Iron in PDB 2bw1: Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.

The structure of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis., PDB code: 2bw1 was solved by A.Kauko, A.Pulliainen, S.Haataja, J.Finne, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.53 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.130, 138.050, 142.550, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23

The structure of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. (pdb code 2bw1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis., PDB code: 2bw1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2000 b:25.8 occ:0.60 OD1 C:ASP74 1.6 28.2 0.6 OE2 C:GLU78 1.9 15.0 0.4 NE2 A:HIS47 2.2 18.2 1.0 O C:HOH2053 2.2 32.8 1.0 OE2 C:GLU78 2.5 20.3 0.6 CG C:ASP74 2.8 24.4 0.6 O A:HOH2034 2.9 34.1 1.0 CD C:GLU78 2.9 18.0 0.4 CE1 A:HIS47 3.2 16.9 1.0 OE1 C:GLU78 3.2 19.1 0.4 CD2 A:HIS47 3.3 18.4 1.0 OD2 C:ASP74 3.4 27.5 0.6 CD C:GLU78 3.7 17.1 0.6 O A:HOH2041 3.9 46.3 1.0 CB C:ASP74 4.0 22.1 0.6 NE2 A:HIS59 4.1 18.4 1.0 OD2 A:ASP63 4.1 32.6 1.0 CG C:GLU78 4.2 16.9 0.6 CG C:GLU78 4.2 17.5 0.4 OD1 C:ASP74 4.2 18.7 0.4 CE1 A:HIS59 4.3 21.3 1.0 ND1 A:HIS47 4.3 17.5 1.0 OD1 A:ASP63 4.4 31.3 1.0 CG A:HIS47 4.4 16.4 1.0 CG C:ASP74 4.5 20.4 0.4 CG A:ASP63 4.7 26.2 1.0 OE1 C:GLU78 4.7 17.4 0.6 NE1 A:TRP48 4.9 18.9 1.0 CB C:ASP74 4.9 19.9 0.4 O C:HOH2060 4.9 33.2 1.0

Iron binding site 2 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2000 b:24.6 occ:0.50 OD1 D:ASP74 1.7 25.7 0.5 OE2 D:GLU78 1.8 15.9 0.5 NE2 B:HIS47 2.3 17.6 1.0 O B:HOH2036 2.3 32.1 1.0 CG D:ASP74 2.4 22.5 0.5 OD2 D:ASP74 2.5 18.5 0.5 OE2 D:GLU78 2.8 21.3 0.5 CD D:GLU78 2.8 18.9 0.5 CD2 B:HIS47 3.1 17.6 1.0 O B:HOH2031 3.2 32.4 1.0 OE1 D:GLU78 3.2 19.6 0.5 CE1 B:HIS47 3.4 19.0 1.0 CD D:GLU78 3.8 19.0 0.5 CB D:ASP74 3.8 22.8 0.5 OD1 D:ASP74 4.0 16.7 0.5 CG D:GLU78 4.0 19.6 0.5 CG D:GLU78 4.1 19.0 0.5 NE2 B:HIS59 4.2 16.1 1.0 OD2 B:ASP63 4.3 28.0 0.7 CE1 B:HIS59 4.3 19.1 1.0 CG B:HIS47 4.4 17.6 1.0 OD1 B:ASP63 4.4 29.2 0.7 CG D:ASP74 4.4 19.8 0.5 ND1 B:HIS47 4.4 17.1 1.0 NE1 B:TRP48 4.6 20.8 1.0 CA D:ASP74 4.8 22.1 0.5 CG B:ASP63 4.8 23.8 0.7 CB D:ASP74 4.8 20.6 0.5 CD1 B:TRP48 4.8 19.9 1.0 O D:ASP74 4.9 21.8 0.5 OE1 D:GLU78 4.9 13.9 0.5 NE2 B:HIS44 5.0 23.0 1.0

Iron binding site 3 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2000 b:26.0 occ:0.60 OE2 A:GLU78 1.9 19.3 0.5 OD1 A:ASP74 2.1 19.9 0.6 NE2 C:HIS47 2.2 17.5 1.0 O C:HOH2036 2.3 32.7 1.0 OD2 A:ASP74 2.3 21.7 0.6 CG A:ASP74 2.5 21.2 0.6 CD A:GLU78 2.8 20.3 0.5 OE2 A:GLU78 2.9 20.6 0.5 O C:HOH2028 2.9 36.1 1.0 OE1 A:GLU78 3.1 22.1 0.5 CD2 C:HIS47 3.2 18.0 1.0 CE1 C:HIS47 3.2 21.1 1.0 O C:HOH2038 3.6 43.7 1.0 CD A:GLU78 4.0 19.3 0.5 CB A:ASP74 4.0 21.6 0.6 CG A:GLU78 4.2 19.6 0.5 OD2 C:ASP63 4.2 34.6 1.0 OD1 A:ASP74 4.2 23.4 0.4 CG A:ASP74 4.2 21.4 0.4 NE2 C:HIS59 4.2 21.2 1.0 CG A:GLU78 4.3 19.8 0.5 ND1 C:HIS47 4.3 20.6 1.0 CG C:HIS47 4.3 19.4 1.0 CE1 C:HIS59 4.4 21.0 1.0 OD1 C:ASP63 4.5 32.4 1.0 OD2 A:ASP74 4.6 22.9 0.4 NE1 C:TRP48 4.6 21.7 1.0 CB A:ASP74 4.6 20.7 0.4 CG C:ASP63 4.8 26.8 1.0 CA A:ASP74 4.8 21.1 0.6 CD1 C:TRP48 4.9 21.8 1.0 O A:ASP74 4.9 21.5 0.6 CA A:ASP74 5.0 20.4 0.4

Iron binding site 4 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2000 b:26.8 occ:0.60 OD1 B:ASP74 1.9 25.6 0.6 OE2 B:GLU78 2.0 15.9 0.6 O D:HOH2042 2.2 28.1 1.0 NE2 D:HIS47 2.2 18.0 1.0 CG B:ASP74 2.6 23.2 0.6 OD2 B:ASP74 2.7 19.3 0.6 CD B:GLU78 2.9 19.1 0.6 OE2 B:GLU78 2.9 16.4 0.4 O D:HOH2034 2.9 28.7 1.0 CD2 D:HIS47 3.1 15.7 1.0 CE1 D:HIS47 3.2 16.0 1.0 OE1 B:GLU78 3.2 19.7 0.6 CD B:GLU78 4.0 17.2 0.4 CB B:ASP74 4.1 23.1 0.6 OD1 B:ASP74 4.1 19.8 0.4 OD2 D:ASP63 4.2 21.8 0.6 CG B:GLU78 4.2 17.9 0.6 O B:HOH2052 4.2 43.9 1.0 NE2 D:HIS59 4.3 16.8 1.0 CG B:GLU78 4.3 16.4 0.4 ND1 D:HIS47 4.3 15.9 1.0 CG D:HIS47 4.3 18.3 1.0 CE1 D:HIS59 4.4 16.7 1.0 O D:HOH2045 4.4 40.6 1.0 CG B:ASP74 4.4 20.5 0.4 OD1 D:ASP63 4.4 18.9 0.6 NE1 D:TRP48 4.6 20.4 1.0 OD2 B:ASP74 4.7 20.8 0.4 CG D:ASP63 4.7 19.5 0.6 CD1 D:TRP48 4.8 19.2 1.0 CB B:ASP74 4.9 20.6 0.4 CA B:ASP74 5.0 22.7 0.6

Iron binding site 5 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe2000 b:26.8 occ:0.50 OD1 G:ASP74 1.9 26.3 0.5 OE2 G:GLU78 2.0 16.4 0.4 O E:HOH2042 2.2 33.4 1.0 NE2 E:HIS47 2.3 19.1 1.0 CG G:ASP74 2.7 25.7 0.5 OD2 G:ASP74 2.8 20.6 0.5 CD G:GLU78 2.8 20.1 0.4 O G:HOH2071 2.8 31.6 1.0 OE2 G:GLU78 2.9 22.8 0.6 OE1 G:GLU78 3.1 22.8 0.4 CE1 E:HIS47 3.2 19.3 1.0 CD2 E:HIS47 3.2 17.6 1.0 CD G:GLU78 3.9 20.7 0.6 O G:HOH2068 3.9 39.0 1.0 OD2 E:ASP63 4.0 33.3 1.0 CB G:ASP74 4.1 25.2 0.5 OD1 G:ASP74 4.1 24.0 0.5 CG G:GLU78 4.2 20.1 0.4 NE2 E:HIS59 4.2 18.3 1.0 CG G:GLU78 4.2 21.9 0.6 ND1 E:HIS47 4.4 18.9 1.0 CE1 E:HIS59 4.4 18.8 1.0 CG E:HIS47 4.4 18.6 1.0 CG G:ASP74 4.5 25.4 0.5 OD1 E:ASP63 4.5 33.1 1.0 O G:HOH2072 4.7 52.0 1.0 CG E:ASP63 4.7 27.5 1.0 NE1 E:TRP48 4.7 23.5 1.0 CB G:ASP74 4.8 25.1 0.5 OE1 G:GLU78 5.0 19.6 0.6 CD1 E:TRP48 5.0 23.0 1.0

Iron binding site 6 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe2000 b:27.2 occ:0.50 OD1 H:ASP74 1.7 32.4 0.6 OE2 H:GLU78 1.8 20.6 0.5 NE2 F:HIS47 2.2 23.9 1.0 O F:HOH2031 2.4 27.4 1.0 CG H:ASP74 2.7 29.1 0.6 CD H:GLU78 2.8 22.6 0.5 OE2 H:GLU78 3.0 26.8 0.5 O F:HOH2026 3.0 29.1 1.0 OD2 H:ASP74 3.1 29.6 0.6 CD2 F:HIS47 3.2 22.9 1.0 CE1 F:HIS47 3.2 23.2 1.0 OE1 H:GLU78 3.3 24.7 0.5 CD H:GLU78 4.0 24.7 0.5 CB H:ASP74 4.0 27.6 0.6 NE2 F:HIS59 4.1 25.3 1.0 CG H:GLU78 4.1 23.6 0.5 OD2 F:ASP63 4.2 35.6 1.0 CG H:GLU78 4.2 24.9 0.5 CE1 F:HIS59 4.3 27.5 1.0 ND1 F:HIS47 4.3 20.0 1.0 CG F:HIS47 4.3 23.6 1.0 OD1 F:ASP63 4.4 36.6 1.0 O F:HOH2030 4.4 42.1 1.0 OD1 H:ASP74 4.5 22.6 0.4 CG F:ASP63 4.7 31.3 1.0 CG H:ASP74 4.7 23.9 0.4 NE1 F:TRP48 4.8 25.9 1.0 CD1 F:TRP48 5.0 25.9 1.0 CB H:ASP74 5.0 25.0 0.4

Iron binding site 7 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe2000 b:26.6 occ:0.50 OD1 E:ASP74 1.6 29.4 0.5 O E:HOH2059 2.0 32.4 1.0 OE2 E:GLU78 2.0 16.1 0.4 NE2 G:HIS47 2.2 21.2 1.0 CG E:ASP74 2.6 24.4 0.5 OE2 E:GLU78 2.9 19.9 0.6 CD E:GLU78 3.0 18.4 0.4 OD2 E:ASP74 3.0 22.2 0.5 O G:HOH2036 3.0 30.5 1.0 CE1 G:HIS47 3.1 24.8 1.0 CD2 G:HIS47 3.2 22.3 1.0 OE1 E:GLU78 3.3 16.9 0.4 O G:HOH2048 3.8 35.4 1.0 CB E:ASP74 3.9 23.2 0.5 CD E:GLU78 4.0 18.9 0.6 NE2 G:HIS59 4.1 19.6 1.0 OD2 G:ASP63 4.1 33.9 1.0 O G:HOH2045 4.2 43.6 1.0 OD1 E:ASP74 4.2 19.3 0.5 CE1 G:HIS59 4.3 19.4 1.0 CG E:GLU78 4.3 17.7 0.6 ND1 G:HIS47 4.3 21.3 1.0 CG E:GLU78 4.3 19.2 0.4 CG G:HIS47 4.4 19.8 1.0 OD1 G:ASP63 4.5 35.3 1.0 CG E:ASP74 4.5 21.9 0.5 CG G:ASP63 4.7 29.0 1.0 NE1 G:TRP48 4.7 22.9 1.0 CB E:ASP74 4.9 21.4 0.5 CD1 G:TRP48 4.9 22.3 1.0 CA E:ASP74 4.9 22.9 0.5 NE2 G:HIS44 5.0 21.5 1.0 OD2 E:ASP74 5.0 20.5 0.5

Iron binding site 8 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe2000 b:26.3 occ:0.50 OE2 F:GLU78 1.9 19.4 0.5 OD1 F:ASP74 1.9 27.6 0.6 O H:HOH2023 2.0 33.5 1.0 NE2 H:HIS47 2.2 19.9 1.0 OE2 F:GLU78 2.7 22.9 0.5 CG F:ASP74 2.7 24.8 0.6 CD F:GLU78 2.8 20.4 0.5 OD2 F:ASP74 2.9 22.8 0.6 O H:HOH2018 3.0 31.9 1.0 OE1 F:GLU78 3.1 19.2 0.5 CD2 H:HIS47 3.2 18.9 1.0 CE1 H:HIS47 3.2 20.0 1.0 CD F:GLU78 3.8 20.9 0.5 O H:HOH2027 3.9 37.1 1.0 OD2 H:ASP63 4.0 24.0 0.6 CB F:ASP74 4.1 23.9 0.6 NE2 H:HIS59 4.1 20.8 1.0 CG F:GLU78 4.2 21.0 0.5 CG F:GLU78 4.2 19.9 0.5 OD1 F:ASP74 4.2 21.5 0.4 CE1 H:HIS59 4.3 20.4 1.0 ND1 H:HIS47 4.4 18.1 1.0 OD1 H:ASP63 4.4 23.7 0.6 CG H:HIS47 4.4 19.9 1.0 O H:HOH2024 4.4 47.7 1.0 CG H:ASP63 4.6 22.4 0.6 CG F:ASP74 4.7 22.9 0.4 NE1 H:TRP48 4.8 24.9 1.0 OE1 F:GLU78 4.9 19.6 0.5 O F:ASP74 4.9 24.3 0.6 CB F:ASP74 4.9 22.1 0.4 CD1 H:TRP48 5.0 23.5 1.0

Iron binding site 9 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe2000 b:26.1 occ:0.60 OE2 K:GLU78 1.9 20.0 0.4 OD1 K:ASP74 2.0 26.6 0.6 NE2 I:HIS47 2.2 19.4 1.0 O I:HOH2034 2.2 32.8 1.0 CG K:ASP74 2.7 23.3 0.6 OD2 K:ASP74 2.8 22.6 0.6 OE2 K:GLU78 2.8 18.3 0.6 CD K:GLU78 2.9 19.1 0.4 CD2 I:HIS47 3.1 18.4 1.0 O K:HOH2068 3.2 32.6 1.0 CE1 I:HIS47 3.2 20.1 1.0 OE1 K:GLU78 3.3 19.3 0.4 O I:HOH2035 3.5 43.2 1.0 CD K:GLU78 3.9 18.2 0.6 CB K:ASP74 4.1 22.6 0.6 OD2 I:ASP63 4.2 33.0 1.0 OD1 K:ASP74 4.2 19.6 0.4 CG K:GLU78 4.2 18.2 0.4 CG K:GLU78 4.2 17.2 0.6 OD1 I:ASP63 4.2 31.4 1.0 CG I:HIS47 4.3 16.6 1.0 NE2 I:HIS59 4.3 17.1 1.0 ND1 I:HIS47 4.3 15.3 1.0 CE1 I:HIS59 4.3 17.4 1.0 O K:HOH2062 4.4 49.7 1.0 CG K:ASP74 4.4 22.0 0.4 NE1 I:TRP48 4.5 19.2 1.0 CG I:ASP63 4.6 27.5 1.0 O K:HOH2070 4.7 46.6 1.0 CB K:ASP74 4.7 22.2 0.4 O K:HOH2069 4.7 43.0 1.0 CD1 I:TRP48 4.9 19.5 1.0 OD2 K:ASP74 5.0 23.5 0.4 OE1 K:GLU78 5.0 16.0 0.6 NE2 I:HIS44 5.0 20.9 1.0 O K:ASP74 5.0 23.1 0.6

Iron binding site 10 out of 12 in the Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Iron-Bound Crystal Structure of Dps-Like Peroxide Resistance Protein (Dpr) From Streptococcus Suis. within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe2000 b:23.9 occ:0.50 OE2 L:GLU78 1.8 17.8 0.5 OD1 L:ASP74 2.0 25.1 0.5 OD2 L:ASP74 2.2 21.9 0.5 O J:HOH2030 2.2 36.3 1.0 NE2 J:HIS47 2.2 23.8 1.0 CG L:ASP74 2.3 24.0 0.5 OE2 L:GLU78 2.6 14.7 0.5 CD L:GLU78 2.8 19.6 0.5 CD2 J:HIS47 3.1 23.3 1.0 OE1 L:GLU78 3.2 19.3 0.5 O J:HOH2025 3.3 29.4 1.0 CE1 J:HIS47 3.3 23.2 1.0 CD L:GLU78 3.7 20.2 0.5 CB L:ASP74 3.8 24.2 0.5 OD1 L:ASP74 4.0 21.2 0.5 OD2 J:ASP63 4.1 35.9 1.0 CG L:GLU78 4.2 19.7 0.5 CG L:GLU78 4.2 20.7 0.5 O L:HOH2049 4.3 41.3 1.0 CG J:HIS47 4.3 21.1 1.0 NE2 J:HIS59 4.3 21.4 1.0 ND1 J:HIS47 4.4 21.7 1.0 OD1 J:ASP63 4.4 34.6 1.0 CE1 J:HIS59 4.4 22.9 1.0 CG L:ASP74 4.5 24.8 0.5 NE1 J:TRP48 4.5 23.6 1.0 CG J:ASP63 4.7 30.2 1.0 CA L:ASP74 4.8 23.7 0.5 CD1 J:TRP48 4.8 22.4 1.0 CB L:ASP74 4.8 23.5 0.5 OE1 L:GLU78 4.8 18.5 0.5 NE2 J:HIS44 4.8 25.7 1.0 O L:ASP74 4.9 23.3 0.5

A.Kauko, A.T.Pulliainen, S.Haataja, W.Meyer-Klaucke, J.Finne, A.C.Papageorgiou. Iron Incorporation in Streptococcus Suis Dps-Like Peroxide Resistance Protein Dpr Requires Mobility in the Ferroxidase Center and Leads to the Formation of A Ferrihydrite-Like Core. J. Mol. Biol. V. 364 97 2006.
ISSN: ISSN 0022-2836
PubMed: 16997323
DOI: 10.1016/J.JMB.2006.08.061