Iron in PDB 4m35: Crystal Structure of Gated-Pore Mutant H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis

The structure of Crystal Structure of Gated-Pore Mutant H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m35 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 / 2.05
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.230, 90.230, 420.312, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.6

The structure of Crystal Structure of Gated-Pore Mutant H126/141D of 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 Gated-Pore Mutant H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis (pdb code 4m35). 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 H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m35:
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 H126/141D 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 H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:68.0 occ:1.00 NE2 B:HIS41 2.6 7.2 1.0 O B:HOH398 2.7 27.7 1.0 OD2 A:ASP68 2.8 15.2 1.0 OE2 A:GLU72 3.0 14.0 1.0 OD1 B:ASP57 3.2 12.0 1.0 OD1 A:ASP68 3.2 14.2 1.0 CE1 B:HIS41 3.4 7.8 1.0 CG A:ASP68 3.4 12.8 1.0 CD A:GLU72 3.5 12.5 1.0 OE1 A:GLU72 3.7 13.1 1.0 CD2 B:HIS41 3.7 7.1 1.0 NZ B:LYS38 4.0 9.3 1.0 CG B:ASP57 4.1 10.8 1.0 OD2 B:ASP57 4.3 11.1 1.0 O B:HOH336 4.4 17.3 1.0 NE2 B:HIS53 4.5 10.4 1.0 ND1 B:HIS41 4.6 7.6 1.0 CG A:GLU72 4.7 10.8 1.0 CE1 B:HIS53 4.7 10.3 1.0 CG B:HIS41 4.8 7.9 1.0 CB A:ASP68 4.9 11.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Gated-Pore Mutant H126/141D 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 H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:84.0 occ:1.00 OD1 B:ASP68 2.7 14.9 1.0 NE2 A:HIS41 2.9 6.8 1.0 OE1 B:GLU72 2.9 13.8 1.0 OD1 A:ASP57 3.1 10.0 1.0 OD2 B:ASP68 3.4 13.2 1.0 CG B:ASP68 3.4 12.2 1.0 CE1 A:HIS41 3.6 7.0 1.0 CD B:GLU72 3.6 12.0 1.0 OE2 B:GLU72 3.8 13.4 1.0 NZ A:LYS38 3.9 9.1 1.0 CD2 A:HIS41 4.0 6.4 1.0 CG A:ASP57 4.1 9.0 1.0 OD2 A:ASP57 4.3 9.4 1.0 O A:HOH369 4.4 24.3 1.0 O B:HOH339 4.7 26.1 1.0 NE2 A:HIS53 4.7 8.1 1.0 CG B:GLU72 4.8 9.7 1.0 ND1 A:HIS41 4.8 6.5 1.0 CB B:ASP68 4.9 10.5 1.0 CE1 A:HIS53 4.9 7.3 1.0 CG A:HIS41 5.0 7.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Gated-Pore Mutant H126/141D 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 H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:74.7 occ:1.00 OD1 C:ASP68 2.6 14.3 1.0 NE2 D:HIS41 2.8 9.7 1.0 OE2 C:GLU72 3.0 14.2 1.0 OD2 C:ASP68 3.3 13.6 1.0 CG C:ASP68 3.3 12.8 1.0 OD1 D:ASP57 3.3 11.6 1.0 CD C:GLU72 3.5 12.7 1.0 OE1 C:GLU72 3.6 13.7 1.0 CE1 D:HIS41 3.8 9.0 1.0 CD2 D:HIS41 3.8 9.3 1.0 NZ D:LYS38 3.9 12.0 1.0 CG D:ASP57 4.3 10.6 1.0 O D:HOH357 4.6 22.7 1.0 OD2 D:ASP57 4.6 12.0 1.0 NE2 D:HIS53 4.6 9.8 1.0 CG C:GLU72 4.7 11.1 1.0 CB C:ASP68 4.8 11.4 1.0 ND1 D:HIS41 4.9 8.9 1.0 CE1 D:HIS53 4.9 10.5 1.0 CG D:HIS41 4.9 9.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Gated-Pore Mutant H126/141D 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 H126/141D of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:75.2 occ:1.00 OD1 D:ASP68 2.6 16.6 1.0 NE2 C:HIS41 2.7 9.2 1.0 OE2 D:GLU72 2.8 13.5 1.0 OD2 D:ASP68 3.3 14.6 1.0 CD D:GLU72 3.3 13.0 1.0 CG D:ASP68 3.3 14.5 1.0 OE1 D:GLU72 3.3 13.9 1.0 OD1 C:ASP57 3.5 12.5 1.0 CE1 C:HIS41 3.6 9.2 1.0 CD2 C:HIS41 3.7 8.9 1.0 NZ C:LYS38 4.0 12.8 1.0 CG C:ASP57 4.4 11.1 1.0 CG D:GLU72 4.5 11.5 1.0 OD2 C:ASP57 4.5 11.8 1.0 NE2 C:HIS53 4.6 9.0 1.0 CE1 C:HIS53 4.7 8.8 1.0 ND1 C:HIS41 4.7 9.8 1.0 CB D:ASP68 4.8 13.2 1.0 CG C:HIS41 4.8 9.1 1.0 O C:HOH372 4.8 22.8 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