Zinc 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:

Iron

(Fe)

8 atoms

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:41.9 occ:1.00 OE1 A:GLU156 2.0 29.9 1.0 ND1 A:HIS73 2.1 23.8 1.0 OD1 A:ASP70 2.2 30.5 1.0 OE1 A:GLU37 2.2 29.0 1.0 OE2 A:GLU37 2.4 34.0 1.0 CD A:GLU37 2.6 28.5 1.0 CD A:GLU156 2.9 27.3 1.0 CE1 A:HIS73 3.0 21.7 1.0 OE2 A:GLU156 3.1 25.2 1.0 CG A:ASP70 3.1 26.7 1.0 CG A:HIS73 3.2 24.0 1.0 O A:HOH2003 3.4 35.3 1.0 O A:HOH2012 3.4 33.2 1.0 CB A:HIS73 3.6 25.9 1.0 CB A:ASP70 3.6 25.9 1.0 CA A:ASP70 3.7 25.4 1.0 FE A:FE1176 3.7 40.2 1.0 OD2 A:ASP70 4.1 27.6 1.0 CG2 A:ILE152 4.1 25.8 1.0 CG A:GLU37 4.1 28.7 1.0 NE2 A:HIS73 4.2 24.2 1.0 CG A:GLU156 4.2 23.6 1.0 CD2 A:HIS73 4.3 24.8 1.0 NE1 A:TRP131 4.5 27.9 1.0 O A:ASP70 4.5 26.6 1.0 N A:ASP70 4.6 25.0 1.0 C A:ASP70 4.6 25.3 1.0 CB A:GLU37 4.9 26.6 1.0 O A:GLU69 4.9 23.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:41.4 occ:1.00 OE1 B:GLU37 2.1 30.5 1.0 OE1 B:GLU156 2.1 27.6 1.0 OD1 B:ASP70 2.2 25.1 1.0 ND1 B:HIS73 2.3 27.6 1.0 OE2 B:GLU37 2.3 35.6 1.0 CD B:GLU37 2.5 30.7 1.0 CD B:GLU156 3.0 28.0 1.0 CG B:ASP70 3.1 26.3 1.0 OE2 B:GLU156 3.1 26.1 1.0 CE1 B:HIS73 3.2 26.4 1.0 CG B:HIS73 3.3 27.2 1.0 O B:HOH2005 3.5 31.1 1.0 CB B:ASP70 3.6 26.3 1.0 CA B:ASP70 3.6 25.7 1.0 CB B:HIS73 3.6 26.8 1.0 FE B:FE1176 3.7 41.3 1.0 O B:HOH2003 3.9 36.7 1.0 CG B:GLU37 4.0 28.0 1.0 OD2 B:ASP70 4.1 29.0 1.0 CG2 B:ILE152 4.3 26.0 1.0 NE2 B:HIS73 4.3 25.4 1.0 CG B:GLU156 4.4 26.3 1.0 O B:ASP70 4.4 26.1 1.0 CD2 B:HIS73 4.4 26.4 1.0 C B:ASP70 4.5 26.0 1.0 N B:ASP70 4.5 25.0 1.0 NE1 B:TRP131 4.6 28.1 1.0 CB B:GLU37 4.8 26.4 1.0 O B:GLU69 5.0 24.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:41.3 occ:1.00 OE1 C:GLU156 2.1 31.1 1.0 ND1 C:HIS73 2.1 28.4 1.0 OE1 C:GLU37 2.1 34.1 1.0 OD1 C:ASP70 2.2 29.0 1.0 OE2 C:GLU37 2.4 35.4 1.0 CD C:GLU37 2.6 32.5 1.0 CD C:GLU156 3.0 25.5 1.0 CE1 C:HIS73 3.0 27.3 1.0 CG C:ASP70 3.1 27.4 1.0 CG C:HIS73 3.2 28.4 1.0 OE2 C:GLU156 3.2 24.2 1.0 CB C:HIS73 3.5 26.8 1.0 CB C:ASP70 3.6 25.9 1.0 CA C:ASP70 3.6 25.9 1.0 O C:HOH2007 3.6 30.1 1.0 FE C:FE1176 3.7 38.6 1.0 O C:HOH2002 3.9 34.7 1.0 CG C:GLU37 4.1 29.2 1.0 OD2 C:ASP70 4.1 33.0 1.0 CG2 C:ILE152 4.1 25.5 1.0 NE2 C:HIS73 4.2 28.5 1.0 CD2 C:HIS73 4.3 27.0 1.0 CG C:GLU156 4.3 24.1 1.0 O C:ASP70 4.4 23.9 1.0 C C:ASP70 4.5 25.3 1.0 N C:ASP70 4.5 25.5 1.0 NE1 C:TRP131 4.6 24.6 1.0 CB C:GLU37 4.8 26.7 1.0 O C:GLU69 4.8 26.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:37.8 occ:1.00 OE1 D:GLU156 2.1 23.6 1.0 ND1 D:HIS73 2.1 26.8 1.0 OD1 D:ASP70 2.2 30.9 1.0 OE1 D:GLU37 2.2 37.2 1.0 OE2 D:GLU37 2.3 37.3 1.0 CD D:GLU37 2.6 35.0 1.0 CD D:GLU156 2.9 25.6 1.0 CE1 D:HIS73 3.0 28.3 1.0 OE2 D:GLU156 3.1 29.9 1.0 CG D:ASP70 3.1 26.4 1.0 CG D:HIS73 3.2 26.9 1.0 O D:HOH2014 3.5 22.5 1.0 CB D:HIS73 3.6 26.8 1.0 CB D:ASP70 3.7 26.5 1.0 CA D:ASP70 3.7 26.0 1.0 FE D:FE1176 3.8 32.8 1.0 O D:HOH2002 3.9 31.1 1.0 CG2 D:ILE152 4.1 26.8 1.0 CG D:GLU37 4.1 31.5 1.0 OD2 D:ASP70 4.1 30.3 1.0 NE2 D:HIS73 4.2 27.8 1.0 CG D:GLU156 4.2 24.3 1.0 CD2 D:HIS73 4.3 28.0 1.0 NE1 D:TRP131 4.5 26.1 1.0 O D:ASP70 4.5 27.2 1.0 N D:ASP70 4.6 26.6 1.0 C D:ASP70 4.7 26.2 1.0 CB D:GLU37 4.9 27.2 1.0 O D:GLU69 5.0 26.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:41.7 occ:1.00 ND1 M:HIS73 2.1 25.2 1.0 OE1 M:GLU156 2.1 33.5 1.0 OE1 M:GLU37 2.2 26.4 1.0 OD1 M:ASP70 2.2 32.0 1.0 OE2 M:GLU37 2.4 29.8 1.0 CD M:GLU37 2.6 27.1 1.0 CD M:GLU156 2.9 29.6 1.0 CE1 M:HIS73 3.0 24.9 1.0 OE2 M:GLU156 3.1 31.2 1.0 CG M:ASP70 3.1 27.3 1.0 CG M:HIS73 3.2 25.2 1.0 O M:HOH2014 3.3 33.7 1.0 CB M:HIS73 3.6 26.0 1.0 O M:HOH2002 3.6 46.2 1.0 FE M:FE1176 3.6 39.0 1.0 CB M:ASP70 3.7 25.2 1.0 CA M:ASP70 3.7 24.8 1.0 CG2 M:ILE152 4.1 24.6 1.0 NE2 M:HIS73 4.1 26.4 1.0 CG M:GLU37 4.1 28.3 1.0 OD2 M:ASP70 4.1 28.1 1.0 CG M:GLU156 4.2 26.0 1.0 CD2 M:HIS73 4.2 25.7 1.0 NE1 M:TRP131 4.5 28.2 1.0 O M:ASP70 4.5 25.4 1.0 N M:ASP70 4.6 23.9 1.0 C M:ASP70 4.6 24.6 1.0 O M:GLU69 4.9 22.3 1.0 CB M:GLU37 4.9 26.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:42.5 occ:1.00 OE1 N:GLU156 2.1 29.0 1.0 OE1 N:GLU37 2.2 29.2 1.0 OD1 N:ASP70 2.2 26.0 1.0 ND1 N:HIS73 2.2 26.3 1.0 OE2 N:GLU37 2.3 32.4 1.0 CD N:GLU37 2.6 30.6 1.0 CD N:GLU156 2.9 29.7 1.0 CG N:ASP70 3.1 27.4 1.0 OE2 N:GLU156 3.1 30.5 1.0 CE1 N:HIS73 3.1 24.8 1.0 CG N:HIS73 3.3 25.8 1.0 O N:HOH2004 3.4 28.2 1.0 CB N:ASP70 3.6 26.3 1.0 CA N:ASP70 3.6 25.5 1.0 CB N:HIS73 3.7 26.2 1.0 FE N:FE1176 3.7 41.4 1.0 O N:HOH2002 3.7 34.4 1.0 OD2 N:ASP70 4.0 31.2 1.0 CG N:GLU37 4.1 28.7 1.0 CG2 N:ILE152 4.3 27.4 1.0 NE2 N:HIS73 4.3 23.9 1.0 CG N:GLU156 4.3 27.9 1.0 CD2 N:HIS73 4.4 25.0 1.0 O N:ASP70 4.4 25.5 1.0 N N:ASP70 4.6 24.7 1.0 C N:ASP70 4.6 25.4 1.0 NE1 N:TRP131 4.6 28.5 1.0 CB N:GLU37 4.8 27.3 1.0 O N:GLU69 5.0 25.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:41.8 occ:1.00 OE1 O:GLU156 2.1 33.5 1.0 OD1 O:ASP70 2.2 32.3 1.0 ND1 O:HIS73 2.2 27.4 1.0 OE1 O:GLU37 2.2 31.3 1.0 OE2 O:GLU37 2.5 34.9 1.0 CD O:GLU37 2.6 31.5 1.0 CD O:GLU156 3.0 26.7 1.0 CG O:ASP70 3.1 27.8 1.0 CE1 O:HIS73 3.1 26.4 1.0 OE2 O:GLU156 3.2 26.4 1.0 CG O:HIS73 3.2 27.6 1.0 O O:HOH2007 3.5 36.0 1.0 CB O:ASP70 3.5 26.3 1.0 CA O:ASP70 3.6 26.2 1.0 CB O:HIS73 3.6 25.8 1.0 FE O:FE1176 3.7 39.6 1.0 O O:HOH2003 3.8 32.2 1.0 OD2 O:ASP70 4.1 33.1 1.0 CG O:GLU37 4.1 29.0 1.0 NE2 O:HIS73 4.2 25.5 1.0 CG2 O:ILE152 4.2 25.4 1.0 CG O:GLU156 4.3 24.5 1.0 CD2 O:HIS73 4.3 25.8 1.0 O O:ASP70 4.4 24.8 1.0 N O:ASP70 4.5 25.7 1.0 C O:ASP70 4.5 25.8 1.0 NE1 O:TRP131 4.6 26.2 1.0 CB O:GLU37 4.8 27.0 1.0 O O:GLU69 4.9 26.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1175 b:35.7 occ:1.00 OE1 P:GLU156 2.0 23.1 1.0 ND1 P:HIS73 2.1 26.2 1.0 OE1 P:GLU37 2.2 34.2 1.0 OD1 P:ASP70 2.2 26.9 1.0 OE2 P:GLU37 2.4 34.5 1.0 CD P:GLU37 2.6 33.6 1.0 CD P:GLU156 2.8 25.0 1.0 CE1 P:HIS73 3.0 27.3 1.0 OE2 P:GLU156 3.1 27.3 1.0 CG P:ASP70 3.2 25.6 1.0 CG P:HIS73 3.2 25.8 1.0 O P:HOH2015 3.5 23.1 1.0 CB P:HIS73 3.6 27.0 1.0 CB P:ASP70 3.7 25.0 1.0 CA P:ASP70 3.7 25.0 1.0 FE P:FE1176 3.8 34.5 1.0 O P:HOH2004 3.8 32.7 1.0 CG2 P:ILE152 4.1 25.5 1.0 CG P:GLU37 4.1 31.4 1.0 OD2 P:ASP70 4.1 27.2 1.0 NE2 P:HIS73 4.2 26.4 1.0 CG P:GLU156 4.2 24.1 1.0 CD2 P:HIS73 4.3 26.1 1.0 NE1 P:TRP131 4.5 26.1 1.0 O P:ASP70 4.5 25.9 1.0 N P:ASP70 4.6 25.2 1.0 C P:ASP70 4.6 24.9 1.0 CB P:GLU37 4.9 28.3 1.0 O P:GLU69 4.9 25.4 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