Iron in PDB 7vp8: Crystal Structure of Ferritin From Ureaplasma Urealyticum

The structure of Crystal Structure of Ferritin From Ureaplasma Urealyticum, PDB code: 7vp8 was solved by W.Wang, X.Liu, Y.Wang, D.Fu, H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.34 / 2.00
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	178.441, 178.441, 178.441, 90, 90, 90
R / Rfree (%)	15.9 / 19.1

The structure of Crystal Structure of Ferritin From Ureaplasma Urealyticum also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Crystal Structure of Ferritin From Ureaplasma Urealyticum (pdb code 7vp8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ferritin From Ureaplasma Urealyticum, PDB code: 7vp8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Ferritin From Ureaplasma Urealyticum


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 Ferritin From Ureaplasma Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:36.8 occ:0.52 OD2 A:ASP51 1.8 30.0 0.4 OD2 A:ASP129 2.0 28.9 1.0 NE2 A:HIS56 2.3 34.5 1.0 O A:HOH308 2.6 39.2 1.0 OD2 A:ASP133 2.7 27.3 1.0 CG A:ASP129 2.9 31.0 1.0 O A:HOH306 2.9 38.5 1.0 CG A:ASP51 2.9 26.4 0.4 FE A:FE202 3.0 85.7 1.0 OD1 A:ASP129 3.1 28.5 1.0 CE1 A:HIS56 3.1 33.0 1.0 CD2 A:HIS56 3.4 26.5 1.0 OD1 A:ASP51 3.4 27.0 0.4 CG A:ASP133 3.5 23.9 1.0 OD1 A:ASP133 3.5 24.6 1.0 CB A:ASP51 4.1 22.2 0.4 CB A:ASP51 4.1 22.5 0.6 O A:HOH406 4.2 27.6 1.0 OD2 A:ASP51 4.2 35.5 0.6 CB A:ASP129 4.2 25.6 1.0 ND1 A:HIS56 4.3 29.4 1.0 CG A:HIS56 4.5 24.1 1.0 CG A:ASP51 4.5 28.2 0.6 CH2 A:TRP125 4.6 30.0 1.0 O A:HOH302 4.6 37.3 1.0 O A:ASP129 4.8 24.9 1.0 CB A:ASP133 4.9 13.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Ferritin From Ureaplasma Urealyticum


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 Ferritin From Ureaplasma Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:85.7 occ:1.00 OD1 A:ASP133 2.7 24.6 1.0 O A:HOH306 3.0 38.5 1.0 OD1 A:ASP129 3.0 28.5 1.0 FE A:FE201 3.0 36.8 0.5 O A:HOH446 3.1 47.2 1.0 O A:HOH308 3.2 39.2 1.0 CD A:LYS132 3.4 38.4 1.0 CE A:LYS132 3.4 46.1 1.0 CG A:ASP133 3.7 23.9 1.0 O A:HOH323 3.7 30.1 1.0 CG A:ASP129 3.8 31.0 1.0 NZ A:LYS132 3.8 38.1 1.0 OD2 A:ASP129 3.8 28.9 1.0 OD2 A:ASP51 3.9 30.0 0.4 OD2 A:ASP51 3.9 35.5 0.6 OD2 A:ASP133 4.0 27.3 1.0 O A:HOH303 4.0 44.5 1.0 O A:HOH441 4.4 43.4 1.0 CG A:ASP51 4.5 26.4 0.4 CG A:LYS132 4.8 32.4 1.0 OD1 A:ASP51 4.9 27.0 0.4 CG A:ASP51 4.9 28.2 0.6

Iron binding site 3 out of 4 in the Crystal Structure of Ferritin From Ureaplasma Urealyticum


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 Ferritin From Ureaplasma Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:61.2 occ:0.68 O A:HOH478 2.5 34.9 1.0 OD1 A:ASP135 3.2 16.0 1.0 O A:HOH504 3.5 27.0 1.0 OD2 A:ASP135 3.6 19.9 1.0 CG A:ASP135 3.8 17.3 1.0 O A:HOH377 3.8 13.9 1.0 O A:HOH336 4.1 27.8 1.0 NH2 A:ARG138 4.4 18.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Ferritin From Ureaplasma Urealyticum


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 Ferritin From Ureaplasma Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:68.1 occ:0.24 O A:HOH415 2.8 45.4 1.0 CE A:LYS124 3.8 20.9 1.0 NZ A:LYS124 3.9 28.4 1.0 CD A:LYS124 4.0 27.3 1.0 O A:HOH482 4.9 27.3 1.0

W.Wang, X.Liu, Y.Wang, Y.Wang, D.Fu, H.Xi, Y.Zhao, H.Wang. Distinct Structural Characteristics Define A New Subfamily of Mycoplasma Ferritin Chin.Chem.Lett. V. 33 4952 2022.
ISSN: ISSN 1001-8417
DOI: 10.1016/J.CCLET.2022.03.119