 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:84.8 occ:0.75 O A:HOH386 2.8 48.3 1.0 OD2 A:ASP43 3.2 47.7 1.0 CG A:ASP43 3.5 49.0 1.0 CB A:ASP43 3.5 37.7 1.0 OD1 A:ASP43 4.2 50.5 1.0 O A:HOH366 4.4 46.1 1.0 NZ A:LYS38 4.9 46.6 1.0

Iron binding site 8 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:68.6 occ:0.50 NZ A:LYS38 2.6 46.6 1.0 O A:HOH358 2.8 45.5 1.0 CE A:LYS38 3.4 46.9 1.0 CD A:LYS38 4.2 36.4 1.0 O A:HOH366 4.4 46.1 1.0 CB A:ASP43 4.6 37.7 1.0 O A:GLY41 4.6 30.6 1.0 O A:LYS38 4.7 30.5 1.0 CA A:GLY41 4.7 29.1 1.0 C A:GLY41 4.7 32.1 1.0 O B:HOH350 4.9 40.2 1.0

Iron binding site 9 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:34.9 occ:0.65 OD2 B:ASP134 2.1 35.2 1.0 NE2 B:HIS60 2.3 30.6 1.0 OD2 B:ASP55 2.3 31.7 0.6 OD2 B:ASP138 2.5 31.5 1.0 OD1 B:ASP138 2.5 25.6 1.0 O B:HOH305 2.5 43.5 1.0 FE B:FE202 2.7 89.5 0.9 CG B:ASP138 2.8 32.7 1.0 CG B:ASP134 3.2 34.6 1.0 CE1 B:HIS60 3.3 32.6 1.0 CD2 B:HIS60 3.3 29.7 1.0 CG B:ASP55 3.3 34.0 0.6 OD1 B:ASP55 3.6 30.2 0.6 OD1 B:ASP134 3.7 31.9 1.0 O B:HOH316 3.7 48.4 1.0 O B:HOH343 4.1 39.1 1.0 O B:HOH306 4.3 46.0 1.0 CB B:ASP138 4.3 27.0 1.0 ND1 B:HIS60 4.4 25.9 1.0 CB B:ASP134 4.5 26.8 1.0 CG B:HIS60 4.5 24.4 1.0 CH2 B:TRP130 4.5 28.8 1.0 O B:ASP134 4.6 27.1 1.0 CB B:ASP55 4.7 27.6 0.6 CB B:ASP55 4.7 27.6 0.4 NZ B:LYS56 4.9 24.6 1.0

Iron binding site 10 out of 36 in the Crystal Structure of M. Penetrans Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of M. Penetrans Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:89.5 occ:0.90 O B:HOH316 2.3 48.4 1.0 OD1 B:ASP138 2.5 25.6 1.0 O B:HOH303 2.7 46.2 1.0 FE B:FE201 2.7 34.9 0.7 O B:HOH306 2.9 46.0 1.0 OD2 B:ASP55 3.3 31.7 0.6 O B:HOH305 3.3 43.5 1.0 CG B:ASP138 3.6 32.7 1.0 CG B:ASP55 3.7 34.0 0.6 OD1 B:ASP55 3.8 30.2 0.6 OE2 B:GLU141 3.8 61.2 1.0 O B:HOH420 3.8 59.4 1.0 OD2 B:ASP134 3.9 35.2 1.0 OD2 B:ASP55 4.1 33.2 0.4 OD1 B:ASP134 4.1 31.9 1.0 OD2 B:ASP138 4.2 31.5 1.0 CG B:ASP134 4.4 34.6 1.0 O B:HOH343 4.6 39.1 1.0 CG B:ASP55 4.7 31.1 0.4 CB B:ASP55 4.7 27.6 0.4 CB B:ASP55 4.7 27.6 0.6 CB B:ASP138 4.8 27.0 1.0 CA B:ASP138 4.8 26.4 1.0 N B:ASP138 4.8 24.6 1.0 CB B:GLU137 4.9 27.6 1.0

W.Wang, Y.Zhang, G.Zhao, H.Wang. Ferritin with Atypical Ferroxidase Centers Takes B-Channels As the Pathway For Fe 2+ Uptake From Mycoplasma . Inorg.Chem. V. 60 7207 2021.
ISSN: ISSN 0020-1669
PubMed: 33852289
DOI: 10.1021/ACS.INORGCHEM.1C00265