Iron in PDB 1o9r: The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding

The structure of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding, PDB code: 1o9r was solved by A.Ilari, P.Ceci, E.Chiancone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.046, 90.349, 105.656, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20

The binding sites of Iron atom in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding (pdb code 1o9r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding, PDB code: 1o9r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1163 b:25.7 occ:0.30 OE2 A:GLU71 2.0 28.9 1.0 O B:HOH2045 2.1 25.7 1.0 O B:HOH2036 2.2 22.8 1.0 OD2 A:ASP67 2.3 11.0 0.3 OD1 A:ASP67 2.7 12.5 0.3 CG A:ASP67 2.9 13.8 0.3 CD A:GLU71 3.3 20.8 1.0 NE2 B:HIS40 3.4 16.8 1.0 CE1 B:HIS40 3.9 15.7 1.0 CG A:GLU71 4.0 19.3 1.0 OD1 B:ASP56 4.1 19.8 1.0 OE1 A:GLU71 4.2 25.3 1.0 NE2 B:HIS52 4.2 16.3 1.0 NZ C:LYS149 4.3 24.0 1.0 NZ B:LYS37 4.3 21.8 1.0 CB A:ASP67 4.4 13.9 0.3 CB A:ASP67 4.5 18.1 0.7 CD2 B:HIS40 4.6 16.2 1.0 CE1 B:HIS52 4.6 14.6 1.0 OD2 A:ASP67 4.6 24.4 0.7 CG A:ASP67 4.7 20.4 0.7 CG B:ASP56 5.0 20.3 1.0 OD2 B:ASP56 5.0 19.5 1.0

Iron binding site 2 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1163 b:27.3 occ:0.30 OE2 B:GLU71 1.9 27.3 1.0 O A:HOH2046 2.1 24.4 1.0 O A:HOH2041 2.1 22.3 1.0 OD1 B:ASP67 2.2 13.9 0.3 OD2 B:ASP67 2.7 10.9 0.3 CG B:ASP67 2.9 15.2 0.3 CD B:GLU71 3.1 22.7 1.0 NE2 A:HIS40 3.6 16.9 1.0 CG B:GLU71 3.9 19.8 1.0 OE1 B:GLU71 4.0 24.9 1.0 CE1 A:HIS40 4.1 15.2 1.0 NZ D:LYS149 4.1 21.3 1.0 OD1 A:ASP56 4.2 19.9 1.0 NE2 A:HIS52 4.3 15.9 1.0 CB B:ASP67 4.3 13.8 0.3 CB B:ASP67 4.5 15.0 0.7 NZ A:LYS37 4.5 22.6 1.0 OD1 B:ASP67 4.7 23.5 0.7 CD2 A:HIS40 4.8 16.4 1.0 CE1 A:HIS52 4.8 15.3 1.0 CG B:ASP67 4.8 17.7 0.7

Iron binding site 3 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1163 b:31.7 occ:0.50 OE2 C:GLU71 2.3 29.4 1.0 OD1 C:ASP67 2.4 16.8 0.5 OD2 C:ASP67 2.4 15.8 0.5 CG C:ASP67 2.8 17.5 0.5 CD C:GLU71 3.4 23.1 1.0 CG C:GLU71 4.0 22.1 1.0 O C:HOH2054 4.3 39.8 1.0 CB C:ASP67 4.3 14.0 0.5 CG C:ASP67 4.4 22.3 0.5 OD1 C:ASP67 4.4 23.5 0.5 OE1 C:GLU71 4.4 28.1 1.0 CB C:ASP67 4.4 17.9 0.5 NZ E:LYS149 4.8 25.3 1.0 OD2 C:ASP67 4.8 24.1 0.5

Iron binding site 4 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1163 b:29.4 occ:0.50 OE2 D:GLU71 2.2 27.8 1.0 O D:HOH2048 2.2 23.0 1.0 OD1 D:ASP67 2.3 16.0 0.5 OD2 D:ASP67 2.6 16.9 0.5 CG D:ASP67 2.9 16.7 0.5 CD D:GLU71 3.3 21.5 1.0 CG D:GLU71 4.0 22.4 1.0 OE1 D:GLU71 4.3 27.1 1.0 OD1 D:ASP67 4.3 22.1 0.5 CB D:ASP67 4.3 14.8 0.5 CB D:ASP67 4.4 15.9 0.5 CG D:ASP67 4.6 18.4 0.5

Iron binding site 5 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1163 b:27.2 occ:0.50 O F:HOH2043 2.1 23.6 1.0 OE2 E:GLU71 2.2 30.2 1.0 O F:HOH2034 2.3 24.9 1.0 OD2 E:ASP67 2.4 14.2 0.5 OD1 E:ASP67 2.5 14.4 0.5 O E:HOH2050 2.7 52.7 1.0 NE2 F:HIS40 2.8 18.0 1.0 CG E:ASP67 2.9 15.0 0.5 CD E:GLU71 3.4 24.1 1.0 CE1 F:HIS40 3.5 16.8 1.0 CD2 F:HIS40 3.9 15.3 1.0 CG E:GLU71 4.0 22.0 1.0 OD1 F:ASP56 4.0 21.4 1.0 NE2 F:HIS52 4.1 15.1 1.0 NZ F:LYS37 4.2 18.2 1.0 OE1 E:GLU71 4.3 29.7 1.0 CB E:ASP67 4.4 11.9 0.5 CG E:ASP67 4.4 21.8 0.5 CE1 F:HIS52 4.4 15.3 1.0 CB E:ASP67 4.4 18.1 0.5 OD1 E:ASP67 4.6 24.4 0.5 NZ A:LYS149 4.7 25.1 1.0 OD2 E:ASP67 4.7 24.2 0.5 NE1 F:TRP41 4.8 14.5 1.0 OD2 F:ASP56 4.8 17.2 1.0 ND1 F:HIS40 4.8 14.6 1.0 CG F:ASP56 4.8 19.8 1.0 CD1 F:TRP41 5.0 14.4 1.0 CG F:HIS40 5.0 15.1 1.0

Iron binding site 6 out of 6 in the The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The X-Ray Crystal Structure of Agrobacterium Tumefaciens Dps, A Member of the Family That Protect Dna Without Binding within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1163 b:28.8 occ:0.50 O E:HOH2035 2.1 21.3 1.0 OE2 F:GLU71 2.2 29.9 1.0 O E:HOH2028 2.3 24.4 1.0 OD1 F:ASP67 2.4 14.4 0.5 OD2 F:ASP67 2.5 15.8 0.5 O F:HOH2057 2.7 45.3 1.0 CG F:ASP67 2.9 16.3 0.5 NE2 E:HIS40 2.9 16.8 1.0 CD F:GLU71 3.3 22.4 1.0 CE1 E:HIS40 3.6 15.9 1.0 CG F:GLU71 4.0 21.7 1.0 CD2 E:HIS40 4.0 15.6 1.0 NE2 E:HIS52 4.1 15.7 1.0 OD1 E:ASP56 4.1 21.0 1.0 NZ E:LYS37 4.3 19.8 1.0 OE1 F:GLU71 4.3 28.9 1.0 CB F:ASP67 4.3 14.4 0.5 CE1 E:HIS52 4.4 15.5 1.0 CG F:ASP67 4.5 21.7 0.5 CB F:ASP67 4.5 17.1 0.5 OD1 F:ASP67 4.6 23.9 0.5 OD2 E:ASP56 4.8 18.4 1.0 NE1 E:TRP41 4.8 14.9 1.0 ND1 E:HIS40 4.8 15.1 1.0 CG E:ASP56 4.9 18.2 1.0 OD2 F:ASP67 4.9 24.6 0.5 CD1 E:TRP41 5.0 14.8 1.0

P.Ceci, A.Ilari, E.Falvo, E.Chiancone. The Dps Protein of Agrobacterium Tumefaciens Does Not Bind to Dna But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties J.Biol.Chem. V. 278 20319 2003.
ISSN: ISSN 0021-9258
PubMed: 12660233
DOI: 10.1074/JBC.M302114200