Iron in PDB 6unc: The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis

The structure of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis, PDB code: 6unc was solved by J.W.Mosior, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.86 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.190, 92.534, 183.626, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.2

The structure of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Iron atom in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis (pdb code 6unc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis, PDB code: 6unc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:28.3 occ:0.37 OD1 A:ASN82 2.2 39.8 1.0 O A:HOH506 2.2 41.0 1.0 O A:HOH531 2.2 36.1 1.0 OD2 A:ASP54 2.2 33.7 1.0 NE2 A:HIS208 2.3 35.9 1.0 ND1 A:HIS249 2.4 34.1 1.0 CG A:ASP54 3.0 41.8 1.0 CE1 A:HIS249 3.2 37.5 1.0 OD1 A:ASP54 3.2 38.4 1.0 CE1 A:HIS208 3.2 34.0 1.0 CG A:ASN82 3.2 32.3 1.0 CD2 A:HIS208 3.3 37.6 1.0 CG A:HIS249 3.5 31.3 1.0 MN A:MN401 3.6 38.8 1.0 CA A:HIS249 3.7 33.7 1.0 ND2 A:ASN82 3.8 32.4 1.0 CB A:HIS249 3.9 32.6 1.0 CD2 A:HIS83 3.9 38.9 1.0 OD2 A:ASP25 3.9 38.0 1.0 O A:HOH561 4.0 40.8 1.0 O A:HOH547 4.1 31.9 1.0 O A:HIS249 4.3 40.4 1.0 CB A:ASP54 4.3 36.5 1.0 N A:ASN82 4.3 35.6 1.0 ND1 A:HIS208 4.4 33.7 1.0 NE2 A:HIS249 4.4 31.8 1.0 CG A:HIS208 4.5 41.3 1.0 CB A:ASN82 4.5 28.9 1.0 O A:HOH571 4.5 48.0 1.0 C A:HIS249 4.5 36.9 1.0 NE2 A:HIS83 4.5 51.0 1.0 CD2 A:HIS249 4.6 26.3 1.0 N A:HIS249 4.7 37.0 1.0 CA A:ASN82 5.0 30.2 1.0

Iron binding site 2 out of 4 in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:35.1 occ:0.44 OD1 B:ASN82 2.1 41.8 1.0 O B:HOH546 2.2 48.6 1.0 O B:HOH526 2.2 42.1 1.0 OD2 B:ASP54 2.2 35.0 1.0 NE2 B:HIS208 2.3 33.7 1.0 ND1 B:HIS249 2.4 41.6 1.0 CG B:ASP54 3.0 40.2 1.0 CE1 B:HIS208 3.1 32.2 1.0 CG B:ASN82 3.2 39.5 1.0 CE1 B:HIS249 3.2 42.9 1.0 OD1 B:ASP54 3.3 37.5 1.0 CD2 B:HIS208 3.4 32.8 1.0 MN B:MN401 3.5 40.5 1.0 CG B:HIS249 3.5 43.3 1.0 ND2 B:ASN82 3.7 41.2 1.0 CA B:HIS249 3.7 35.5 1.0 O B:HOH569 3.7 44.0 1.0 OD1 B:ASP25 3.8 39.6 1.0 CB B:HIS249 3.9 31.0 1.0 ND1 B:HIS83 4.0 44.6 1.0 O B:HOH566 4.1 44.0 1.0 O B:HIS249 4.2 37.4 1.0 ND1 B:HIS208 4.3 32.0 1.0 CE1 B:HIS83 4.3 45.2 1.0 CB B:ASP54 4.3 39.4 1.0 O B:HOH592 4.4 44.4 1.0 N B:ASN82 4.4 41.2 1.0 NE2 B:HIS249 4.4 40.0 1.0 CB B:ASN82 4.5 32.6 1.0 CG B:HIS208 4.5 31.0 1.0 C B:HIS249 4.5 34.8 1.0 CD2 B:HIS249 4.6 37.9 1.0 N B:HIS249 4.7 34.5 1.0 CA B:ASN82 5.0 38.8 1.0

Iron binding site 3 out of 4 in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:38.4 occ:0.36 OD1 C:ASN82 2.1 53.8 1.0 O C:HOH517 2.1 53.5 1.0 O C:HOH505 2.2 46.7 1.0 OD2 C:ASP54 2.2 43.1 1.0 NE2 C:HIS208 2.3 51.6 1.0 ND1 C:HIS249 2.4 43.1 1.0 CG C:ASP54 3.0 49.2 1.0 CE1 C:HIS208 3.1 43.6 1.0 CG C:ASN82 3.2 47.9 1.0 CE1 C:HIS249 3.2 54.0 1.0 OD1 C:ASP54 3.2 46.1 1.0 CD2 C:HIS208 3.4 44.8 1.0 MN C:MN401 3.5 52.0 1.0 CG C:HIS249 3.5 46.8 1.0 ND2 C:ASN82 3.7 52.2 1.0 CA C:HIS249 3.8 42.3 1.0 O C:HOH531 3.9 51.1 1.0 OD1 C:ASP25 3.9 51.6 1.0 CB C:HIS249 3.9 40.3 1.0 ND1 C:HIS83 3.9 55.6 1.0 O C:HOH541 4.2 50.1 1.0 CE1 C:HIS83 4.3 60.3 1.0 O C:HIS249 4.3 46.2 1.0 CB C:ASP54 4.3 51.4 1.0 O C:HOH544 4.3 40.7 1.0 ND1 C:HIS208 4.3 48.2 1.0 N C:ASN82 4.3 48.6 1.0 NE2 C:HIS249 4.4 53.4 1.0 CB C:ASN82 4.4 46.3 1.0 CG C:HIS208 4.5 44.3 1.0 C C:HIS249 4.6 44.3 1.0 CD2 C:HIS249 4.6 47.1 1.0 N C:HIS249 4.8 42.4 1.0 CA C:ASN82 4.9 51.0 1.0

Iron binding site 4 out of 4 in the The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Phosphopantetheinyl Hydrolase (Ppth) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:43.5 occ:0.32 OD1 D:ASN82 2.1 56.7 1.0 OD2 D:ASP54 2.2 49.5 1.0 O D:HOH511 2.2 59.6 1.0 O D:HOH504 2.2 55.9 1.0 NE2 D:HIS208 2.3 59.8 1.0 ND1 D:HIS249 2.3 54.6 1.0 CG D:ASP54 3.0 52.5 1.0 CE1 D:HIS208 3.1 50.9 1.0 CE1 D:HIS249 3.1 56.8 1.0 OD1 D:ASP54 3.2 50.8 1.0 CG D:ASN82 3.2 52.7 1.0 CD2 D:HIS208 3.4 56.6 1.0 CG D:HIS249 3.5 54.4 1.0 MN D:MN401 3.5 48.9 1.0 ND2 D:ASN82 3.7 42.9 1.0 CA D:HIS249 3.8 56.8 1.0 ND1 D:HIS83 3.8 51.1 1.0 O D:HOH517 3.9 38.3 1.0 CB D:HIS249 3.9 56.5 1.0 OD2 D:ASP25 4.0 48.9 1.0 CE1 D:HIS83 4.2 49.6 1.0 O D:HIS249 4.3 54.6 1.0 O D:HOH521 4.3 47.7 1.0 ND1 D:HIS208 4.3 51.1 1.0 CB D:ASP54 4.3 43.9 1.0 O D:HOH531 4.3 40.6 1.0 NE2 D:HIS249 4.3 49.3 1.0 N D:ASN82 4.4 52.8 1.0 CG D:HIS208 4.5 59.2 1.0 CB D:ASN82 4.5 51.9 1.0 CD2 D:HIS249 4.5 52.9 1.0 C D:HIS249 4.5 52.0 1.0 N D:HIS249 4.8 58.5 1.0 N D:HIS83 5.0 48.5 1.0 CA D:ASN82 5.0 46.7 1.0

J.Mosior, R.Bourland, S.Soma, C.Nathan, J.Sacchettini. Structural Insights Into Phosphopantetheinyl Hydrolase Ppth From Mycobacterium Tuberculosis. Protein Sci. V. 29 744 2020.
ISSN: ESSN 1469-896X
PubMed: 31886928
DOI: 10.1002/PRO.3813