Iron in PDB 2iy4: X-Ray Structure of Dps From Listeria Monocytogenes

The structure of X-Ray Structure of Dps From Listeria Monocytogenes, PDB code: 2iy4 was solved by A.Ilari, G.Bellapadrona, S.Stefanini, E.Chiancone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.288, 172.708, 135.312, 90.00, 92.11, 90.00
R / Rfree (%)	18.2 / 23.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the X-Ray Structure of Dps From Listeria Monocytogenes (pdb code 2iy4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the X-Ray Structure of Dps From Listeria Monocytogenes, PDB code: 2iy4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1157 b:11.9 occ:0.20 OD2 B:ASP58 1.8 35.1 1.0 OE2 B:GLU62 2.1 34.3 1.0 NE2 D:HIS31 2.4 28.0 1.0 CG B:ASP58 3.0 31.1 1.0 CE1 D:HIS31 3.1 27.6 1.0 CD B:GLU62 3.2 31.3 1.0 O B:HOH2030 3.2 36.0 1.0 OD1 B:ASP58 3.4 31.6 1.0 CD2 D:HIS31 3.5 26.6 1.0 OE1 B:GLU62 3.8 31.1 1.0 OD1 D:ASP47 3.8 31.0 1.0 NE2 D:HIS43 4.0 28.6 1.0 OD2 D:ASP47 4.1 32.1 1.0 CB B:ASP58 4.3 27.9 1.0 CE1 D:HIS43 4.3 29.1 1.0 CG B:GLU62 4.3 27.9 1.0 ND1 D:HIS31 4.3 26.3 1.0 CG D:ASP47 4.4 28.5 1.0 CG D:HIS31 4.6 25.3 1.0 O D:HOH2019 4.6 31.1 1.0

Iron binding site 2 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1157 b:24.8 occ:0.20 NE2 A:HIS31 2.0 26.8 1.0 OE2 C:GLU62 2.3 33.9 1.0 OD2 C:ASP58 2.5 36.3 1.0 CD2 A:HIS31 3.0 27.0 1.0 OD1 C:ASP58 3.0 30.5 1.0 CE1 A:HIS31 3.1 28.0 1.0 CG C:ASP58 3.1 30.5 1.0 CD C:GLU62 3.4 30.6 1.0 OD1 A:ASP47 3.8 31.9 1.0 NE2 A:HIS43 4.1 29.2 1.0 OD2 A:ASP47 4.1 31.9 1.0 O C:HOH2028 4.1 38.3 1.0 CG A:HIS31 4.1 26.4 1.0 ND1 A:HIS31 4.1 28.3 1.0 CE1 A:HIS43 4.1 29.4 1.0 CG C:GLU62 4.2 27.7 1.0 OE1 C:GLU62 4.2 32.4 1.0 CG A:ASP47 4.4 29.5 1.0 CB C:ASP58 4.6 28.3 1.0 O A:HOH2020 4.7 37.1 1.0 NE1 A:TRP32 4.9 24.2 1.0

Iron binding site 3 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1157 b:26.0 occ:0.20 OD2 D:ASP58 1.9 34.4 1.0 NE2 B:HIS31 2.2 26.2 1.0 OE2 D:GLU62 2.2 33.6 1.0 CG D:ASP58 2.8 31.2 1.0 OD1 D:ASP58 3.0 33.7 1.0 CD D:GLU62 3.1 30.5 1.0 CE1 B:HIS31 3.1 26.4 1.0 CD2 B:HIS31 3.2 26.4 1.0 O D:HOH2034 3.3 31.2 1.0 OE1 D:GLU62 3.6 31.4 1.0 OD1 B:ASP47 4.0 31.2 1.0 NE2 B:HIS43 4.0 29.9 1.0 CG D:GLU62 4.1 27.2 1.0 CE1 B:HIS43 4.2 30.0 1.0 CB D:ASP58 4.2 28.4 1.0 ND1 B:HIS31 4.2 26.9 1.0 OD2 B:ASP47 4.3 31.8 1.0 CG B:HIS31 4.3 26.1 1.0 CG B:ASP47 4.6 28.9 1.0 NE1 B:TRP32 4.8 24.6 1.0

Iron binding site 4 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1157 b:17.9 occ:0.20 OE2 E:GLU62 2.5 33.1 1.0 NE2 G:HIS31 2.5 28.3 1.0 OD1 E:ASP58 2.8 35.9 1.0 CG E:ASP58 3.4 33.2 1.0 CE1 G:HIS31 3.4 27.7 1.0 CD E:GLU62 3.4 30.3 1.0 CD2 G:HIS31 3.5 27.0 1.0 OD1 G:ASP47 3.7 30.4 1.0 OD2 E:ASP58 3.7 38.9 1.0 OD2 G:ASP47 3.8 32.0 1.0 OE1 E:GLU62 4.0 32.2 1.0 O E:HOH2029 4.2 42.1 1.0 CG G:ASP47 4.2 28.9 1.0 CB E:ASP58 4.4 29.2 1.0 NE2 G:HIS43 4.4 30.5 1.0 CG E:GLU62 4.4 28.0 1.0 O E:HOH2028 4.5 35.4 1.0 ND1 G:HIS31 4.5 27.0 1.0 CG G:HIS31 4.6 25.8 1.0 CE1 G:HIS43 4.7 30.2 1.0

Iron binding site 5 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1158 b:23.0 occ:0.20 OD2 G:ASP58 2.0 28.6 0.7 NE2 E:HIS31 2.1 27.7 1.0 OE2 G:GLU62 2.4 33.4 1.0 CG G:ASP58 2.8 26.6 0.7 CE1 E:HIS31 3.0 27.3 1.0 OD1 G:ASP58 3.0 22.0 0.7 CD2 E:HIS31 3.2 26.6 1.0 CD G:GLU62 3.5 30.8 1.0 OD1 E:ASP47 3.7 30.7 1.0 OD2 E:ASP47 3.9 31.6 1.0 ND1 E:HIS31 4.1 26.2 1.0 NE2 E:HIS43 4.2 28.5 1.0 OE1 G:GLU62 4.2 30.5 1.0 CG E:HIS31 4.2 25.3 1.0 CG E:ASP47 4.2 28.9 1.0 CB G:ASP58 4.3 25.9 0.7 CE1 E:HIS43 4.3 29.1 1.0 CB G:ASP58 4.3 26.0 0.3 CG G:GLU62 4.4 28.0 1.0 OD2 G:ASP58 4.6 25.9 0.3 CG G:ASP58 4.6 25.6 0.3 NE1 E:TRP32 4.7 24.3 1.0

Iron binding site 6 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1157 b:16.6 occ:0.20 OD2 F:ASP58 2.1 35.1 1.0 OE2 F:GLU62 2.3 34.3 1.0 O F:HOH2036 2.4 40.2 1.0 NE2 H:HIS31 2.6 28.5 1.0 CG F:ASP58 3.0 31.2 1.0 CD F:GLU62 3.0 31.0 1.0 OD1 F:ASP58 3.1 32.8 1.0 OE1 F:GLU62 3.4 32.3 1.0 CE1 H:HIS31 3.5 27.7 1.0 CD2 H:HIS31 3.7 27.0 1.0 CG F:GLU62 4.1 27.9 1.0 OD1 H:ASP47 4.2 31.1 1.0 NE2 H:HIS43 4.4 28.0 1.0 CB F:ASP58 4.4 27.5 1.0 OD2 H:ASP47 4.4 31.0 1.0 ND1 H:HIS31 4.7 27.7 1.0 CG H:ASP47 4.7 28.5 1.0 CG H:HIS31 4.8 25.7 1.0 CE1 H:HIS43 4.8 28.5 1.0

Iron binding site 7 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe1157 b:16.6 occ:0.20 OD2 H:ASP58 1.9 35.6 1.0 NE2 F:HIS31 2.4 27.3 1.0 OE2 H:GLU62 2.6 34.1 1.0 CG H:ASP58 2.8 31.7 1.0 OD1 H:ASP58 3.1 31.8 1.0 CE1 F:HIS31 3.4 26.5 1.0 CD H:GLU62 3.4 31.1 1.0 CD2 F:HIS31 3.4 26.9 1.0 OD1 F:ASP47 3.8 31.2 1.0 OD2 F:ASP47 3.9 32.5 1.0 OE1 H:GLU62 4.0 31.5 1.0 NE2 F:HIS43 4.2 28.1 1.0 CB H:ASP58 4.3 27.9 1.0 CG F:ASP47 4.3 29.1 1.0 CG H:GLU62 4.3 28.1 1.0 CE1 F:HIS43 4.5 30.0 1.0 ND1 F:HIS31 4.5 27.7 1.0 CG F:HIS31 4.6 26.3 1.0 O F:HOH2023 4.6 33.4 1.0

Iron binding site 8 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe1157 b:24.0 occ:0.20 NE2 K:HIS31 2.5 27.5 1.0 OD2 I:ASP58 2.5 33.1 0.7 OE2 I:GLU62 2.5 33.7 1.0 CD I:GLU62 3.1 31.1 1.0 CG I:ASP58 3.2 29.6 0.7 CE1 K:HIS31 3.2 27.0 1.0 OD1 I:ASP58 3.4 29.1 0.7 OE1 I:GLU62 3.5 31.4 1.0 O I:HOH2034 3.6 42.3 1.0 CD2 K:HIS31 3.6 27.1 1.0 CG I:GLU62 4.1 28.0 1.0 OD1 K:ASP47 4.1 30.7 1.0 NE2 K:HIS43 4.1 29.7 1.0 OD2 K:ASP47 4.2 30.8 1.0 CE1 K:HIS43 4.4 29.9 1.0 CB I:ASP58 4.4 28.3 0.7 CB I:ASP58 4.4 27.8 0.3 ND1 K:HIS31 4.4 27.3 1.0 CG K:ASP47 4.6 28.4 1.0 CG K:HIS31 4.6 26.6 1.0 CG I:ASP58 4.7 27.2 0.3 OD1 I:ASP58 4.8 26.2 0.3

Iron binding site 9 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe1157 b:22.9 occ:0.20 OE2 J:GLU62 2.0 34.0 1.0 OD2 J:ASP58 2.3 34.5 1.0 NE2 L:HIS31 2.4 28.3 1.0 CG J:ASP58 3.1 31.4 1.0 CD J:GLU62 3.1 30.1 1.0 CE1 L:HIS31 3.3 26.8 1.0 OD1 J:ASP58 3.3 34.8 1.0 CD2 L:HIS31 3.4 26.8 1.0 OE1 J:GLU62 3.9 30.3 1.0 OD2 L:ASP47 4.0 32.1 1.0 NE2 L:HIS43 4.0 28.5 1.0 OD1 L:ASP47 4.1 30.5 1.0 CG J:GLU62 4.1 27.6 1.0 ND1 L:HIS31 4.4 27.4 1.0 CE1 L:HIS43 4.4 28.9 1.0 CG L:ASP47 4.5 29.4 1.0 CG L:HIS31 4.5 26.4 1.0 CB J:ASP58 4.5 29.1 1.0 O L:HOH2017 4.8 32.6 1.0 NE1 L:TRP32 5.0 23.5 1.0 CD2 L:HIS43 5.0 28.6 1.0

Iron binding site 10 out of 24 in the X-Ray Structure of Dps From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of X-Ray Structure of Dps From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ K:Fe1157 b:27.7 occ:0.20 OD2 K:ASP58 2.3 39.0 1.0 OE2 K:GLU62 2.3 34.6 1.0 NE2 I:HIS31 2.4 27.6 1.0 CG K:ASP58 3.1 32.8 1.0 CE1 I:HIS31 3.1 26.8 1.0 CD K:GLU62 3.3 30.8 1.0 OD1 K:ASP58 3.4 33.1 1.0 O K:HOH2029 3.4 42.9 1.0 CD2 I:HIS31 3.6 27.3 1.0 OD2 I:ASP47 3.9 30.5 1.0 OD1 I:ASP47 3.9 31.6 1.0 OE1 K:GLU62 4.0 31.9 1.0 NE2 I:HIS43 4.1 28.5 1.0 CG K:GLU62 4.1 27.7 1.0 CB K:ASP58 4.3 29.3 1.0 CG I:ASP47 4.4 28.4 1.0 ND1 I:HIS31 4.4 27.2 1.0 CE1 I:HIS43 4.5 28.5 1.0 CG I:HIS31 4.6 27.0 1.0 O I:HOH2019 4.9 33.8 1.0

G.Bellapadrona, R.Chiaraluce, V.Consalvi, A.Ilari, S.Stefanini, E.Chiancone. The Mutations Lys 114 --> Gln and Asp 126 --> Asn Disrupt An Intersubunit Salt Bridge and Convert Listeria Innocua Dps Into Its Natural Mutant Listeria Monocytogenes Dps. Effects on Protein Stability at Low pH. Proteins V. 66 975 2007.
ISSN: ISSN 0887-3585
PubMed: 17186524
DOI: 10.1002/PROT.21305