Iron in PDB 4s1c: Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain

The structure of Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain, PDB code: 4s1c was solved by S.Luo, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.60 / 2.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	116.562, 116.562, 91.783, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 23.1

The binding sites of Iron atom in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain (pdb code 4s1c). 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 L. Monocytogenes Phosphodiesterase Pgph Hd Domain, PDB code: 4s1c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain


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 L. Monocytogenes Phosphodiesterase Pgph Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe801 b:29.0 occ:1.00 O D:HOH965 1.8 22.5 1.0 NE2 D:HIS605 2.2 30.5 1.0 NE2 D:HIS580 2.2 27.8 1.0 OD1 D:ASP544 2.3 25.9 1.0 NE2 D:HIS604 2.3 28.0 1.0 CD2 D:HIS605 3.1 26.7 1.0 CE1 D:HIS580 3.2 29.4 1.0 CE1 D:HIS605 3.2 23.9 1.0 CD2 D:HIS604 3.2 25.6 1.0 CD2 D:HIS580 3.2 29.4 1.0 CG D:ASP544 3.3 26.9 1.0 CE1 D:HIS604 3.3 24.3 1.0 OD2 D:ASP544 3.6 24.1 1.0 FE D:FE802 3.7 28.8 1.0 CD2 D:HIS543 4.2 27.2 1.0 OD2 D:ASP648 4.2 29.1 1.0 CE D:LYS547 4.3 23.6 1.0 ND1 D:HIS605 4.3 26.9 1.0 CG D:HIS605 4.3 25.4 1.0 ND1 D:HIS580 4.3 26.8 1.0 NE2 D:HIS543 4.4 26.5 1.0 CG D:HIS580 4.4 29.0 1.0 NZ D:LYS547 4.4 22.1 1.0 ND1 D:HIS604 4.4 30.8 1.0 CG D:HIS604 4.4 28.3 1.0 CB D:ASP544 4.6 23.1 1.0 CA D:ASP544 4.9 26.3 1.0 OD1 D:ASP648 4.9 31.2 1.0 CG D:ASP648 4.9 29.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain


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 L. Monocytogenes Phosphodiesterase Pgph Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe802 b:28.8 occ:1.00 OD1 D:ASP648 2.1 31.2 1.0 O D:HOH965 2.2 22.5 1.0 OD2 D:ASP544 2.2 24.1 1.0 NE2 D:HIS543 2.3 26.5 1.0 NE2 D:HIS514 2.3 27.3 1.0 CG D:ASP648 3.0 29.9 1.0 CG D:ASP544 3.0 26.9 1.0 CE1 D:HIS543 3.1 26.5 1.0 CD2 D:HIS514 3.2 24.8 1.0 OD2 D:ASP648 3.2 29.1 1.0 CE1 D:HIS514 3.3 24.6 1.0 CD2 D:HIS543 3.3 27.2 1.0 OD1 D:ASP544 3.4 25.9 1.0 FE D:FE801 3.7 29.0 1.0 NZ D:LYS547 4.1 22.1 1.0 CB D:ASP544 4.2 23.1 1.0 ND1 D:HIS543 4.3 27.4 1.0 CB D:ASP648 4.3 27.4 1.0 ND1 D:HIS514 4.4 24.0 1.0 CG D:HIS514 4.4 24.1 1.0 CG D:HIS543 4.4 31.7 1.0 NE2 D:HIS604 4.6 28.0 1.0 CD2 D:HIS604 4.7 25.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain


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 L. Monocytogenes Phosphodiesterase Pgph Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:29.1 occ:1.00 O A:HOH955 2.0 24.9 1.0 OD1 A:ASP648 2.0 30.9 1.0 OD2 A:ASP544 2.1 22.5 1.0 NE2 A:HIS543 2.3 25.6 1.0 NE2 A:HIS514 2.3 28.2 1.0 CG A:ASP648 3.0 31.3 1.0 CG A:ASP544 3.0 28.2 1.0 CE1 A:HIS543 3.2 26.2 1.0 CD2 A:HIS514 3.2 24.6 1.0 CE1 A:HIS514 3.2 25.5 1.0 CD2 A:HIS543 3.2 26.2 1.0 OD2 A:ASP648 3.3 30.6 1.0 OD1 A:ASP544 3.4 25.8 1.0 FE A:FE802 3.7 30.1 1.0 NZ A:LYS547 4.2 22.5 1.0 CB A:ASP544 4.2 23.1 1.0 ND1 A:HIS543 4.3 27.4 1.0 CB A:ASP648 4.3 27.6 1.0 ND1 A:HIS514 4.3 23.9 1.0 CG A:HIS543 4.4 31.1 1.0 CG A:HIS514 4.4 22.5 1.0 NE2 A:HIS604 4.6 31.4 1.0 CD2 A:HIS604 4.7 26.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain


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 L. Monocytogenes Phosphodiesterase Pgph Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:30.1 occ:1.00 O A:HOH955 1.9 24.9 1.0 NE2 A:HIS605 2.2 30.1 1.0 OD1 A:ASP544 2.2 25.8 1.0 NE2 A:HIS580 2.2 28.2 1.0 NE2 A:HIS604 2.3 31.4 1.0 CD2 A:HIS605 3.1 25.3 1.0 CE1 A:HIS605 3.2 23.8 1.0 CD2 A:HIS604 3.2 26.7 1.0 CE1 A:HIS580 3.2 26.8 1.0 CG A:ASP544 3.2 28.2 1.0 CD2 A:HIS580 3.3 29.0 1.0 CE1 A:HIS604 3.3 24.1 1.0 OD2 A:ASP544 3.5 22.5 1.0 FE A:FE801 3.7 29.1 1.0 CD2 A:HIS543 4.2 26.2 1.0 ND1 A:HIS605 4.2 26.3 1.0 OD2 A:ASP648 4.2 30.6 1.0 CG A:HIS605 4.3 23.4 1.0 CE A:LYS547 4.3 24.8 1.0 ND1 A:HIS580 4.3 25.7 1.0 CG A:HIS604 4.4 29.9 1.0 ND1 A:HIS604 4.4 32.1 1.0 CG A:HIS580 4.4 29.7 1.0 NE2 A:HIS543 4.4 25.6 1.0 NZ A:LYS547 4.5 22.5 1.0 CB A:ASP544 4.6 23.1 1.0 CA A:ASP544 4.9 25.1 1.0 OD1 A:ASP648 4.9 30.9 1.0 O A:HIS543 4.9 27.3 1.0 CG A:ASP648 5.0 31.3 1.0

T.N.Huynh, S.Luo, D.Pensinger, J.D.Sauer, L.Tong, J.J.Woodward. An Hd-Domain Phosphodiesterase Mediates Cooperative Hydrolysis of C-Di-Amp to Affect Bacterial Growth and Virulence. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25583510
DOI: 10.1073/PNAS.1416485112