Iron in PDB 1n1q: Crystal Structure of A Dps Protein From Bacillus Brevis

The structure of Crystal Structure of A Dps Protein From Bacillus Brevis, PDB code: 1n1q was solved by B.Ren, G.Tibbelin, T.Kajino, O.Asami, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.53 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	86.911, 86.911, 220.808, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 20.9

The binding sites of Iron atom in the Crystal Structure of A Dps Protein From Bacillus Brevis (pdb code 1n1q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of A Dps Protein From Bacillus Brevis, PDB code: 1n1q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:15.9 occ:1.00 FE1 A:FEO516 0.0 15.9 1.0 O A:FEO516 1.9 17.2 1.0 OE2 A:GLU62 2.1 15.2 1.0 NE2 B:HIS31 2.2 13.3 1.0 OD2 A:ASP58 2.2 12.7 1.0 OD1 A:ASP58 2.7 15.4 1.0 CG A:ASP58 2.8 14.4 1.0 CD A:GLU62 3.0 16.7 1.0 CD2 B:HIS31 3.1 13.2 1.0 CE1 B:HIS31 3.2 12.5 1.0 FE2 A:FEO516 3.3 45.0 1.0 OE1 A:GLU62 3.3 17.0 1.0 OH B:TYR50 3.9 19.8 1.0 CE1 B:HIS43 3.9 14.2 1.0 NE2 B:HIS43 4.0 15.3 1.0 CG A:GLU62 4.2 15.9 1.0 O B:HOH612 4.3 24.1 1.0 CG B:HIS31 4.3 14.0 1.0 ND1 B:HIS31 4.3 13.6 1.0 CB A:ASP58 4.3 13.7 1.0 O B:HOH611 4.4 38.8 1.0 NE1 B:TRP32 4.7 11.2 1.0 CD1 B:TRP32 4.9 11.8 1.0

Iron binding site 2 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:45.0 occ:1.00 FE2 A:FEO516 0.0 45.0 1.0 O A:FEO516 2.0 17.2 1.0 O B:HOH611 2.2 38.8 1.0 FE1 A:FEO516 3.3 15.9 1.0 OE1 A:GLU62 3.6 17.0 1.0 OE2 A:GLU62 3.8 15.2 1.0 NE2 B:HIS43 3.8 15.3 1.0 O B:HOH612 3.9 24.1 1.0 CD A:GLU62 4.1 16.7 1.0 OD2 A:ASP58 4.4 12.7 1.0 CE1 B:HIS43 4.7 14.2 1.0 NE2 B:HIS31 4.8 13.3 1.0 CD2 B:HIS43 4.8 13.7 1.0

Iron binding site 3 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe515 b:15.4 occ:1.00 FE1 B:FEO515 0.0 15.4 1.0 O B:FEO515 2.0 14.2 1.0 OD2 B:ASP58 2.1 12.5 1.0 OE2 B:GLU62 2.1 15.3 1.0 NE2 A:HIS31 2.2 12.9 1.0 OD1 B:ASP58 2.7 15.7 1.0 CG B:ASP58 2.7 14.2 1.0 CD B:GLU62 3.0 16.9 1.0 CD2 A:HIS31 3.0 13.4 1.0 CE1 A:HIS31 3.2 12.8 1.0 OE1 B:GLU62 3.3 16.6 1.0 FE2 B:FEO515 3.3 39.2 1.0 OH A:TYR50 3.9 20.1 1.0 CE1 A:HIS43 4.0 14.8 1.0 O A:HOH641 4.1 39.6 1.0 O A:HOH640 4.1 42.7 1.0 NE2 A:HIS43 4.1 15.4 1.0 CB B:ASP58 4.2 13.6 1.0 CG B:GLU62 4.2 15.7 1.0 CG A:HIS31 4.2 14.1 1.0 ND1 A:HIS31 4.3 13.6 1.0 NE1 A:TRP32 4.6 11.4 1.0 CD1 A:TRP32 4.8 11.9 1.0

Iron binding site 4 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe515 b:39.2 occ:1.00 FE2 B:FEO515 0.0 39.2 1.0 O B:FEO515 2.0 14.2 1.0 O A:HOH640 2.2 42.7 1.0 FE1 B:FEO515 3.3 15.4 1.0 O A:HOH641 3.6 39.6 1.0 OE1 B:GLU62 3.6 16.6 1.0 NE2 A:HIS43 3.7 15.4 1.0 OE2 B:GLU62 3.9 15.3 1.0 CD B:GLU62 4.2 16.9 1.0 OD2 B:ASP58 4.3 12.5 1.0 CE1 A:HIS43 4.5 14.8 1.0 NE2 A:HIS31 4.6 12.9 1.0 CD2 A:HIS43 4.7 13.8 1.0 CE1 A:HIS31 4.9 12.8 1.0

Iron binding site 5 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe518 b:13.9 occ:1.00 FE1 C:FEO518 0.0 13.9 1.0 O C:FEO518 2.0 16.4 1.0 OD2 C:ASP58 2.1 12.5 1.0 OE2 C:GLU62 2.1 14.7 1.0 NE2 D:HIS31 2.2 12.9 1.0 OD1 C:ASP58 2.7 14.9 1.0 CG C:ASP58 2.7 13.9 1.0 CD C:GLU62 2.9 16.6 1.0 CD2 D:HIS31 3.1 13.3 1.0 CE1 D:HIS31 3.2 12.9 1.0 OE1 C:GLU62 3.2 16.5 1.0 FE2 C:FEO518 3.3 38.5 1.0 O D:HOH633 3.8 27.8 1.0 OH D:TYR50 3.9 19.6 1.0 CE1 D:HIS43 3.9 14.6 1.0 NE2 D:HIS43 4.0 15.4 1.0 CG C:GLU62 4.2 15.6 1.0 CB C:ASP58 4.2 13.5 1.0 ND1 D:HIS31 4.3 14.0 1.0 CG D:HIS31 4.3 14.2 1.0 O D:HOH634 4.3 24.6 1.0 NE1 D:TRP32 4.7 11.4 1.0 CD1 D:TRP32 4.9 11.9 1.0

Iron binding site 6 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe518 b:38.5 occ:1.00 FE2 C:FEO518 0.0 38.5 1.0 O C:FEO518 2.0 16.4 1.0 O D:HOH633 2.1 27.8 1.0 FE1 C:FEO518 3.3 13.9 1.0 O D:HOH634 3.6 24.6 1.0 OE1 C:GLU62 3.8 16.5 1.0 NZ B:LYS139 3.8 21.7 1.0 NE2 D:HIS43 4.0 15.4 1.0 OE2 C:GLU62 4.0 14.7 1.0 OD2 C:ASP58 4.2 12.5 1.0 CD C:GLU62 4.3 16.6 1.0 CE B:LYS139 4.4 20.1 1.0 NE2 D:HIS31 4.7 12.9 1.0 CE1 D:HIS43 4.8 14.6 1.0 O C:HOH532 4.8 37.8 1.0 CD2 D:HIS43 4.9 13.8 1.0 CE1 D:HIS31 5.0 12.9 1.0

Iron binding site 7 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe517 b:13.0 occ:1.00 FE1 D:FEO517 0.0 13.0 1.0 O D:FEO517 2.0 14.3 1.0 OD2 D:ASP58 2.1 12.9 1.0 OE2 D:GLU62 2.1 15.0 1.0 NE2 C:HIS31 2.1 13.7 1.0 CG D:ASP58 2.7 13.9 1.0 OD1 D:ASP58 2.7 15.3 1.0 CD D:GLU62 2.9 16.9 1.0 CD2 C:HIS31 3.1 13.3 1.0 CE1 C:HIS31 3.1 12.5 1.0 OE1 D:GLU62 3.2 16.1 1.0 FE2 D:FEO517 3.3 38.9 1.0 OH C:TYR50 3.9 19.9 1.0 CE1 C:HIS43 3.9 14.6 1.0 NE2 C:HIS43 4.0 15.5 1.0 CG D:GLU62 4.2 15.8 1.0 CB D:ASP58 4.2 13.2 1.0 CG C:HIS31 4.2 14.0 1.0 ND1 C:HIS31 4.2 13.7 1.0 O C:HOH658 4.5 27.2 1.0 O D:HOH527 4.6 35.7 1.0 NE1 C:TRP32 4.7 11.3 1.0 O C:HOH657 4.7 46.8 1.0 CD1 C:TRP32 4.8 11.8 1.0

Iron binding site 8 out of 8 in the Crystal Structure of A Dps Protein From Bacillus Brevis


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 A Dps Protein From Bacillus Brevis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe517 b:38.9 occ:1.00 FE2 D:FEO517 0.0 38.9 1.0 O D:FEO517 2.0 14.3 1.0 O C:HOH657 2.3 46.8 1.0 FE1 D:FEO517 3.3 13.0 1.0 OE1 D:GLU62 3.6 16.1 1.0 NE2 C:HIS43 3.7 15.5 1.0 O C:HOH658 3.8 27.2 1.0 O C:HOH628 3.8 47.4 1.0 OE2 D:GLU62 3.9 15.0 1.0 CD D:GLU62 4.2 16.9 1.0 OD2 D:ASP58 4.3 12.9 1.0 CE1 C:HIS43 4.6 14.6 1.0 O D:HOH527 4.6 35.7 1.0 CD2 C:HIS43 4.7 13.6 1.0 NE2 C:HIS31 4.7 13.7 1.0 CE1 C:HIS31 4.9 12.5 1.0

B.Ren, G.Tibbelin, T.Kajino, O.Asami, R.Ladenstein. The Multi-Layered Structure of Dps with A Novel Di-Nuclear Ferroxidase Center J.Mol.Biol. V. 329 467 2003.
ISSN: ISSN 0022-2836
PubMed: 12767829
DOI: 10.1016/S0022-2836(03)00466-2