Iron in PDB 8w1d: Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form)

The structure of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form), PDB code: 8w1d was solved by S.Lovell, K.P.Battaile, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.76 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.938, 44.58, 51.468, 90, 96.97, 90
R / Rfree (%)	14.5 / 17.9

The binding sites of Iron atom in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form) (pdb code 8w1d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form), PDB code: 8w1d:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric 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 Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:17.8 occ:1.00 OE2 A:GLU162 1.9 18.8 1.0 OE1 A:GLU47 1.9 18.3 1.0 ND1 A:HIS83 2.0 17.1 1.0 OE1 A:GLU80 2.1 18.4 1.0 O A:HOH301 2.2 27.7 1.0 OE2 A:GLU47 2.4 21.2 1.0 CD A:GLU47 2.5 18.1 1.0 CD A:GLU162 2.8 17.2 1.0 CE1 A:HIS83 2.9 17.8 1.0 CD A:GLU80 3.1 17.2 1.0 CG A:HIS83 3.1 16.1 1.0 OE1 A:GLU162 3.1 17.7 1.0 CB A:HIS83 3.6 15.6 1.0 OE2 A:GLU80 3.7 17.3 1.0 O A:HOH305 3.9 31.2 1.0 FE A:FE2202 3.9 16.3 1.0 CG A:GLU47 4.0 17.4 1.0 CA A:GLU80 4.0 14.2 1.0 NE2 A:HIS83 4.0 18.5 1.0 CG2 A:ILE158 4.1 17.3 1.0 CG A:GLU162 4.2 16.3 1.0 CG A:GLU80 4.2 16.0 1.0 CD2 A:HIS83 4.2 17.4 1.0 CB A:GLU80 4.3 14.9 1.0 CB A:GLU47 4.7 15.2 1.0 O A:GLU80 4.7 14.5 1.0 N A:GLU80 4.8 14.7 1.0 O A:GLN79 4.8 15.6 1.0 CE1 A:HIS165 4.9 15.4 1.0 C A:GLU80 4.9 13.5 1.0 ND1 A:HIS165 5.0 15.5 1.0 CA A:GLU47 5.0 14.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric 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 Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dimeric Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:16.3 occ:1.00 OE2 A:GLU80 1.9 17.3 1.0 OE1 A:GLU162 2.0 17.7 1.0 ND1 A:HIS165 2.1 15.5 1.0 OE1 A:GLU130 2.1 18.1 1.0 O A:HOH305 2.2 31.2 1.0 OE2 A:GLU130 2.4 17.7 1.0 CD A:GLU130 2.6 16.9 1.0 CD A:GLU80 2.8 17.2 1.0 OE1 A:GLU80 2.9 18.4 1.0 CE1 A:HIS165 3.0 15.4 1.0 CD A:GLU162 3.1 17.2 1.0 CG A:HIS165 3.1 15.2 1.0 O A:HOH301 3.2 27.7 1.0 CB A:HIS165 3.5 14.2 1.0 OE2 A:GLU162 3.6 18.8 1.0 FE A:FE2201 3.9 17.8 1.0 O A:HOH378 4.0 24.7 1.0 CG A:GLU130 4.1 16.4 1.0 NE2 A:HIS165 4.1 16.6 1.0 CG A:GLU80 4.2 16.0 1.0 CA A:GLU162 4.2 14.7 1.0 CD2 A:HIS165 4.2 15.4 1.0 CG A:GLU162 4.3 16.3 1.0 CB A:GLU162 4.4 15.9 1.0 CE2 A:TYR54 4.5 14.8 1.0 OH A:TYR54 4.7 16.5 1.0 CE1 A:HIS83 4.8 17.8 1.0 CB A:GLU130 4.9 16.0 1.0 ND1 A:HIS83 5.0 17.1 1.0

N.Rajapaksha, H.Yao, A.Cook, S.Seibold, L.Liu, K.P.Battaile, L.Fontenot, F.Donnarumma, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Gene PA4880 Encodes A Dps-Like Protein with A Dps Fold, Bacterioferritin-Type Ferroxidase Centers, and Endonuclease Activity Front Mol Biosci 2024.
ISSN: ESSN 2296-889X
DOI: 10.3389/FMOLB.2024.1390745