Iron in PDB 3gvy: Crystal Structure of Bacterioferritin From R.Sphaeroides

The structure of Crystal Structure of Bacterioferritin From R.Sphaeroides, PDB code: 3gvy was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.57 / 2.80
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	160.495, 160.495, 116.276, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 28.4

The binding sites of Iron atom in the Crystal Structure of Bacterioferritin From R.Sphaeroides (pdb code 3gvy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Bacterioferritin From R.Sphaeroides, PDB code: 3gvy:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of Bacterioferritin From R.Sphaeroides


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 Bacterioferritin From R.Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe162 b:44.5 occ:1.00 FE A:HEM162 0.0 44.5 1.0 SD C:MET52 2.0 26.9 1.0 NC A:HEM162 2.0 42.5 1.0 NB A:HEM162 2.1 42.7 1.0 SD A:MET52 2.1 20.3 1.0 ND A:HEM162 2.1 44.4 1.0 NA A:HEM162 2.3 45.3 1.0 C4C A:HEM162 3.0 42.0 1.0 C4B A:HEM162 3.0 42.9 1.0 C1D A:HEM162 3.0 45.8 1.0 C1C A:HEM162 3.1 40.7 1.0 CE A:MET52 3.1 19.5 1.0 C1B A:HEM162 3.1 44.6 1.0 C4D A:HEM162 3.2 46.2 1.0 CE C:MET52 3.2 26.0 1.0 C4A A:HEM162 3.3 45.3 1.0 C1A A:HEM162 3.3 47.0 1.0 CHD A:HEM162 3.4 44.6 1.0 CHC A:HEM162 3.4 42.2 1.0 CG C:MET52 3.5 25.4 1.0 CHB A:HEM162 3.6 44.9 1.0 CHA A:HEM162 3.6 47.8 1.0 CG A:MET52 3.8 18.8 1.0 CB C:MET52 4.1 25.2 1.0 C3C A:HEM162 4.2 38.9 1.0 C3B A:HEM162 4.3 45.1 1.0 C2C A:HEM162 4.3 38.7 1.0 C2B A:HEM162 4.3 45.5 1.0 C2D A:HEM162 4.3 47.1 1.0 C3D A:HEM162 4.4 47.4 1.0 C3A A:HEM162 4.5 46.2 1.0 C2A A:HEM162 4.5 46.7 1.0 CB A:MET52 4.5 18.8 1.0

Iron binding site 2 out of 5 in the Crystal Structure of Bacterioferritin From R.Sphaeroides


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 Bacterioferritin From R.Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe163 b:43.9 occ:1.00 OE2 A:GLU127 1.8 37.2 1.0 CD A:GLU127 2.6 34.5 1.0 ND1 A:HIS54 2.7 26.4 1.0 OE1 A:GLU18 2.7 25.6 1.0 OE1 A:GLU51 2.7 31.4 1.0 CE1 A:HIS54 2.7 29.4 1.0 OE1 A:GLU127 2.7 34.7 1.0 OE2 A:GLU51 2.9 28.9 1.0 OE2 A:GLU18 3.0 24.3 1.0 CD A:GLU51 3.1 29.0 1.0 CD A:GLU18 3.3 24.5 1.0 OE1 A:GLU94 3.8 29.7 1.0 CG A:HIS54 4.0 25.2 1.0 NE2 A:HIS54 4.1 30.1 1.0 CG A:GLU127 4.1 30.0 1.0 CG A:GLU51 4.5 24.8 1.0 CD2 A:HIS54 4.7 28.7 1.0 CB A:ASP126 4.7 26.6 1.0 CG A:GLU18 4.8 21.8 1.0 N A:GLU127 4.8 25.4 1.0 CB A:HIS54 4.9 22.6 1.0 OD2 A:ASP126 4.9 34.0 1.0 CA A:GLU127 4.9 26.1 1.0 CE2 A:TYR101 5.0 22.6 1.0 CD A:GLU94 5.0 29.9 1.0

Iron binding site 3 out of 5 in the Crystal Structure of Bacterioferritin From R.Sphaeroides


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 Bacterioferritin From R.Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe162 b:58.2 occ:0.50 FE B:HEM162 0.0 58.2 0.5 SD B:MET52 1.5 10.3 1.0 NC B:HEM162 2.0 59.2 0.5 NB B:HEM162 2.1 59.4 0.5 NA B:HEM162 2.2 59.8 0.5 ND B:HEM162 2.3 60.0 0.5 CE B:MET52 2.7 18.6 1.0 C4C B:HEM162 3.0 59.6 0.5 C1C B:HEM162 3.0 59.2 0.5 C4B B:HEM162 3.1 59.3 0.5 C1B B:HEM162 3.1 59.8 0.5 C4A B:HEM162 3.1 60.2 0.5 C1D B:HEM162 3.1 60.2 0.5 C1A B:HEM162 3.3 60.0 0.5 C4D B:HEM162 3.3 60.3 0.5 CG B:MET52 3.3 17.6 1.0 CHC B:HEM162 3.4 59.7 0.5 CHD B:HEM162 3.4 59.9 0.5 CHB B:HEM162 3.4 60.0 0.5 CHA B:HEM162 3.7 60.1 0.5 C3C B:HEM162 4.2 59.4 0.5 C2C B:HEM162 4.2 58.9 0.5 CB B:MET52 4.2 20.7 1.0 C3B B:HEM162 4.3 59.5 0.5 C2B B:HEM162 4.3 59.9 0.5 C3A B:HEM162 4.3 60.5 0.5 C2D B:HEM162 4.3 60.7 0.5 C2A B:HEM162 4.4 60.6 0.5 C3D B:HEM162 4.5 61.1 0.5

Iron binding site 4 out of 5 in the Crystal Structure of Bacterioferritin From R.Sphaeroides


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 Bacterioferritin From R.Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe163 b:48.2 occ:1.00 OE2 B:GLU51 2.2 36.3 1.0 ND1 B:HIS54 2.3 22.7 1.0 OE2 B:GLU18 2.4 23.1 1.0 CE1 B:HIS54 2.8 24.7 1.0 CD B:GLU127 3.0 32.6 1.0 OE1 B:GLU127 3.0 33.8 1.0 CD B:GLU51 3.1 33.6 1.0 OE2 B:GLU127 3.2 33.6 1.0 CD B:GLU18 3.4 25.5 1.0 OE1 B:GLU51 3.4 33.1 1.0 CG B:HIS54 3.5 22.3 1.0 OE1 B:GLU18 3.6 26.7 1.0 CG B:GLU127 3.7 27.7 1.0 NE2 B:HIS54 4.0 24.6 1.0 OH B:TYR101 4.1 22.2 1.0 CB B:HIS54 4.2 22.6 1.0 CD2 B:LEU123 4.2 21.5 1.0 CD2 B:HIS54 4.4 22.3 1.0 CG B:GLU51 4.5 29.7 1.0 CE2 B:TYR101 4.6 18.8 1.0 CG B:GLU18 4.7 22.8 1.0 CZ B:TYR101 4.8 20.5 1.0 O B:LEU123 4.9 23.9 1.0 CB B:ASP126 5.0 26.4 1.0 CA B:GLU51 5.0 26.4 1.0

Iron binding site 5 out of 5 in the Crystal Structure of Bacterioferritin From R.Sphaeroides


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 Bacterioferritin From R.Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe162 b:46.5 occ:1.00 OE1 C:GLU18 2.2 25.5 1.0 OE2 C:GLU18 2.4 28.0 1.0 OE1 C:GLU127 2.4 35.4 1.0 OE1 C:GLU51 2.5 37.0 1.0 OE2 C:GLU127 2.6 34.0 1.0 CD C:GLU18 2.7 26.1 1.0 CD C:GLU51 2.7 35.2 1.0 CD C:GLU127 2.9 33.2 1.0 ND1 C:HIS54 2.9 28.2 1.0 OE2 C:GLU51 3.1 35.6 1.0 CG C:GLU51 3.5 31.2 1.0 CE1 C:HIS54 3.5 28.3 1.0 CG C:HIS54 3.9 27.3 1.0 CD2 C:LEU123 4.2 24.7 1.0 CG C:GLU18 4.2 23.6 1.0 CB C:HIS54 4.3 26.2 1.0 CG C:GLU127 4.4 29.8 1.0 CA C:GLU51 4.4 26.9 1.0 CB C:GLU51 4.5 27.9 1.0 NE2 C:HIS54 4.6 29.9 1.0 OH C:TYR101 4.8 21.1 1.0 CD2 C:HIS54 4.9 29.1 1.0 N C:GLU51 4.9 27.0 1.0 OE1 C:GLU50 4.9 38.8 1.0

K.H.Nam, Y.Xu, S.Piao, A.Priyadarshi, E.H.Lee, H.-Y.Kim, Y.H.Jeon, N.-C.Ha, K.Y.Hwang. Crystal Structure of Bacterioferritin From Rhodobacter Sphaeroides Biochem.Biophys.Res.Commun. V. 391 990 2010.
ISSN: ISSN 0006-291X
PubMed: 19968959
DOI: 10.1016/J.BBRC.2009.12.003