Iron in PDB 4m32: Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis

The structure of Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m32 was solved by S.M.Williams, A.V.Chandran, M.S.Vijayabaskar, S.Roy, H.Balaram, S.Vishveshwara, M.Vijayan, D.Chatterji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.86
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.650, 89.650, 421.071, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.8

The structure of Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis (pdb code 4m32). 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m32:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Gated-Pore Mutant D138N of 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:71.2 occ:1.00 NE2 B:HIS41 2.8 9.8 1.0 O B:HOH391 2.8 21.9 1.0 OE2 A:GLU72 2.9 19.2 1.0 NE1 B:TRP42 3.3 10.4 1.0 CD2 B:HIS41 3.3 10.3 1.0 CG A:ASP68 3.3 13.7 1.0 OD1 A:ASP68 3.3 16.2 1.0 NZ B:LYS38 3.4 14.1 1.0 CB A:ASP68 3.5 12.0 1.0 CD A:GLU72 3.6 16.8 1.0 CD1 B:TRP42 3.8 10.4 1.0 OD2 A:ASP68 3.8 16.6 1.0 CG A:GLU72 3.8 14.1 1.0 CE1 B:HIS41 4.0 10.1 1.0 CA A:ASP68 4.0 11.4 1.0 O A:ASP68 4.4 11.3 1.0 CE2 B:TRP42 4.5 10.2 1.0 OE1 A:GLU72 4.5 19.0 1.0 CG B:HIS41 4.6 9.8 1.0 C A:ASP68 4.6 11.3 1.0 OD2 B:ASP57 4.6 11.0 1.0 OD1 B:ASP57 4.6 12.2 1.0 CE B:LYS38 4.6 14.1 1.0 CD B:LYS38 4.7 12.7 1.0 O A:HOH414 4.7 34.0 1.0 ND1 B:HIS41 4.9 10.0 1.0 O A:HOH390 4.9 20.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Gated-Pore Mutant D138N of 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:82.1 occ:1.00 OE1 B:GLU72 2.8 18.5 1.0 O A:HOH407 3.0 23.2 1.0 NE2 A:HIS41 3.2 9.9 1.0 OD1 B:ASP68 3.2 15.7 1.0 CG B:ASP68 3.2 13.6 1.0 NE1 A:TRP42 3.3 10.0 1.0 CB B:ASP68 3.3 12.0 1.0 CD B:GLU72 3.5 15.7 1.0 NZ A:LYS38 3.5 9.6 1.0 CG B:GLU72 3.6 13.1 1.0 CD2 A:HIS41 3.6 10.4 1.0 CA B:ASP68 3.8 11.5 1.0 CD1 A:TRP42 3.8 9.4 1.0 OD2 B:ASP68 3.9 15.1 1.0 O B:ASP68 4.2 11.1 1.0 C B:ASP68 4.3 11.2 1.0 CE1 A:HIS41 4.3 10.4 1.0 CE2 A:TRP42 4.5 9.7 1.0 OE2 B:GLU72 4.5 17.7 1.0 O B:HOH372 4.7 22.3 1.0 OD1 A:ASP57 4.7 11.5 1.0 CE A:LYS38 4.8 10.8 1.0 CD A:LYS38 4.8 10.1 1.0 OD2 A:ASP57 4.9 10.2 1.0 CG A:HIS41 4.9 10.0 1.0 CB B:GLU72 5.0 10.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Gated-Pore Mutant D138N of 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:76.1 occ:1.00 OE2 D:GLU72 2.6 21.2 1.0 NE2 C:HIS41 2.7 11.8 1.0 O C:HOH377 2.9 19.5 1.0 CD2 C:HIS41 3.2 11.9 1.0 CD D:GLU72 3.4 18.7 1.0 NE1 C:TRP42 3.5 13.5 1.0 NZ C:LYS38 3.5 15.4 1.0 CG D:ASP68 3.6 16.6 1.0 OD1 D:ASP68 3.7 19.7 1.0 CG D:GLU72 3.7 16.3 1.0 CB D:ASP68 3.7 15.0 1.0 CD1 C:TRP42 3.9 13.8 1.0 CE1 C:HIS41 3.9 11.8 1.0 OD2 D:ASP68 4.1 19.1 1.0 CA D:ASP68 4.3 14.5 1.0 OE1 D:GLU72 4.4 20.9 1.0 O D:HOH380 4.5 19.5 1.0 OD1 C:ASP57 4.5 14.0 1.0 CG C:HIS41 4.5 11.7 1.0 O D:ASP68 4.5 14.3 1.0 OD2 C:ASP57 4.7 13.4 1.0 CE2 C:TRP42 4.7 13.8 1.0 C D:ASP68 4.8 14.2 1.0 CE C:LYS38 4.8 16.2 1.0 ND1 C:HIS41 4.8 10.8 1.0 CD C:LYS38 4.9 14.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Gated-Pore Mutant D138N of 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:89.0 occ:1.00 O D:HOH394 2.7 21.5 1.0 OE2 C:GLU72 2.7 22.1 1.0 NE2 D:HIS41 3.0 12.4 1.0 CD2 D:HIS41 3.4 12.6 1.0 CG C:ASP68 3.4 14.6 1.0 CD C:GLU72 3.5 19.1 1.0 NE1 D:TRP42 3.5 12.9 1.0 OD1 C:ASP68 3.5 17.2 1.0 CB C:ASP68 3.6 13.2 1.0 NZ D:LYS38 3.6 13.3 1.0 CG C:GLU72 3.7 15.9 1.0 OD2 C:ASP68 3.9 16.2 1.0 CD1 D:TRP42 4.0 12.7 1.0 CA C:ASP68 4.2 12.7 1.0 CE1 D:HIS41 4.2 12.3 1.0 O C:ASP68 4.4 12.7 1.0 OE1 C:GLU72 4.5 20.4 1.0 OD1 D:ASP57 4.5 14.4 1.0 C C:ASP68 4.6 12.6 1.0 CE2 D:TRP42 4.7 13.0 1.0 O C:HOH374 4.7 19.3 1.0 CG D:HIS41 4.7 12.0 1.0 OD2 D:ASP57 4.8 14.0 1.0 CE D:LYS38 4.8 13.7 1.0 CD D:LYS38 5.0 12.8 1.0

S.M.Williams, A.V.Chandran, M.S.Vijayabaskar, S.Roy, H.Balaram, S.Vishveshwara, M.Vijayan, D.Chatterji. A Histidine Aspartate Ionic Lock Gates the Iron Passage in Miniferritins From Mycobacterium Smegmatis J.Biol.Chem. V. 289 11042 2014.
ISSN: ISSN 0021-9258
PubMed: 24573673
DOI: 10.1074/JBC.M113.524421