Iron in PDB 4m34: Crystal Structure of Gated-Pore Mutant D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis

The structure of Crystal Structure of Gated-Pore Mutant D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m34 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 (°)	89.490, 89.490, 420.400, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.7

The structure of Crystal Structure of Gated-Pore Mutant D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Crystal Structure of Gated-Pore Mutant D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis (pdb code 4m34). 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 D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m34:
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 D138H 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 D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:43.3 occ:1.00 O A:HOH382 2.1 18.9 1.0 O B:HOH368 2.2 15.3 1.0 OE2 A:GLU72 2.2 12.3 1.0 NE2 B:HIS41 2.3 5.5 1.0 OD2 A:ASP68 2.4 10.7 1.0 OD1 A:ASP68 2.5 10.1 1.0 CG A:ASP68 2.8 9.6 1.0 CD A:GLU72 3.2 10.2 1.0 CE1 B:HIS41 3.2 6.1 1.0 CD2 B:HIS41 3.3 5.3 1.0 OE1 A:GLU72 3.7 10.9 1.0 OD2 B:ASP57 3.8 8.6 1.0 NZ B:LYS38 3.9 7.3 1.0 O B:HOH353 4.0 16.5 1.0 CG A:GLU72 4.2 8.2 1.0 CB A:ASP68 4.3 8.5 1.0 CE1 B:HIS53 4.4 7.2 1.0 ND1 B:HIS41 4.4 6.2 1.0 OD1 B:ASP57 4.4 8.5 1.0 CG B:ASP57 4.4 7.6 1.0 CG B:HIS41 4.4 6.2 1.0 NE2 B:HIS53 4.5 7.0 1.0 NE1 B:TRP42 4.6 5.6 1.0 O A:HOH338 4.7 20.1 1.0 CD1 B:TRP42 4.9 4.8 1.0 CE B:LYS38 5.0 7.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Gated-Pore Mutant D138H 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 D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:50.5 occ:1.00 OE1 B:GLU72 2.1 12.1 1.0 O A:HOH383 2.3 12.8 1.0 OD1 B:ASP68 2.4 11.8 1.0 NE2 A:HIS41 2.5 5.5 1.0 OD2 B:ASP68 2.8 10.3 1.0 CG B:ASP68 2.9 10.1 1.0 CD B:GLU72 3.0 10.3 1.0 CE1 A:HIS41 3.3 5.3 1.0 O B:HOH369 3.4 24.7 1.0 OE2 B:GLU72 3.5 10.5 1.0 CD2 A:HIS41 3.6 5.3 1.0 OD2 A:ASP57 3.7 8.7 1.0 NZ A:LYS38 3.8 7.6 1.0 CG B:GLU72 4.2 8.3 1.0 NE2 A:HIS53 4.4 6.8 1.0 CE1 A:HIS53 4.4 6.8 1.0 CB B:ASP68 4.4 8.7 1.0 CG A:ASP57 4.4 7.7 1.0 ND1 A:HIS41 4.5 5.5 1.0 OD1 A:ASP57 4.5 8.0 1.0 CG A:HIS41 4.6 5.8 1.0 NE1 A:TRP42 4.8 5.3 1.0 O A:HOH352 4.9 19.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Gated-Pore Mutant D138H 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 D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:37.9 occ:1.00 O C:HOH368 2.1 22.8 1.0 OE2 C:GLU72 2.2 13.0 1.0 O D:HOH380 2.3 16.5 1.0 NE2 D:HIS41 2.3 7.7 1.0 OD2 C:ASP68 2.4 10.9 1.0 OD1 C:ASP68 2.5 9.5 1.0 CG C:ASP68 2.8 9.7 1.0 CD C:GLU72 3.0 11.6 1.0 CD2 D:HIS41 3.2 7.7 1.0 CE1 D:HIS41 3.4 7.6 1.0 OE1 C:GLU72 3.5 13.1 1.0 O D:HOH306 3.9 14.6 1.0 OD2 D:ASP57 3.9 9.6 1.0 NZ D:LYS38 4.1 9.7 1.0 CG C:GLU72 4.1 9.8 1.0 CB C:ASP68 4.3 8.9 1.0 CE1 D:HIS53 4.3 8.0 1.0 CG D:HIS41 4.4 7.6 1.0 NE2 D:HIS53 4.4 7.7 1.0 ND1 D:HIS41 4.5 7.6 1.0 CG D:ASP57 4.6 8.2 1.0 NE1 D:TRP42 4.6 7.9 1.0 OD1 D:ASP57 4.6 8.8 1.0 CD1 D:TRP42 4.8 7.2 1.0 O D:HOH357 4.9 18.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Gated-Pore Mutant D138H 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 D138H of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:39.7 occ:1.00 O D:HOH381 2.2 20.8 1.0 OE2 D:GLU72 2.2 9.6 1.0 O C:HOH369 2.3 16.4 1.0 NE2 C:HIS41 2.3 6.8 1.0 OD2 D:ASP68 2.4 9.9 1.0 OD1 D:ASP68 2.5 9.7 1.0 CG D:ASP68 2.8 9.5 1.0 CD D:GLU72 3.0 8.9 1.0 CD2 C:HIS41 3.2 7.4 1.0 CE1 C:HIS41 3.4 7.1 1.0 OE1 D:GLU72 3.4 9.1 1.0 O D:HOH382 3.8 20.4 1.0 NZ C:LYS38 3.9 11.9 1.0 OD2 C:ASP57 3.9 11.3 1.0 CG D:GLU72 4.2 8.0 1.0 CB D:ASP68 4.3 8.7 1.0 CG C:HIS41 4.4 7.1 1.0 CE1 C:HIS53 4.4 8.1 1.0 O D:HOH364 4.4 31.8 1.0 ND1 C:HIS41 4.5 6.5 1.0 NE2 C:HIS53 4.5 7.0 1.0 CG C:ASP57 4.5 9.2 1.0 OD1 C:ASP57 4.5 9.7 1.0 NE1 C:TRP42 4.6 7.0 1.0 O D:HOH354 4.7 22.9 1.0 CD1 C:TRP42 4.8 7.2 1.0 CE C:LYS38 4.9 11.8 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