Iron in PDB 5ww9: Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis

The structure of Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 5ww9 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)	30.00 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.950, 90.950, 421.065, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.4

The structure of Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis 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 R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis (pdb code 5ww9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 5ww9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:55.5 occ:1.00 OE2 A:GLU72 2.3 17.7 1.0 NE2 B:HIS41 2.3 8.0 1.0 OD1 A:ASP68 2.5 13.1 1.0 O B:HOH308 2.6 16.6 1.0 OD2 A:ASP68 2.7 13.8 1.0 CG A:ASP68 2.9 13.2 1.0 CD A:GLU72 3.2 16.4 1.0 CD2 B:HIS41 3.3 8.0 1.0 CE1 B:HIS41 3.3 8.0 1.0 NZ B:LYS38 3.8 8.2 1.0 O B:HOH348 4.0 14.2 1.0 CG A:GLU72 4.0 15.2 1.0 OE1 A:GLU72 4.0 16.8 1.0 OD1 B:ASP57 4.1 12.1 1.0 ND1 B:HIS41 4.4 8.1 1.0 CG B:HIS41 4.5 8.0 1.0 CB A:ASP68 4.5 12.4 1.0 NE1 B:TRP42 4.5 8.2 1.0 OD2 B:ASP57 4.5 12.0 1.0 CE1 B:HIS53 4.5 7.7 1.0 NE2 B:HIS53 4.5 7.7 1.0 CG B:ASP57 4.6 11.7 1.0 CD1 B:TRP42 4.6 8.2 1.0 CE B:LYS38 4.8 8.3 1.0 O A:HOH407 5.0 27.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:56.1 occ:1.00 O A:HOH301 2.2 18.5 1.0 NE1 A:TRP42 3.0 6.8 1.0 CG B:ASP68 3.0 14.5 1.0 OD1 B:ASP68 3.1 15.7 1.0 CB B:ASP68 3.1 13.4 1.0 NZ A:LYS38 3.2 9.0 1.0 OE1 B:GLU72 3.3 15.6 1.0 NE2 A:HIS41 3.4 6.8 1.0 O A:HOH331 3.5 17.8 1.0 CA B:ASP68 3.5 12.1 1.0 OD2 B:ASP68 3.6 15.9 1.0 CD2 A:HIS41 3.7 6.7 1.0 CD B:GLU72 3.7 13.2 1.0 CD1 A:TRP42 3.8 6.8 1.0 CG B:GLU72 3.8 11.7 1.0 O B:ASP68 3.9 11.7 1.0 C B:ASP68 4.1 11.6 1.0 CE2 A:TRP42 4.1 7.0 1.0 CE A:LYS38 4.2 9.0 1.0 CD A:LYS38 4.3 8.5 1.0 O B:HOH412 4.4 24.3 1.0 CZ2 A:TRP42 4.6 7.0 1.0 OE2 B:GLU72 4.7 12.9 1.0 CE1 A:HIS41 4.7 6.8 1.0 N B:ASP68 4.8 11.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:60.0 occ:1.00 OE2 C:GLU72 2.2 17.8 1.0 NE2 D:HIS41 2.3 10.2 1.0 O D:HOH304 2.4 22.4 1.0 OD2 C:ASP68 2.7 14.8 1.0 OD1 C:ASP68 2.7 14.0 1.0 CG C:ASP68 3.1 13.9 1.0 CD C:GLU72 3.1 16.6 1.0 CE1 D:HIS41 3.2 10.2 1.0 CD2 D:HIS41 3.4 10.1 1.0 OD1 D:ASP57 3.7 11.7 1.0 OE1 C:GLU72 3.7 16.3 1.0 O D:HOH339 3.8 24.5 1.0 NZ D:LYS38 3.8 11.8 1.0 CG C:GLU72 4.2 15.5 1.0 ND1 D:HIS41 4.3 10.0 1.0 OD2 D:ASP57 4.4 11.7 1.0 CG D:ASP57 4.4 11.5 1.0 CG D:HIS41 4.5 10.1 1.0 NE2 D:HIS53 4.5 8.9 1.0 CE1 D:HIS53 4.5 8.9 1.0 CB C:ASP68 4.6 13.0 1.0 NE1 D:TRP42 4.7 9.2 1.0 O D:HOH419 4.7 25.1 1.0 CD1 D:TRP42 4.9 9.2 1.0 CE D:LYS38 4.9 11.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 R73E Mutant of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:68.4 occ:1.00 OE2 D:GLU72 2.3 19.6 1.0 NE2 C:HIS41 2.4 9.4 1.0 O C:HOH304 2.6 18.3 1.0 OD2 D:ASP68 2.6 15.1 1.0 OD1 D:ASP68 2.8 14.2 1.0 CG D:ASP68 3.1 14.3 1.0 CD D:GLU72 3.1 18.3 1.0 CE1 C:HIS41 3.4 9.2 1.0 CD2 C:HIS41 3.4 9.3 1.0 OE1 D:GLU72 3.6 19.0 1.0 NZ C:LYS38 3.7 10.7 1.0 O C:HOH359 3.7 21.2 1.0 OD1 C:ASP57 3.9 12.4 1.0 CG D:GLU72 4.1 16.6 1.0 ND1 C:HIS41 4.5 9.2 1.0 CE1 C:HIS53 4.5 8.9 1.0 OD2 C:ASP57 4.5 12.4 1.0 CG C:HIS41 4.5 9.2 1.0 CG C:ASP57 4.5 12.0 1.0 NE2 C:HIS53 4.6 9.1 1.0 CB D:ASP68 4.6 13.6 1.0 NE1 C:TRP42 4.7 9.2 1.0 CD1 C:TRP42 4.8 9.2 1.0 O D:HOH394 4.9 31.5 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