Iron in PDB 8ffc: Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)

The structure of Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form), PDB code: 8ffc was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.91 / 1.85
Space group	P 21 3 1
Cell size a, b, c (Å), α, β, γ (°)	223.9, 223.9, 223.9, 90, 90, 90
R / Rfree (%)	16.2 / 19.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 63;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) (pdb code 8ffc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 63 binding sites of Iron where determined in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form), PDB code: 8ffc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:26.7 occ:0.81 OE2 A:GLU68 2.1 33.0 1.0 OD2 A:ASP64 2.2 28.6 1.0 NE2 E:HIS37 2.2 26.1 1.0 O E:HOH301 2.3 30.7 1.0 OD1 A:ASP64 2.4 24.0 1.0 FE A:FE2202 2.6 41.4 0.6 CG A:ASP64 2.6 31.0 1.0 CD A:GLU68 3.0 28.5 1.0 CE1 E:HIS37 3.2 25.1 1.0 CD2 E:HIS37 3.3 26.1 1.0 OE1 A:GLU68 3.4 25.6 1.0 O K:HOH336 3.8 38.8 1.0 OE2 E:GLU53 4.0 40.2 1.0 CE1 E:HIS49 4.0 30.8 1.0 NE2 E:HIS49 4.1 26.1 1.0 CG A:GLU68 4.1 26.0 1.0 CB A:ASP64 4.1 26.2 1.0 OH E:TYR56 4.2 35.6 1.0 O E:HOH390 4.2 43.5 1.0 ND1 E:HIS37 4.3 21.5 1.0 CG E:HIS37 4.4 24.7 1.0 NE1 E:TRP38 4.5 26.0 1.0 CD1 E:TRP38 4.5 22.6 1.0 O A:HOH349 4.5 43.8 1.0 O E:HOH382 4.8 35.4 1.0

Iron binding site 2 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:41.4 occ:0.57 O E:HOH390 2.4 43.5 1.0 O E:HOH382 2.5 35.4 1.0 O K:HOH336 2.5 38.8 1.0 NE2 E:HIS49 2.6 26.1 1.0 FE A:FE2201 2.6 26.7 0.8 OE2 A:GLU68 2.8 33.0 1.0 OE1 A:GLU68 3.1 25.6 1.0 CE1 E:HIS49 3.3 30.8 1.0 CD A:GLU68 3.3 28.5 1.0 O K:HOH404 3.5 47.6 1.0 CD2 E:HIS49 3.7 29.1 1.0 NE2 E:HIS37 3.7 26.1 1.0 O E:HOH301 3.8 30.7 1.0 CE1 E:HIS37 3.8 25.1 1.0 OD2 A:ASP64 4.0 28.6 1.0 OE2 E:GLU53 4.1 40.2 1.0 ND1 E:HIS49 4.4 20.9 1.0 CG E:HIS49 4.7 22.7 1.0 NZ K:LYS145 4.7 46.4 1.0 CG A:GLU68 4.8 26.0 1.0 CE K:LYS145 4.9 41.2 1.0 CG A:ASP64 4.9 31.0 1.0 OD1 A:ASP64 5.0 24.0 1.0

Iron binding site 3 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:47.6 occ:0.30 FE C:FE2203 2.3 41.8 0.4 OD1 A:ASP134 2.4 41.6 1.0 NE2 A:GLN138 2.4 48.4 1.0 FE K:FE2203 2.4 46.0 0.3 FE A:FE2204 2.6 87.9 0.7 OD1 C:ASP134 2.6 39.0 1.0 FE C:FE2204 2.9 66.7 0.5 CG C:ASP134 3.0 36.3 1.0 OD2 C:ASP134 3.0 40.3 1.0 CG A:ASP134 3.4 37.5 1.0 CD A:GLN138 3.4 59.5 1.0 OD2 A:ASP134 3.7 37.6 1.0 OD1 K:ASP134 3.9 39.6 1.0 OE1 A:GLN138 4.1 56.7 1.0 CB C:ASP134 4.3 31.8 1.0 CG A:GLN138 4.3 42.8 1.0 NE2 C:GLN138 4.6 53.0 1.0 NE2 K:GLN138 4.6 52.1 1.0 CB A:ASP134 4.7 26.5 1.0 CG K:ASP134 4.8 36.3 1.0 O A:ASP134 4.9 24.9 1.0

Iron binding site 4 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:87.9 occ:0.73 FE K:FE2203 2.5 46.0 0.3 FE A:FE2203 2.6 47.6 0.3 FE C:FE2204 2.9 66.7 0.5 FE C:FE2203 3.3 41.8 0.4 OD2 A:ASP134 3.6 37.6 1.0 NE2 A:GLN138 3.7 48.4 1.0 OD1 A:ASP134 3.8 41.6 1.0 NE2 K:GLN138 3.8 52.1 1.0 CD A:GLN138 3.9 59.5 1.0 CG A:ASP134 4.1 37.5 1.0 CD K:GLN138 4.1 57.3 1.0 OE1 K:GLN138 4.2 51.1 1.0 CG A:GLN138 4.3 42.8 1.0 OE1 A:GLN138 4.3 56.7 1.0 OD1 K:ASP134 4.7 39.6 1.0 OD2 C:ASP134 4.8 40.3 1.0 OD1 C:ASP134 4.9 39.0 1.0

Iron binding site 5 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:23.5 occ:0.86 OE2 B:GLU68 2.2 24.6 1.0 NE2 L:HIS37 2.2 18.3 1.0 O L:HOH311 2.2 28.7 1.0 OD2 B:ASP64 2.3 25.1 1.0 OD1 B:ASP64 2.4 23.6 1.0 FE B:FE2202 2.5 42.5 0.6 CG B:ASP64 2.6 24.8 1.0 CD B:GLU68 3.0 23.5 1.0 CE1 L:HIS37 3.1 21.5 1.0 CD2 L:HIS37 3.2 18.8 1.0 OE1 B:GLU68 3.4 24.6 1.0 O B:HOH356 3.9 36.7 1.0 CE1 L:HIS49 4.0 25.9 1.0 NE2 L:HIS49 4.1 24.8 1.0 OE2 L:GLU53 4.1 42.0 1.0 CB B:ASP64 4.1 22.4 1.0 OH L:TYR56 4.2 32.2 1.0 CG B:GLU68 4.2 19.4 1.0 O L:HOH371 4.2 36.7 1.0 ND1 L:HIS37 4.2 17.8 1.0 CG L:HIS37 4.3 17.0 1.0 O B:HOH303 4.4 44.5 1.0 NE1 L:TRP38 4.5 20.8 1.0 CD1 L:TRP38 4.6 20.3 1.0 O L:HOH358 4.7 29.8 1.0

Iron binding site 6 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:42.5 occ:0.61 FE B:FE2201 2.5 23.5 0.9 O L:HOH358 2.5 29.8 1.0 O B:HOH356 2.6 36.7 1.0 NE2 L:HIS49 2.7 24.8 1.0 O L:HOH371 2.7 36.7 1.0 OE2 B:GLU68 2.7 24.6 1.0 OE1 B:GLU68 3.1 24.6 1.0 CD B:GLU68 3.3 23.5 1.0 CE1 L:HIS49 3.4 25.9 1.0 O L:HOH311 3.6 28.7 1.0 NE2 L:HIS37 3.6 18.3 1.0 CE1 L:HIS37 3.7 21.5 1.0 CD2 L:HIS49 3.8 25.2 1.0 OD2 B:ASP64 3.9 25.1 1.0 OE2 L:GLU53 4.1 42.0 1.0 ND1 L:HIS49 4.6 22.4 1.0 CG L:HIS49 4.8 19.8 1.0 CG B:ASP64 4.8 24.8 1.0 CG B:GLU68 4.8 19.4 1.0 OD1 B:ASP64 4.8 23.6 1.0 CD2 L:HIS37 4.9 18.8 1.0 ND1 L:HIS37 5.0 17.8 1.0 NZ I:LYS145 5.0 41.3 1.0

Iron binding site 7 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:47.7 occ:0.65 FE L:FE2201 2.4 24.6 0.9 O E:HOH332 2.5 30.6 1.0 O B:HOH363 2.5 32.8 1.0 O B:HOH306 2.7 35.0 1.0 NE2 B:HIS49 2.8 20.7 1.0 OE2 L:GLU68 2.8 24.3 1.0 OE1 L:GLU68 3.2 28.0 1.0 CD L:GLU68 3.4 27.9 1.0 CE1 B:HIS49 3.4 26.1 1.0 NE2 B:HIS37 3.5 18.6 1.0 O E:HOH407 3.5 43.2 1.0 O B:HOH305 3.5 27.4 1.0 CE1 B:HIS37 3.7 20.5 1.0 OE2 B:GLU53 3.8 41.2 1.0 OD2 L:ASP64 3.8 23.6 1.0 CD2 B:HIS49 3.8 24.4 1.0 ND1 B:HIS49 4.6 19.9 1.0 CG L:ASP64 4.7 27.6 1.0 OD1 L:ASP64 4.7 26.0 1.0 CD2 B:HIS37 4.8 19.4 1.0 CG B:HIS49 4.8 18.7 1.0 NZ E:LYS145 4.8 32.9 1.0 CG L:GLU68 4.8 19.7 1.0 CD B:GLU53 4.9 38.5 1.0 ND1 B:HIS37 4.9 18.8 1.0

Iron binding site 8 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


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 Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe204 b:99.7 occ:0.86 FE B:FE2205 2.5 45.5 0.4 FE I:FE2203 2.6 61.0 0.6 FE B:FE2206 2.8 59.0 0.4 OD1 B:ASP134 2.8 40.4 1.0 OD1 H:ASP134 3.2 37.6 1.0 OD2 B:ASP134 3.5 32.1 1.0 CG B:ASP134 3.5 27.9 1.0 OD2 H:ASP134 3.5 36.9 1.0 CG H:ASP134 3.7 34.2 1.0 OD1 I:ASP134 4.1 41.6 1.0 CG B:GLN138 4.4 37.3 1.0 NE2 B:GLN138 4.6 46.4 1.0 O H:HOH391 4.7 35.3 1.0 OD2 I:ASP134 4.9 35.9 1.0 CG I:ASP134 4.9 27.0 1.0 CB B:ASP134 5.0 19.7 1.0 CD B:GLN138 5.0 57.9 1.0

Iron binding site 9 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe205 b:45.5 occ:0.41 OD1 I:ASP134 2.3 41.6 1.0 FE B:FE2204 2.5 99.7 0.9 FE I:FE2203 2.9 61.0 0.6 OD1 B:ASP134 2.9 40.4 1.0 OD2 B:ASP134 3.0 32.1 1.0 CG B:ASP134 3.1 27.9 1.0 CG I:ASP134 3.1 27.0 1.0 OD2 I:ASP134 3.4 35.9 1.0 CG I:GLN138 3.8 28.1 1.0 OD1 H:ASP134 4.3 37.6 1.0 CB B:ASP134 4.3 19.7 1.0 O I:ASP134 4.4 16.9 1.0 CB I:ASP134 4.5 20.3 1.0 FE B:FE2206 4.7 59.0 0.4 FE I:FE2204 4.8 49.5 0.5 CA I:ASP134 4.9 17.1 1.0 C I:ASP134 5.0 18.1 1.0

Iron binding site 10 out of 63 in the Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Iron Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe206 b:59.0 occ:0.40 FE B:FE2204 2.8 99.7 0.9 OD1 B:ASP134 2.8 40.4 1.0 O H:HOH391 2.8 35.3 1.0 CG B:GLN138 3.0 37.3 1.0 O B:ASP134 3.2 17.7 1.0 N B:GLN138 3.4 19.3 1.0 OD2 H:ASP134 3.5 36.9 1.0 CG B:ASP134 3.6 27.9 1.0 CG H:ASP134 3.6 34.2 1.0 CA B:GLN138 3.7 21.8 1.0 OD1 H:ASP134 3.8 37.6 1.0 CB B:GLN138 3.8 23.8 1.0 CG2 B:THR137 3.8 24.6 1.0 CB B:THR137 4.0 20.7 1.0 OD2 B:ASP134 4.0 32.1 1.0 C B:THR137 4.1 19.0 1.0 CD B:GLN138 4.2 57.9 1.0 C B:ASP134 4.2 16.9 1.0 NE2 B:GLN138 4.3 46.4 1.0 CB H:ASP134 4.4 20.8 1.0 CA B:ASP134 4.5 18.3 1.0 CA B:THR137 4.6 17.9 1.0 CB B:ASP134 4.7 19.7 1.0 O B:THR137 4.7 17.8 1.0 FE B:FE2205 4.7 45.5 0.4 FE I:FE2203 4.8 61.0 0.6 FE B:FE2207 4.9 65.5 0.8

N.Rajapaksha, A.Soldano, H.Yao, F.Donnarumma, M.M.Kashipathy, S.Seibold, K.P.Battaile, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits in Vitro Dna Cleaving Activity Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24054669