Iron in PDB 4s1b: Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp

The structure of Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp, PDB code: 4s1b 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)	24.69 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	124.286, 124.286, 58.019, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.2

The binding sites of Iron atom in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp (pdb code 4s1b). 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 in Complex with Cyclic-Di-Amp, PDB code: 4s1b:
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 in Complex with Cyclic-Di-Amp


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 in Complex with Cyclic-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:21.8 occ:1.00 O A:HOH972 2.1 20.4 1.0 O1P A:2BA803 2.1 21.6 1.0 OD1 A:ASP544 2.3 20.0 1.0 NE2 A:HIS604 2.3 21.9 1.0 NE2 A:HIS580 2.3 23.6 1.0 NE2 A:HIS605 2.4 23.2 1.0 CD2 A:HIS604 3.2 19.7 1.0 CE1 A:HIS580 3.2 22.4 1.0 CG A:ASP544 3.2 22.4 1.0 CD2 A:HIS605 3.3 19.4 1.0 CE1 A:HIS605 3.3 22.3 1.0 CE1 A:HIS604 3.3 20.3 1.0 P A:2BA803 3.3 25.4 1.0 CD2 A:HIS580 3.4 22.1 1.0 OD2 A:ASP544 3.5 18.3 1.0 FE A:FE802 3.6 19.3 1.0 O2P A:2BA803 3.9 22.5 1.0 O5' A:2BA803 3.9 24.3 1.0 CD2 A:HIS543 4.2 19.6 1.0 CE A:LYS547 4.3 23.0 1.0 ND1 A:HIS580 4.3 23.6 1.0 OD2 A:ASP648 4.4 18.2 1.0 ND1 A:HIS605 4.4 21.3 1.0 CG A:HIS604 4.4 18.3 1.0 CG A:HIS605 4.4 23.6 1.0 ND1 A:HIS604 4.4 19.7 1.0 NZ A:LYS547 4.4 22.7 1.0 CG A:HIS580 4.5 21.8 1.0 NE2 A:HIS543 4.5 20.6 1.0 CB A:ASP544 4.6 20.4 1.0 O3'1 A:2BA803 4.7 21.7 1.0 C5'1 A:2BA803 4.7 23.6 1.0 CA A:ASP544 4.9 20.0 1.0 OD1 A:ASP648 4.9 18.1 1.0 C4'1 A:2BA803 4.9 24.1 1.0 CG A:ASP648 5.0 20.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp


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 in Complex with Cyclic-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:19.3 occ:1.00 O A:HOH972 2.0 20.4 1.0 OD1 A:ASP648 2.2 18.1 1.0 NE2 A:HIS543 2.2 20.6 1.0 O2P A:2BA803 2.2 22.5 1.0 NE2 A:HIS514 2.2 20.0 1.0 OD2 A:ASP544 2.2 18.3 1.0 CG A:ASP648 3.1 20.2 1.0 CG A:ASP544 3.1 22.4 1.0 CD2 A:HIS543 3.1 19.6 1.0 CE1 A:HIS514 3.2 20.0 1.0 CD2 A:HIS514 3.2 20.8 1.0 CE1 A:HIS543 3.3 21.0 1.0 P A:2BA803 3.3 25.4 1.0 OD2 A:ASP648 3.4 18.2 1.0 OD1 A:ASP544 3.5 20.0 1.0 FE A:FE801 3.6 21.8 1.0 O1P A:2BA803 3.7 21.6 1.0 O5' A:2BA803 4.0 24.3 1.0 NZ A:LYS547 4.2 22.7 1.0 ND1 A:HIS514 4.3 18.4 1.0 CG A:HIS543 4.3 20.6 1.0 CB A:ASP544 4.3 20.4 1.0 ND1 A:HIS543 4.3 19.3 1.0 CG A:HIS514 4.4 23.2 1.0 CB A:ASP648 4.4 19.2 1.0 O A:HOH1004 4.4 35.0 1.0 O3'1 A:2BA803 4.6 21.7 1.0 C5' A:2BA803 4.6 22.8 1.0 NE2 A:HIS604 4.7 21.9 1.0 CD2 A:HIS604 4.8 19.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp


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 in Complex with Cyclic-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe801 b:17.0 occ:1.00 O D:HOH968 2.0 19.7 1.0 O1P D:2BA803 2.2 16.6 1.0 OD1 D:ASP544 2.3 15.1 1.0 NE2 D:HIS605 2.3 15.7 1.0 NE2 D:HIS580 2.3 17.2 1.0 NE2 D:HIS604 2.4 16.2 1.0 CD2 D:HIS605 3.1 16.6 1.0 CG D:ASP544 3.2 18.9 1.0 CE1 D:HIS580 3.2 15.9 1.0 CD2 D:HIS604 3.2 14.5 1.0 CE1 D:HIS605 3.3 18.4 1.0 CD2 D:HIS580 3.3 16.4 1.0 P D:2BA803 3.4 18.4 1.0 OD2 D:ASP544 3.4 17.6 1.0 CE1 D:HIS604 3.4 17.1 1.0 FE D:FE802 3.6 18.4 1.0 O5' D:2BA803 3.9 20.6 1.0 O2P D:2BA803 3.9 19.2 1.0 CD2 D:HIS543 4.2 15.6 1.0 CG D:HIS605 4.3 18.5 1.0 CE D:LYS547 4.3 17.9 1.0 ND1 D:HIS605 4.3 17.4 1.0 ND1 D:HIS580 4.3 18.3 1.0 OD2 D:ASP648 4.4 18.6 1.0 CG D:HIS604 4.4 15.1 1.0 CG D:HIS580 4.4 18.6 1.0 NE2 D:HIS543 4.5 15.5 1.0 ND1 D:HIS604 4.5 16.2 1.0 NZ D:LYS547 4.6 18.8 1.0 CB D:ASP544 4.6 17.6 1.0 C5'1 D:2BA803 4.7 17.7 1.0 O3'1 D:2BA803 4.7 17.5 1.0 OD1 D:ASP648 4.9 17.9 1.0 CA D:ASP544 4.9 15.2 1.0 C4'1 D:2BA803 4.9 18.3 1.0 CG D:ASP648 5.0 19.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of L. Monocytogenes Phosphodiesterase Pgph Hd Domain in Complex with Cyclic-Di-Amp


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 in Complex with Cyclic-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe802 b:18.4 occ:1.00 O D:HOH968 2.0 19.7 1.0 OD1 D:ASP648 2.2 17.9 1.0 NE2 D:HIS514 2.2 20.0 1.0 OD2 D:ASP544 2.2 17.6 1.0 NE2 D:HIS543 2.2 15.5 1.0 O2P D:2BA803 2.3 19.2 1.0 CE1 D:HIS514 3.1 20.2 1.0 CG D:ASP648 3.1 19.0 1.0 CD2 D:HIS543 3.1 15.6 1.0 CG D:ASP544 3.1 18.9 1.0 CE1 D:HIS543 3.2 17.4 1.0 CD2 D:HIS514 3.3 20.8 1.0 P D:2BA803 3.3 18.4 1.0 OD2 D:ASP648 3.4 18.6 1.0 OD1 D:ASP544 3.5 15.1 1.0 FE D:FE801 3.6 17.0 1.0 O1P D:2BA803 3.6 16.6 1.0 O5' D:2BA803 4.1 20.6 1.0 ND1 D:HIS514 4.2 17.0 1.0 NZ D:LYS547 4.3 18.8 1.0 CG D:HIS543 4.3 18.9 1.0 ND1 D:HIS543 4.3 16.4 1.0 CB D:ASP544 4.3 17.6 1.0 CG D:HIS514 4.4 17.9 1.0 CB D:ASP648 4.4 18.7 1.0 O D:HOH929 4.4 28.6 1.0 C5' D:2BA803 4.6 19.1 1.0 O3'1 D:2BA803 4.6 17.5 1.0 NE2 D:HIS604 4.7 16.2 1.0 CD2 D:HIS604 4.8 14.5 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