Iron in PDB 2clb: The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly

The structure of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly, PDB code: 2clb was solved by G.H.Gauss, P.Benas, B.Wiedenheft, M.Young, T.Douglas, C.M.Lawrence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.4
Space group	I 21 3 1
Cell size a, b, c (Å), α, β, γ (°)	212.928, 212.928, 212.928, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.2

The structure of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Iron atom in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly (pdb code 2clb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly, PDB code: 2clb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1176 b:40.2 occ:1.00 OE1 A:GLU124 2.3 26.9 1.0 OE2 A:GLU156 2.3 25.2 1.0 O A:HOH2012 2.4 33.2 1.0 OD1 A:ASP70 2.4 30.5 1.0 OD2 A:ASP70 2.5 27.6 1.0 ND1 A:HIS159 2.5 24.0 1.0 OE2 A:GLU124 2.6 29.2 1.0 CD A:GLU124 2.8 26.9 1.0 CG A:ASP70 2.8 26.7 1.0 CE1 A:HIS159 3.3 22.8 1.0 CD A:GLU156 3.4 27.3 1.0 CG A:HIS159 3.6 22.4 1.0 ZN A:ZN1175 3.7 41.9 1.0 OE1 A:GLU156 3.8 29.9 1.0 CB A:HIS159 4.0 23.6 1.0 CG A:GLU124 4.3 25.7 1.0 CB A:ASP70 4.3 25.9 1.0 NE2 A:HIS159 4.5 20.5 1.0 O A:ALA66 4.6 26.2 1.0 OH A:TYR44 4.6 22.9 1.0 CA A:GLU156 4.6 23.4 1.0 O A:HOH2003 4.7 35.3 1.0 CG A:GLU156 4.7 23.6 1.0 CD2 A:HIS159 4.7 21.8 1.0 CE2 A:TYR44 4.8 20.7 1.0 CB A:ALA66 4.8 25.1 1.0 CB A:GLU156 4.9 23.3 1.0 CB A:GLU124 5.0 25.8 1.0 CE1 A:HIS73 5.0 21.7 1.0

Iron binding site 2 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1176 b:41.3 occ:1.00 OE1 B:GLU124 2.3 34.8 1.0 OD1 B:ASP70 2.4 25.1 1.0 OE2 B:GLU124 2.5 28.8 1.0 OE2 B:GLU156 2.5 26.1 1.0 OD2 B:ASP70 2.5 29.0 1.0 ND1 B:HIS159 2.5 22.1 1.0 O B:HOH2005 2.5 31.1 1.0 CD B:GLU124 2.7 31.1 1.0 CG B:ASP70 2.8 26.3 1.0 CE1 B:HIS159 3.3 23.5 1.0 CD B:GLU156 3.5 28.0 1.0 CG B:HIS159 3.7 22.4 1.0 ZN B:ZN1175 3.7 41.4 1.0 OE1 B:GLU156 3.9 27.6 1.0 CB B:HIS159 4.0 22.7 1.0 CG B:GLU124 4.2 28.8 1.0 CB B:ASP70 4.3 26.3 1.0 NE2 B:HIS159 4.5 23.1 1.0 OH B:TYR44 4.6 23.1 1.0 CA B:GLU156 4.6 25.0 1.0 O B:ALA66 4.7 26.8 1.0 CG B:GLU156 4.7 26.3 1.0 CD2 B:HIS159 4.7 23.2 1.0 CE2 B:TYR44 4.8 24.0 1.0 CB B:GLU156 4.8 24.9 1.0 CB B:ALA66 4.9 26.6 1.0 CB B:GLU124 5.0 27.1 1.0

Iron binding site 3 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1176 b:38.6 occ:1.00 OE2 C:GLU156 2.2 24.2 1.0 OE1 C:GLU124 2.3 31.7 1.0 OD1 C:ASP70 2.4 29.0 1.0 ND1 C:HIS159 2.5 24.1 1.0 O C:HOH2007 2.5 30.1 1.0 OE2 C:GLU124 2.6 29.4 1.0 OD2 C:ASP70 2.6 33.0 1.0 CD C:GLU124 2.8 28.8 1.0 CG C:ASP70 2.9 27.4 1.0 CD C:GLU156 3.2 25.5 1.0 CE1 C:HIS159 3.3 20.8 1.0 OE1 C:GLU156 3.6 31.1 1.0 CG C:HIS159 3.6 24.8 1.0 ZN C:ZN1175 3.7 41.3 1.0 CB C:HIS159 4.0 24.1 1.0 CG C:GLU124 4.3 28.5 1.0 CB C:ASP70 4.4 25.9 1.0 CG C:GLU156 4.5 24.1 1.0 CA C:GLU156 4.5 23.2 1.0 NE2 C:HIS159 4.5 25.5 1.0 CB C:GLU156 4.7 23.3 1.0 CD2 C:HIS159 4.7 26.1 1.0 O C:ALA66 4.7 26.7 1.0 OH C:TYR44 4.7 26.5 1.0 CE2 C:TYR44 4.9 25.1 1.0 CE1 C:HIS73 4.9 27.3 1.0 OE1 C:GLU37 5.0 34.1 1.0 ND1 C:HIS73 5.0 28.4 1.0 CB C:GLU124 5.0 26.6 1.0 CB C:ALA127 5.0 26.2 1.0

Iron binding site 4 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1176 b:32.8 occ:1.00 OE1 D:GLU124 2.2 26.8 1.0 O D:HOH2014 2.3 22.5 1.0 OE2 D:GLU156 2.3 29.9 1.0 ND1 D:HIS159 2.5 21.6 1.0 OE2 D:GLU124 2.5 28.6 1.0 OD1 D:ASP70 2.5 30.9 1.0 OD2 D:ASP70 2.6 30.3 1.0 CD D:GLU124 2.7 23.8 1.0 CG D:ASP70 2.9 26.4 1.0 CE1 D:HIS159 3.3 22.1 1.0 CD D:GLU156 3.4 25.6 1.0 CG D:HIS159 3.6 21.6 1.0 ZN D:ZN1175 3.8 37.8 1.0 OE1 D:GLU156 3.9 23.6 1.0 CB D:HIS159 4.0 20.6 1.0 CG D:GLU124 4.2 25.4 1.0 CB D:ASP70 4.4 26.5 1.0 NE2 D:HIS159 4.5 20.6 1.0 CA D:GLU156 4.5 23.9 1.0 CD2 D:HIS159 4.6 22.0 1.0 CG D:GLU156 4.6 24.3 1.0 OH D:TYR44 4.7 25.1 1.0 O D:ALA66 4.7 25.5 1.0 CB D:GLU156 4.7 23.8 1.0 CE2 D:TYR44 4.9 25.8 1.0 O D:HOH2002 4.9 31.1 1.0 CB D:ALA66 4.9 25.3 1.0 CB D:GLU124 4.9 25.8 1.0

Iron binding site 5 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe1176 b:39.0 occ:1.00 OE2 M:GLU156 2.3 31.2 1.0 OE1 M:GLU124 2.3 23.6 1.0 OD1 M:ASP70 2.3 32.0 1.0 OD2 M:ASP70 2.5 28.1 1.0 ND1 M:HIS159 2.5 21.8 1.0 O M:HOH2014 2.6 33.7 1.0 OE2 M:GLU124 2.6 25.4 1.0 CG M:ASP70 2.8 27.3 1.0 CD M:GLU124 2.8 25.2 1.0 CE1 M:HIS159 3.3 22.3 1.0 CD M:GLU156 3.3 29.6 1.0 ZN M:ZN1175 3.6 41.7 1.0 CG M:HIS159 3.7 22.4 1.0 OE1 M:GLU156 3.7 33.5 1.0 CB M:HIS159 4.1 22.3 1.0 CB M:ASP70 4.3 25.2 1.0 CG M:GLU124 4.3 25.4 1.0 NE2 M:HIS159 4.5 21.4 1.0 CG M:GLU156 4.6 26.0 1.0 CA M:GLU156 4.6 23.2 1.0 O M:ALA66 4.6 24.5 1.0 CD2 M:HIS159 4.7 22.8 1.0 OH M:TYR44 4.7 22.9 1.0 CB M:GLU156 4.8 23.6 1.0 CE2 M:TYR44 4.9 21.2 1.0 CE1 M:HIS73 4.9 24.9 1.0 OE1 M:GLU37 4.9 26.4 1.0 ND1 M:HIS73 4.9 25.2 1.0 O M:HOH2002 4.9 46.2 1.0 CB M:ALA66 5.0 24.1 1.0

Iron binding site 6 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe1176 b:41.4 occ:1.00 OE1 N:GLU124 2.3 31.0 1.0 O N:HOH2004 2.4 28.2 1.0 ND1 N:HIS159 2.4 23.1 1.0 OD1 N:ASP70 2.4 26.0 1.0 OE2 N:GLU156 2.5 30.5 1.0 OD2 N:ASP70 2.5 31.2 1.0 OE2 N:GLU124 2.6 26.1 1.0 CD N:GLU124 2.7 28.0 1.0 CG N:ASP70 2.8 27.4 1.0 CE1 N:HIS159 3.2 22.8 1.0 CD N:GLU156 3.4 29.7 1.0 CG N:HIS159 3.5 22.8 1.0 ZN N:ZN1175 3.7 42.5 1.0 OE1 N:GLU156 3.8 29.0 1.0 CB N:HIS159 3.9 22.5 1.0 CG N:GLU124 4.2 28.0 1.0 CB N:ASP70 4.4 26.3 1.0 NE2 N:HIS159 4.4 21.7 1.0 CA N:GLU156 4.5 25.5 1.0 CD2 N:HIS159 4.6 22.5 1.0 CG N:GLU156 4.7 27.9 1.0 O N:ALA66 4.7 27.2 1.0 OH N:TYR44 4.7 25.1 1.0 CB N:GLU156 4.8 25.8 1.0 CE2 N:TYR44 4.9 25.1 1.0 CB N:ALA66 4.9 26.3 1.0 O N:HOH2002 5.0 34.4 1.0 CB N:GLU124 5.0 27.4 1.0 CE1 N:HIS73 5.0 24.8 1.0

Iron binding site 7 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ O:Fe1176 b:39.6 occ:1.00 OE2 O:GLU156 2.3 26.4 1.0 OE1 O:GLU124 2.3 28.3 1.0 O O:HOH2007 2.4 36.0 1.0 OD1 O:ASP70 2.4 32.3 1.0 OE2 O:GLU124 2.5 27.3 1.0 ND1 O:HIS159 2.5 23.5 1.0 OD2 O:ASP70 2.6 33.1 1.0 CD O:GLU124 2.7 27.5 1.0 CG O:ASP70 2.9 27.8 1.0 CE1 O:HIS159 3.3 20.4 1.0 CD O:GLU156 3.3 26.7 1.0 CG O:HIS159 3.6 23.9 1.0 ZN O:ZN1175 3.7 41.8 1.0 OE1 O:GLU156 3.8 33.5 1.0 CB O:HIS159 4.0 24.0 1.0 CG O:GLU124 4.2 26.9 1.0 CB O:ASP70 4.4 26.3 1.0 NE2 O:HIS159 4.5 24.3 1.0 CA O:GLU156 4.6 23.0 1.0 OH O:TYR44 4.6 26.4 1.0 CG O:GLU156 4.6 24.5 1.0 CD2 O:HIS159 4.7 25.3 1.0 O O:ALA66 4.7 25.9 1.0 CB O:GLU156 4.7 23.5 1.0 CE2 O:TYR44 4.8 24.7 1.0 O O:HOH2003 5.0 32.2 1.0 CB O:GLU124 5.0 25.6 1.0 CB O:ALA66 5.0 25.9 1.0 CE1 O:HIS73 5.0 26.4 1.0

Iron binding site 8 out of 8 in the The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Di-Metal Binding Site Within A Dps-Like Dodecameric Assembly within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe1176 b:34.5 occ:1.00 OE1 P:GLU124 2.2 28.3 1.0 OE2 P:GLU156 2.2 27.3 1.0 O P:HOH2015 2.4 23.1 1.0 OE2 P:GLU124 2.5 27.5 1.0 OD1 P:ASP70 2.5 26.9 1.0 ND1 P:HIS159 2.5 21.9 1.0 OD2 P:ASP70 2.5 27.2 1.0 CD P:GLU124 2.7 26.6 1.0 CG P:ASP70 2.9 25.6 1.0 CD P:GLU156 3.3 25.0 1.0 CE1 P:HIS159 3.3 22.6 1.0 CG P:HIS159 3.6 21.5 1.0 ZN P:ZN1175 3.8 35.7 1.0 OE1 P:GLU156 3.8 23.1 1.0 CB P:HIS159 4.0 22.2 1.0 CG P:GLU124 4.2 27.2 1.0 CB P:ASP70 4.4 25.0 1.0 CA P:GLU156 4.5 23.8 1.0 NE2 P:HIS159 4.5 21.7 1.0 CG P:GLU156 4.6 24.1 1.0 OH P:TYR44 4.6 26.1 1.0 CD2 P:HIS159 4.7 21.6 1.0 CB P:GLU156 4.7 23.3 1.0 O P:ALA66 4.7 24.5 1.0 O P:HOH2004 4.9 32.7 1.0 CE2 P:TYR44 4.9 25.8 1.0 CB P:GLU124 4.9 26.3 1.0 CB P:ALA66 5.0 24.0 1.0 CA P:GLU124 5.0 26.4 1.0 OE1 P:GLU37 5.0 34.2 1.0

G.H.Gauss, P.Benas, B.Wiedenheft, M.Young, T.Douglas, C.M.Lawrence. Structure of the Dps-Like Protein From Sulfolobus Solfataricus Reveals A Bacterioferritin-Like Dimetal Binding Site Within A Dps-Like Dodecameric Assembly. Biochemistry V. 45 10815 2006.
ISSN: ISSN 0006-2960
PubMed: 16953567
DOI: 10.1021/BI060782U