Iron in PDB 4mln: Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid

The structure of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid, PDB code: 4mln was solved by L.M.Van Staalduinen, F.R.Mcsorley, D.L.Zechel, Z.Jia, Montreal-Kingstonbacterial Structural Genomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.630, 74.910, 75.810, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.4

The binding sites of Iron atom in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid (pdb code 4mln). 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 of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid, PDB code: 4mln:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.7 occ:1.00 NE2 A:HIS58 2.1 23.1 1.0 OD1 A:ASP161 2.1 23.6 1.0 OD2 A:ASP59 2.1 22.0 1.0 O A:HOH301 2.1 28.4 1.0 O A:HOH347 2.1 26.5 1.0 NE2 A:HIS34 2.2 24.5 1.0 CG A:ASP161 2.9 28.1 1.0 CG A:ASP59 3.0 20.4 1.0 CE1 A:HIS58 3.0 23.6 1.0 CD2 A:HIS58 3.1 20.3 1.0 OD2 A:ASP161 3.2 32.1 1.0 CD2 A:HIS34 3.2 27.2 1.0 HAC A:ODV203 3.2 28.2 1.0 CE1 A:HIS34 3.2 26.8 1.0 OD1 A:ASP59 3.4 17.6 1.0 HAG A:ODV203 3.6 38.3 1.0 FE A:FE202 3.7 21.8 1.0 OAC A:ODV203 4.0 23.5 1.0 O A:HOH348 4.1 31.8 1.0 ND1 A:HIS58 4.1 20.4 1.0 CB A:ASP59 4.2 19.9 1.0 CG A:HIS58 4.2 17.8 1.0 CAG A:ODV203 4.2 31.9 1.0 CB A:ASP161 4.3 23.9 1.0 O A:HOH363 4.3 29.1 1.0 CG A:HIS34 4.3 24.7 1.0 ND1 A:HIS34 4.3 22.1 1.0 NE2 A:HIS104 4.7 21.6 1.0 CA A:ASP161 4.7 27.3 1.0 HAI A:ODV203 4.8 44.6 1.0 CD2 A:HIS104 4.8 24.6 1.0 O A:ASP161 4.9 30.8 1.0

Iron binding site 2 out of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:21.8 occ:1.00 HAC A:ODV203 1.6 28.2 1.0 O A:HOH301 2.1 28.4 1.0 NE2 A:HIS104 2.1 21.6 1.0 OD1 A:ASP59 2.2 17.6 1.0 OAC A:ODV203 2.2 23.5 1.0 NE2 A:HIS80 2.2 23.5 1.0 OAE A:ODV203 2.3 23.0 1.0 CAG A:ODV203 3.0 31.9 1.0 CD2 A:HIS104 3.1 24.6 1.0 PAH A:ODV203 3.1 25.6 1.0 CE1 A:HIS104 3.2 19.3 1.0 CG A:ASP59 3.2 20.4 1.0 CE1 A:HIS80 3.2 20.2 1.0 CD2 A:HIS80 3.2 21.3 1.0 HAG A:ODV203 3.2 38.3 1.0 OD2 A:ASP59 3.5 22.0 1.0 FE A:FE201 3.7 22.7 1.0 OAD A:ODV203 4.0 25.9 1.0 CD2 A:HIS58 4.0 20.3 1.0 NE2 A:HIS62 4.2 22.1 1.0 O A:HOH347 4.2 26.5 1.0 ND1 A:HIS104 4.2 25.9 1.0 OD2 A:ASP161 4.2 32.1 1.0 CG A:HIS104 4.3 23.2 1.0 OAB A:ODV203 4.3 31.1 1.0 ND1 A:HIS80 4.3 19.9 1.0 NE2 A:HIS58 4.4 23.1 1.0 CAF A:ODV203 4.4 33.7 1.0 CG A:HIS80 4.4 20.7 1.0 NH1 A:ARG158 4.4 30.6 1.0 HAH A:ODV203 4.5 40.5 1.0 CB A:ASP59 4.5 19.9 1.0 O A:HOH348 4.7 31.8 1.0 CG2 A:VAL105 4.8 25.6 1.0 HAJ A:ODV203 4.8 44.6 1.0 O A:HIS58 4.8 17.3 1.0 CA A:ASP59 4.9 17.4 1.0 CD2 A:HIS62 4.9 25.2 1.0 HAF A:ODV203 5.0 40.5 1.0

Iron binding site 3 out of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:19.6 occ:1.00 OD2 B:ASP59 2.0 19.6 1.0 NE2 B:HIS58 2.1 15.8 1.0 OH B:TYR24 2.1 25.2 1.0 NE2 B:HIS34 2.1 23.3 1.0 OD1 B:ASP161 2.2 22.6 1.0 O B:HOH301 2.3 19.0 1.0 CG B:ASP59 3.0 18.9 1.0 CG B:ASP161 3.0 22.0 1.0 CD2 B:HIS58 3.0 13.9 1.0 CZ B:TYR24 3.1 32.6 1.0 CE1 B:HIS58 3.1 19.2 1.0 HAC B:ODV203 3.1 24.9 1.0 CD2 B:HIS34 3.1 21.6 1.0 CE1 B:HIS34 3.1 22.5 1.0 OD2 B:ASP161 3.3 20.5 1.0 OD1 B:ASP59 3.4 18.7 1.0 CE1 B:TYR24 3.7 30.2 1.0 FE B:FE202 3.8 18.4 1.0 OAC B:ODV203 4.0 20.8 1.0 CE2 B:TYR24 4.0 27.1 1.0 HAG B:ODV203 4.0 33.1 1.0 ND1 B:HIS58 4.2 15.2 1.0 CG B:HIS58 4.2 16.8 1.0 ND1 B:HIS34 4.2 20.9 1.0 CB B:ASP59 4.2 16.9 1.0 CG B:HIS34 4.2 21.0 1.0 CB B:ASP161 4.4 18.5 1.0 CAG B:ODV203 4.5 27.6 1.0 CA B:ASP161 4.8 17.7 1.0 NE2 B:HIS104 4.8 17.5 1.0 O B:ASP161 4.9 19.3 1.0 CD1 B:TYR24 5.0 32.9 1.0 CD2 B:HIS104 5.0 20.0 1.0

Iron binding site 4 out of 4 in the Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal of Phnz Bound to (R)-2-Amino-1-Hydroxyethylphosphonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:18.4 occ:1.00 HAC B:ODV203 1.9 24.9 1.0 O B:HOH301 2.0 19.0 1.0 OAC B:ODV203 2.1 20.8 1.0 OD1 B:ASP59 2.2 18.7 1.0 NE2 B:HIS104 2.2 17.5 1.0 NE2 B:HIS80 2.2 20.1 1.0 OAE B:ODV203 2.2 22.2 1.0 CAG B:ODV203 3.0 27.6 1.0 PAH B:ODV203 3.1 23.7 1.0 CD2 B:HIS104 3.1 20.0 1.0 CE1 B:HIS104 3.1 20.9 1.0 CE1 B:HIS80 3.1 19.5 1.0 CD2 B:HIS80 3.2 19.6 1.0 CG B:ASP59 3.2 18.9 1.0 HAG B:ODV203 3.4 33.1 1.0 OD2 B:ASP59 3.5 19.6 1.0 FE B:FE201 3.8 19.6 1.0 CD2 B:HIS58 4.0 13.9 1.0 OAD B:ODV203 4.1 26.6 1.0 NE2 B:HIS62 4.2 26.5 1.0 OD2 B:ASP161 4.2 20.5 1.0 OAB B:ODV203 4.2 21.7 1.0 OH B:TYR24 4.2 25.2 1.0 ND1 B:HIS104 4.3 20.0 1.0 CAF B:ODV203 4.3 31.6 1.0 HAH B:ODV203 4.3 37.9 1.0 ND1 B:HIS80 4.3 19.0 1.0 CG B:HIS104 4.3 18.6 1.0 CG B:HIS80 4.3 20.7 1.0 NH1 B:ARG158 4.4 20.1 1.0 NE2 B:HIS58 4.4 15.8 1.0 CB B:ASP59 4.5 16.9 1.0 CG2 B:VAL105 4.7 21.1 1.0 O B:HIS58 4.8 17.3 1.0 CD2 B:HIS62 4.8 23.8 1.0 CA B:ASP59 4.8 18.7 1.0 HAF B:ODV203 4.8 37.9 1.0 HAJ B:ODV203 4.9 48.0 1.0 CE1 B:HIS62 5.0 24.4 1.0

L.M.Van Staalduinen, F.R.Mcsorley, K.Schiessl, J.Seguin, P.B.Wyatt, F.Hammerschmidt, D.L.Zechel, Z.Jia. Crystal Structure of Phnz in Complex with Substrate Reveals A Di-Iron Oxygenase Mechanism For Catabolism of Organophosphonates. Proc.Natl.Acad.Sci.Usa V. 111 5171 2014.
ISSN: ISSN 0027-8424
PubMed: 24706911
DOI: 10.1073/PNAS.1320039111