Iron in PDB 5ww4: Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer

The structure of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer, PDB code: 5ww4 was solved by S.M.Williams, D.Chatterji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 2.05
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.410, 89.410, 420.780, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 21.2

The structure of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer (pdb code 5ww4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer, PDB code: 5ww4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:57.1 occ:1.00 OE2 A:GLU72 2.2 19.4 1.0 O B:HOH302 2.2 19.2 1.0 NE2 B:HIS41 2.3 10.5 1.0 OD2 A:ASP68 2.5 17.8 1.0 OD1 A:ASP68 2.6 17.4 1.0 CG A:ASP68 2.9 17.1 1.0 CD A:GLU72 3.1 17.9 1.0 CE1 B:HIS41 3.2 10.6 1.0 CD2 B:HIS41 3.3 10.6 1.0 OE1 A:GLU72 3.6 19.1 1.0 OD1 B:ASP57 3.7 13.4 1.0 NZ B:LYS38 3.9 13.8 1.0 O B:HOH321 3.9 20.8 1.0 CG A:GLU72 4.3 16.1 1.0 CB A:ASP68 4.3 15.8 1.0 ND1 B:HIS41 4.4 10.8 1.0 CG B:ASP57 4.4 12.6 1.0 CE1 B:HIS53 4.4 14.2 1.0 NE2 B:HIS53 4.4 14.1 1.0 OD2 B:ASP57 4.4 12.7 1.0 CG B:HIS41 4.5 10.8 1.0 NE1 B:TRP42 4.7 11.6 1.0 O B:HOH328 4.9 21.9 1.0 CD1 B:TRP42 4.9 11.5 1.0 CE B:LYS38 5.0 13.8 1.0

Iron binding site 2 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:66.2 occ:1.00 OE1 B:GLU72 2.1 18.3 1.0 O A:HOH304 2.2 20.1 1.0 NE2 A:HIS41 2.5 11.7 1.0 OD2 B:ASP68 2.6 18.9 1.0 OD1 B:ASP68 2.8 17.0 1.0 CD B:GLU72 2.9 17.2 1.0 CG B:ASP68 3.1 17.7 1.0 CE1 A:HIS41 3.3 11.7 1.0 OE2 B:GLU72 3.4 16.8 1.0 O A:HOH327 3.4 27.4 1.0 CD2 A:HIS41 3.5 11.6 1.0 NZ A:LYS38 3.7 11.7 1.0 OD1 A:ASP57 3.7 13.7 1.0 CG B:GLU72 4.1 15.7 1.0 CE1 A:HIS53 4.4 12.3 1.0 NE2 A:HIS53 4.4 12.4 1.0 CG A:ASP57 4.4 13.2 1.0 OD2 A:ASP57 4.5 13.3 1.0 ND1 A:HIS41 4.5 11.7 1.0 CB B:ASP68 4.6 16.4 1.0 CG A:HIS41 4.6 11.7 1.0 NE1 A:TRP42 4.7 10.7 1.0 O A:HOH325 4.9 26.0 1.0 CD1 A:TRP42 5.0 10.9 1.0

Iron binding site 3 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:78.2 occ:0.75 OD1 B:ASP138 2.6 13.3 0.3 OD2 B:ASP138 3.0 13.1 0.3 O B:HOH301 3.1 31.5 1.0 CG B:ASP138 3.2 13.0 0.3 OD2 B:ASP138 4.1 12.3 0.7 CB B:ASP138 4.5 12.5 0.7 CG B:ASP138 4.6 12.5 0.7 CB B:ASP138 4.7 12.8 0.3

Iron binding site 4 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:78.1 occ:0.75 O B:HOH330 3.0 29.2 1.0 O B:HOH338 3.3 32.3 1.0 OD1 B:ASP138 3.9 12.5 0.7 CE1 B:HIS141 4.3 13.3 1.0 CG B:ASP138 4.9 12.5 0.7 ND1 B:HIS141 5.0 13.1 1.0

Iron binding site 5 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:51.0 occ:1.00 O C:HOH365 2.0 22.3 1.0 OE2 C:GLU72 2.1 20.0 1.0 NE2 D:HIS41 2.3 13.4 1.0 O D:HOH311 2.4 21.3 1.0 OD2 C:ASP68 2.4 17.4 1.0 OD1 C:ASP68 2.7 16.5 1.0 CG C:ASP68 2.9 16.4 1.0 CD C:GLU72 3.0 18.4 1.0 CE1 D:HIS41 3.3 13.5 1.0 CD2 D:HIS41 3.3 13.4 1.0 OE1 C:GLU72 3.4 18.6 1.0 O D:HOH352 3.8 20.8 1.0 OD1 D:ASP57 3.8 16.3 1.0 NZ D:LYS38 4.1 15.8 1.0 CG C:GLU72 4.2 17.0 1.0 CE1 D:HIS53 4.3 13.3 1.0 NE2 D:HIS53 4.4 13.1 1.0 ND1 D:HIS41 4.4 13.4 1.0 CB C:ASP68 4.4 15.4 1.0 CG D:HIS41 4.4 13.6 1.0 CG D:ASP57 4.5 15.5 1.0 OD2 D:ASP57 4.6 15.7 1.0 NE1 D:TRP42 4.6 13.5 1.0 CD1 D:TRP42 4.8 13.3 1.0

Iron binding site 6 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:55.1 occ:1.00 OE2 D:GLU72 2.2 16.8 1.0 O C:HOH302 2.3 17.9 1.0 NE2 C:HIS41 2.3 12.9 1.0 OD2 D:ASP68 2.5 16.9 1.0 OD1 D:ASP68 2.6 16.6 1.0 CG D:ASP68 2.9 16.6 1.0 CD D:GLU72 3.0 16.9 1.0 CD2 C:HIS41 3.2 12.7 1.0 CE1 C:HIS41 3.4 12.8 1.0 OE1 D:GLU72 3.4 17.1 1.0 OD1 C:ASP57 3.7 17.1 1.0 O C:HOH345 3.8 18.5 1.0 NZ C:LYS38 3.9 17.6 1.0 CG D:GLU72 4.2 15.6 1.0 CB D:ASP68 4.3 15.9 1.0 CG C:HIS41 4.4 12.8 1.0 CE1 C:HIS53 4.4 13.5 1.0 ND1 C:HIS41 4.4 12.6 1.0 NE2 C:HIS53 4.5 13.2 1.0 CG C:ASP57 4.5 16.0 1.0 OD2 C:ASP57 4.5 15.9 1.0 NE1 C:TRP42 4.6 13.1 1.0 CD1 C:TRP42 4.8 13.0 1.0 CE C:LYS38 4.9 17.1 1.0

Iron binding site 7 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:71.8 occ:0.33 OD1 D:ASP138 2.7 15.8 0.3 O D:HOH305 3.0 40.9 1.0 CG D:ASP138 3.5 15.6 0.3 OD2 D:ASP138 3.6 15.9 0.3 OD1 D:ASP138 4.4 15.6 0.7 CB D:ASP138 4.8 15.3 0.7 CG D:ASP138 4.8 15.3 0.7 CB D:ASP138 5.0 15.5 0.3

Iron binding site 8 out of 8 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer


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 the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 48 Iron Atoms Per Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe203 b:71.2 occ:0.23 O D:HOH351 2.7 30.2 1.0 O D:HOH348 3.1 32.2 1.0 OD2 D:ASP138 4.4 15.9 0.7 CE1 D:HIS141 4.5 14.5 1.0 OD1 D:ASP130 5.0 19.8 1.0 OD2 D:ASP130 5.0 22.0 1.0

S.M.Williams, D.Chatterji. Flexible Aspartates Propel Iron to the Ferroxidation Sites Along Pathways Stabilized By A Conserved Arginine in Dps Proteins From Mycobacterium Smegmatis Metallomics V. 9 685 2017.
ISSN: ESSN 1756-591X
PubMed: 28418062
DOI: 10.1039/C7MT00008A