Iron in PDB 1uvh: X-Ray Structure of Dps From Mycobacterium Smegmatis

The structure of X-Ray Structure of Dps From Mycobacterium Smegmatis, PDB code: 1uvh was solved by A.Ilari, P.Ceci, E.Falvo, E.Chiancone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40 / 2.8
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	124.300, 124.300, 304.650, 90.00, 90.00, 120.00
R / Rfree (%)	26 / 34

The binding sites of Iron atom in the X-Ray Structure of Dps From Mycobacterium Smegmatis (pdb code 1uvh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of Dps From Mycobacterium Smegmatis, PDB code: 1uvh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the X-Ray Structure of 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 X-Ray Structure of Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1162 b:56.1 occ:0.30 OE1 A:GLU70 1.2 58.4 1.0 OD2 A:ASP66 1.2 55.8 1.0 CD A:GLU70 2.4 57.9 1.0 CG A:ASP66 2.4 52.5 1.0 NE2 B:HIS39 2.8 63.7 1.0 CG A:GLU70 3.2 55.4 1.0 CE1 B:HIS39 3.2 63.8 1.0 CB A:ASP66 3.3 48.9 1.0 OE2 A:GLU70 3.4 56.1 1.0 OD1 A:ASP66 3.5 56.0 1.0 O B:HOH2002 3.5 53.7 1.0 NZ B:LYS36 3.8 40.5 1.0 CD2 B:HIS39 4.0 63.1 1.0 CA A:ASP66 4.2 48.0 1.0 CE3 B:TRP40 4.4 61.4 1.0 ND1 B:HIS39 4.4 62.5 1.0 NE2 B:HIS51 4.5 60.1 1.0 OD2 B:ASP55 4.5 52.8 1.0 CE B:LYS36 4.6 37.1 1.0 C A:ASP66 4.7 48.8 1.0 CB A:GLU70 4.7 53.5 1.0 O A:ASP66 4.7 48.4 1.0 CG B:HIS39 4.8 58.7 1.0

Iron binding site 2 out of 4 in the X-Ray Structure of 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 X-Ray Structure of Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1162 b:56.1 occ:0.30 OE1 B:GLU70 1.3 57.7 1.0 OD2 B:ASP66 1.4 52.9 1.0 NE2 A:HIS39 2.0 60.6 1.0 CD B:GLU70 2.4 58.5 1.0 CG B:ASP66 2.6 49.9 1.0 CE1 A:HIS39 2.7 60.4 1.0 CD2 A:HIS39 3.2 59.1 1.0 CG B:GLU70 3.2 55.3 1.0 OD1 B:ASP66 3.3 54.3 1.0 OE2 B:GLU70 3.5 58.0 1.0 CB B:ASP66 3.7 45.9 1.0 NZ A:LYS36 3.8 43.6 1.0 ND1 A:HIS39 3.9 56.9 1.0 CE3 A:TRP40 4.1 61.3 1.0 CG A:HIS39 4.2 56.1 1.0 NE2 A:HIS51 4.3 58.7 1.0 CA B:ASP66 4.4 44.7 1.0 O B:ASP66 4.6 45.0 1.0 OD2 A:ASP55 4.7 56.9 1.0 CB B:GLU70 4.7 53.0 1.0 CZ3 A:TRP40 4.8 62.5 1.0 C B:ASP66 4.8 45.6 1.0 CB A:TRP40 4.9 58.6 1.0 OD1 A:ASP55 4.9 52.0 1.0 CE A:LYS36 5.0 42.8 1.0

Iron binding site 3 out of 4 in the X-Ray Structure of 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 X-Ray Structure of Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1162 b:55.6 occ:0.30 OE1 C:GLU70 1.2 58.5 1.0 OD2 C:ASP66 1.3 55.0 1.0 CD C:GLU70 2.3 57.1 1.0 CG C:ASP66 2.5 53.4 1.0 OD1 C:ASP66 3.1 60.0 1.0 NE2 D:HIS39 3.1 60.6 1.0 CG C:GLU70 3.2 54.1 1.0 OE2 C:GLU70 3.2 57.5 1.0 CE1 D:HIS39 3.4 60.7 1.0 CB C:ASP66 3.7 49.1 1.0 CD2 D:HIS39 4.2 60.9 1.0 CE1 D:HIS51 4.3 57.6 1.0 NE2 D:HIS51 4.3 57.3 1.0 ND1 D:HIS39 4.5 59.9 1.0 CA C:ASP66 4.5 48.3 1.0 CE3 D:TRP40 4.5 60.1 1.0 O C:ASP66 4.6 49.0 1.0 CB C:GLU70 4.6 52.5 1.0 C C:ASP66 4.8 48.9 1.0 CG D:HIS39 4.9 57.1 1.0

Iron binding site 4 out of 4 in the X-Ray Structure of 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 X-Ray Structure of Dps From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1162 b:55.8 occ:0.30 OE1 D:GLU70 1.3 59.0 1.0 OD2 D:ASP66 1.3 55.1 1.0 CD D:GLU70 2.4 60.4 1.0 CG D:ASP66 2.5 50.1 1.0 NE2 C:HIS39 3.0 57.6 1.0 CG D:GLU70 3.3 56.7 1.0 OE2 D:GLU70 3.4 60.6 1.0 CB D:ASP66 3.4 46.3 1.0 OD1 D:ASP66 3.5 52.1 1.0 CE1 C:HIS39 3.8 56.2 1.0 NZ C:LYS36 3.9 38.3 1.0 CD2 C:HIS39 4.0 56.8 1.0 CA D:ASP66 4.3 45.3 1.0 O D:ASP66 4.5 46.2 1.0 CE C:LYS36 4.6 35.4 1.0 CE1 C:HIS51 4.6 61.2 1.0 C D:ASP66 4.6 46.6 1.0 OD2 C:ASP55 4.6 51.4 1.0 CE3 C:TRP40 4.6 62.4 1.0 CB D:GLU70 4.7 53.7 1.0 NE2 C:HIS51 4.9 60.0 1.0

P.Ceci, A.Ilari, E.Falvo, L.Giangiacomo, E.Chiancone. Reassessment of Protein Stability, Dna Binding, and Protection of Mycobacterium Smegmatis Dps. J.Biol.Chem. V. 280 34776 2005.
ISSN: ISSN 0021-9258
PubMed: 16030020
DOI: 10.1074/JBC.M502343200