Iron in PDB 2z90: Crystal Structure of the Second Dps From Mycobacterium Smegmatis

The structure of Crystal Structure of the Second Dps From Mycobacterium Smegmatis, PDB code: 2z90 was solved by S.Roy, R.Saraswathi, D.Chatterji, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.008, 90.008, 421.522, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.7

The structure of Crystal Structure of the Second Dps 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 the Second Dps From Mycobacterium Smegmatis (pdb code 2z90). 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 the Second Dps From Mycobacterium Smegmatis, PDB code: 2z90:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Second Dps 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 the Second Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe162 b:49.4 occ:1.00 OE2 A:GLU72 2.0 26.2 1.0 NE2 B:HIS41 2.3 21.6 1.0 OD1 A:ASP68 2.4 29.9 1.0 O A:HOH244 2.4 25.9 1.0 OD2 A:ASP68 2.6 29.0 1.0 CG A:ASP68 2.8 28.8 1.0 CD2 B:HIS41 3.2 18.8 1.0 CD A:GLU72 3.2 24.1 1.0 CE1 B:HIS41 3.4 18.6 1.0 NZ B:LYS38 3.7 24.2 1.0 OD1 B:ASP57 3.7 27.4 1.0 OE1 A:GLU72 3.7 22.8 1.0 OD2 B:ASP57 4.3 23.4 1.0 CB A:ASP68 4.3 24.9 1.0 CG A:GLU72 4.3 22.2 1.0 CG B:HIS41 4.4 20.0 1.0 CG B:ASP57 4.4 24.3 1.0 O A:HOH246 4.4 40.5 1.0 ND1 B:HIS41 4.4 20.8 1.0 NE2 B:HIS53 4.5 25.2 1.0 CE1 B:HIS53 4.5 26.2 1.0 NE1 B:TRP42 4.5 20.2 1.0 CE B:LYS38 4.8 25.4 1.0 CD1 B:TRP42 4.9 21.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Second Dps 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 the Second Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe162 b:44.5 occ:1.00 OE1 B:GLU72 2.1 25.4 1.0 OD2 B:ASP68 2.3 24.3 1.0 O B:HOH258 2.4 41.3 1.0 NE2 A:HIS41 2.4 23.9 1.0 OD1 B:ASP68 2.5 22.2 1.0 CG B:ASP68 2.7 25.0 1.0 CD B:GLU72 3.0 24.8 1.0 CD2 A:HIS41 3.2 22.9 1.0 NZ A:LYS38 3.5 21.8 1.0 CE1 A:HIS41 3.5 21.9 1.0 OE2 B:GLU72 3.5 24.4 1.0 OD1 A:ASP57 3.7 29.2 1.0 CG B:GLU72 4.2 22.8 1.0 O B:HOH218 4.2 40.4 1.0 CB B:ASP68 4.2 23.1 1.0 NE2 A:HIS53 4.3 24.0 1.0 CE1 A:HIS53 4.4 22.7 1.0 OD2 A:ASP57 4.4 29.9 1.0 CG A:ASP57 4.4 29.1 1.0 CG A:HIS41 4.4 22.2 1.0 ND1 A:HIS41 4.5 23.9 1.0 NE1 A:TRP42 4.5 15.9 1.0 CD1 A:TRP42 4.8 16.7 1.0 CE A:LYS38 4.9 25.1 1.0 O B:ASP68 4.9 22.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Second Dps 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 the Second Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe162 b:45.9 occ:1.00 OE2 C:GLU72 2.2 28.9 1.0 NE2 D:HIS41 2.4 18.9 1.0 OD1 C:ASP68 2.4 30.9 1.0 OD2 C:ASP68 2.5 28.5 1.0 O C:HOH241 2.7 34.2 1.0 CG C:ASP68 2.8 29.1 1.0 CD C:GLU72 2.8 27.0 1.0 CD2 D:HIS41 3.1 20.8 1.0 OE1 C:GLU72 3.2 28.1 1.0 CE1 D:HIS41 3.5 19.6 1.0 CG C:GLU72 3.9 24.3 1.0 NZ D:LYS38 4.0 21.2 1.0 OD1 D:ASP57 4.0 22.9 1.0 CB C:ASP68 4.3 27.3 1.0 CG D:HIS41 4.4 21.0 1.0 CE1 D:HIS53 4.5 22.7 1.0 NE1 D:TRP42 4.5 22.6 1.0 NE2 D:HIS53 4.5 23.0 1.0 ND1 D:HIS41 4.5 21.9 1.0 OD2 D:ASP57 4.7 21.5 1.0 CG D:ASP57 4.7 22.3 1.0 CD1 D:TRP42 4.7 22.5 1.0 O C:ASP68 4.9 23.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Second Dps 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 the Second Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe162 b:46.5 occ:1.00 NE2 C:HIS41 2.3 25.5 1.0 OE2 D:GLU72 2.5 29.2 1.0 OD1 D:ASP68 2.5 23.2 1.0 OD2 D:ASP68 2.5 23.5 1.0 CG D:ASP68 2.8 24.2 1.0 CD2 C:HIS41 3.1 25.5 1.0 CD D:GLU72 3.2 27.4 1.0 CE1 C:HIS41 3.4 24.5 1.0 OE1 D:GLU72 3.7 27.4 1.0 O D:HOH249 3.7 56.3 1.0 OD1 C:ASP57 3.7 30.4 1.0 NZ C:LYS38 3.9 27.2 1.0 CG D:GLU72 4.1 25.9 1.0 NE1 C:TRP42 4.1 25.1 1.0 CG C:HIS41 4.3 24.2 1.0 CB D:ASP68 4.3 23.2 1.0 ND1 C:HIS41 4.4 25.5 1.0 CD1 C:TRP42 4.4 26.0 1.0 CE1 C:HIS53 4.5 26.1 1.0 CG C:ASP57 4.5 28.4 1.0 OD2 C:ASP57 4.5 25.9 1.0 NE2 C:HIS53 4.6 25.4 1.0 CE C:LYS38 4.9 29.0 1.0

S.Roy, R.Saraswathi, D.Chatterji, M.Vijayan. Structural Studies on the Second Mycobacterium Smegmatis Dps: Invariant and Variable Features of Structure, Assembly and Function. J.Mol.Biol. V. 375 948 2008.
ISSN: ISSN 0022-2836
PubMed: 18061613
DOI: 10.1016/J.JMB.2007.10.023