Iron in PDB 4n71: X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz

The structure of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz, PDB code: 4n71 was solved by B.Woersdoerfer, M.Lingaraju, N.Yennawar, A.K.Boal, C.Krebs, J.M.Bollingerjr, M.-E.Pandelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 2.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.761, 65.423, 109.355, 90.00, 124.83, 90.00
R / Rfree (%)	27.8 / 33.3

The binding sites of Iron atom in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz (pdb code 4n71). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz, PDB code: 4n71:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:37.0 occ:1.00 OD1 A:ASP59 2.1 70.4 1.0 NE2 A:HIS104 2.2 71.3 1.0 OAD A:ODV203 2.2 73.5 1.0 OAC A:ODV203 2.3 63.4 1.0 NE2 A:HIS80 2.3 59.4 1.0 CG A:ASP59 2.9 66.0 1.0 CAG A:ODV203 3.0 64.4 1.0 CD2 A:HIS104 3.0 72.6 1.0 OD2 A:ASP59 3.1 64.6 1.0 CE1 A:HIS80 3.1 59.8 1.0 PAH A:ODV203 3.1 75.3 1.0 CE1 A:HIS104 3.2 69.6 1.0 CD2 A:HIS80 3.4 56.8 1.0 FE A:FE202 3.5 40.7 1.0 OD2 A:ASP161 3.7 70.9 1.0 NH1 A:ARG158 3.9 45.4 1.0 OAE A:ODV203 4.0 73.0 1.0 CD2 A:HIS58 4.0 44.9 1.0 CG A:HIS104 4.2 70.9 1.0 ND1 A:HIS104 4.3 69.4 1.0 ND1 A:HIS80 4.3 57.3 1.0 CB A:ASP59 4.3 60.4 1.0 OAB A:ODV203 4.3 77.8 1.0 NE2 A:HIS58 4.3 45.2 1.0 NE2 A:HIS62 4.4 60.8 1.0 CAF A:ODV203 4.4 63.2 1.0 CG A:HIS80 4.5 56.4 1.0 O A:HIS58 4.7 55.7 1.0 CA A:ASP59 4.8 60.7 1.0 CG A:ASP161 4.9 70.4 1.0 CG2 A:VAL105 4.9 43.4 1.0 CZ A:ARG158 5.0 48.1 1.0 CD2 A:HIS62 5.0 61.2 1.0

Iron binding site 2 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:40.7 occ:1.00 OD2 A:ASP59 2.0 64.6 1.0 OD1 A:ASP161 2.1 69.8 1.0 OD2 A:ASP161 2.1 70.9 1.0 NE2 A:HIS58 2.1 45.2 1.0 NE2 A:HIS34 2.1 51.3 1.0 CG A:ASP161 2.4 70.4 1.0 CD2 A:HIS58 3.0 44.9 1.0 CG A:ASP59 3.0 66.0 1.0 CD2 A:HIS34 3.1 59.2 1.0 CE1 A:HIS34 3.1 68.8 1.0 CE1 A:HIS58 3.2 48.7 1.0 FE A:FE201 3.5 37.0 1.0 OD1 A:ASP59 3.5 70.4 1.0 CB A:ASP161 3.9 69.4 1.0 OAC A:ODV203 4.1 63.4 1.0 CG A:HIS58 4.2 45.9 1.0 ND1 A:HIS34 4.2 66.4 1.0 CB A:ASP59 4.2 60.4 1.0 ND1 A:HIS58 4.2 47.3 1.0 CG A:HIS34 4.3 60.8 1.0 CAG A:ODV203 4.4 64.4 1.0 O A:ASP161 4.6 65.7 1.0 CA A:ASP161 4.7 67.9 1.0 NH1 A:ARG158 4.8 45.4 1.0 CD2 A:HIS104 4.9 72.6 1.0 NE2 A:HIS104 4.9 71.3 1.0 OAD A:ODV203 5.0 73.5 1.0

Iron binding site 3 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:54.1 occ:1.00 OD1 B:ASP59 2.0 51.3 1.0 NE2 B:HIS80 2.2 51.5 1.0 NE2 B:HIS104 2.2 71.3 1.0 OAC B:ODV203 2.2 46.8 1.0 OAD B:ODV203 2.2 54.2 1.0 CAG B:ODV203 2.8 41.2 1.0 CE1 B:HIS80 2.9 54.6 1.0 CG B:ASP59 2.9 48.8 1.0 CE1 B:HIS104 3.0 70.9 1.0 PAH B:ODV203 3.1 51.0 1.0 OD2 B:ASP59 3.2 46.3 1.0 CD2 B:HIS104 3.3 71.7 1.0 CD2 B:HIS80 3.3 49.6 1.0 FE B:FE202 3.5 60.3 1.0 OD2 B:ASP161 3.6 72.8 1.0 OAE B:ODV203 4.0 51.0 1.0 ND1 B:HIS80 4.1 52.8 1.0 CD2 B:HIS58 4.1 75.4 1.0 ND1 B:HIS104 4.2 72.5 1.0 OAB B:ODV203 4.2 52.7 1.0 CB B:ASP59 4.3 48.7 1.0 CAF B:ODV203 4.3 38.2 1.0 CG B:HIS104 4.3 72.8 1.0 CG B:HIS80 4.3 50.1 1.0 NH2 B:ARG158 4.5 57.6 1.0 NE2 B:HIS58 4.6 76.5 1.0 CG B:ASP161 4.7 70.5 1.0 O B:HIS58 4.7 65.7 1.0 NE2 B:HIS62 4.8 46.9 1.0 CA B:ASP59 4.8 52.0 1.0 NAA B:ODV203 4.9 33.4 1.0 CG2 B:VAL105 5.0 63.0 1.0 OD1 B:ASP161 5.0 76.1 1.0

Iron binding site 4 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:60.3 occ:1.00 OD2 B:ASP161 2.1 72.8 1.0 OD1 B:ASP161 2.1 76.1 1.0 OD2 B:ASP59 2.1 46.3 1.0 NE2 B:HIS58 2.1 76.5 1.0 NE2 B:HIS34 2.2 71.1 1.0 CG B:ASP161 2.3 70.5 1.0 CD2 B:HIS58 2.8 75.4 1.0 CG B:ASP59 3.0 48.8 1.0 CE1 B:HIS34 3.1 72.7 1.0 CD2 B:HIS34 3.3 69.0 1.0 CE1 B:HIS58 3.3 75.6 1.0 OD1 B:ASP59 3.4 51.3 1.0 FE B:FE201 3.5 54.1 1.0 CB B:ASP161 3.7 61.5 1.0 CG B:HIS58 4.0 73.5 1.0 ND1 B:HIS34 4.2 71.2 1.0 ND1 B:HIS58 4.2 73.4 1.0 CB B:ASP59 4.4 48.7 1.0 CG B:HIS34 4.4 66.9 1.0 OAC B:ODV203 4.4 46.8 1.0 CA B:ASP161 4.4 59.2 1.0 CAG B:ODV203 4.6 41.2 1.0 NE2 B:HIS104 4.7 71.3 1.0 O B:ASP161 4.8 65.2 1.0 CD2 B:HIS104 4.8 71.7 1.0 OAD B:ODV203 5.0 54.2 1.0 NH1 B:ARG158 5.0 55.0 1.0

Iron binding site 5 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:46.7 occ:1.00 OD1 D:ASP59 1.9 79.0 1.0 OAC D:ODV203 2.1 65.2 1.0 NE2 D:HIS104 2.1 51.1 1.0 OAD D:ODV203 2.2 64.3 1.0 OD2 D:ASP59 2.3 67.5 1.0 NE2 D:HIS80 2.4 64.3 1.0 CG D:ASP59 2.4 71.7 1.0 CAG D:ODV203 2.7 63.1 1.0 PAH D:ODV203 2.8 65.7 1.0 CE1 D:HIS104 2.8 53.4 1.0 CE1 D:HIS80 3.2 66.2 1.0 FE D:FE202 3.2 54.1 1.0 CD2 D:HIS104 3.3 52.3 1.0 CD2 D:HIS80 3.4 60.0 1.0 OAE D:ODV203 3.5 64.9 1.0 OD2 D:ASP161 3.8 67.9 1.0 CB D:ASP59 3.9 68.8 1.0 ND1 D:HIS104 4.1 52.7 1.0 CD2 D:HIS58 4.1 42.1 1.0 CAF D:ODV203 4.1 61.4 1.0 NE2 D:HIS62 4.1 43.2 1.0 OAB D:ODV203 4.2 68.6 1.0 ND1 D:HIS80 4.3 51.4 1.0 CG D:HIS104 4.3 52.2 1.0 CG D:HIS80 4.4 57.0 1.0 NH1 D:ARG158 4.5 42.4 1.0 NE2 D:HIS58 4.6 41.4 1.0 CA D:ASP59 4.6 43.6 1.0 CD2 D:HIS62 4.7 62.4 1.0 NAA D:ODV203 4.8 59.4 1.0 NE2 D:HIS34 4.8 40.3 1.0 CG D:ASP161 4.8 65.2 1.0 O D:HIS58 5.0 51.6 1.0 OD1 D:ASP161 5.0 67.1 1.0

Iron binding site 6 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:54.1 occ:1.00 OD2 D:ASP161 2.1 67.9 1.0 OD1 D:ASP161 2.1 67.1 1.0 OD2 D:ASP59 2.1 67.5 1.0 NE2 D:HIS58 2.1 41.4 1.0 NE2 D:HIS34 2.3 40.3 1.0 CG D:ASP161 2.3 65.2 1.0 CD2 D:HIS58 2.6 42.1 1.0 CE1 D:HIS34 2.7 41.4 1.0 CG D:ASP59 3.2 71.7 1.0 FE D:FE201 3.2 46.7 1.0 CE1 D:HIS58 3.4 35.0 1.0 CD2 D:HIS34 3.6 46.5 1.0 CB D:ASP161 3.8 61.1 1.0 OD1 D:ASP59 3.9 79.0 1.0 CG D:HIS58 3.9 44.5 1.0 NE2 D:HIS104 3.9 51.1 1.0 ND1 D:HIS34 4.0 45.3 1.0 CD2 D:HIS104 4.1 52.3 1.0 OAD D:ODV203 4.1 64.3 1.0 CB D:ASP59 4.1 68.8 1.0 ND1 D:HIS58 4.2 48.8 1.0 OAC D:ODV203 4.3 65.2 1.0 CAG D:ODV203 4.3 63.1 1.0 CG D:HIS34 4.4 47.5 1.0 CA D:ASP161 4.5 58.9 1.0 PAH D:ODV203 4.9 65.7 1.0 O D:ASP161 4.9 54.5 1.0 NH1 D:ARG158 5.0 42.4 1.0

Iron binding site 7 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:48.0 occ:1.00 OD1 E:ASP59 2.0 60.9 1.0 OAD E:ODV203 2.2 51.2 1.0 NE2 E:HIS104 2.2 39.9 1.0 NE2 E:HIS80 2.2 72.3 1.0 OAC E:ODV203 2.3 18.6 1.0 CE1 E:HIS80 3.0 74.3 1.0 CG E:ASP59 3.0 54.9 1.0 CAG E:ODV203 3.1 19.9 1.0 CD2 E:HIS104 3.1 41.1 1.0 PAH E:ODV203 3.1 49.6 1.0 CE1 E:HIS104 3.2 41.7 1.0 OD2 E:ASP59 3.3 50.1 1.0 CD2 E:HIS80 3.3 70.6 1.0 FE E:FE202 3.7 48.3 1.0 NH1 E:ARG158 3.8 48.2 1.0 OAE E:ODV203 3.8 49.0 1.0 OD2 E:ASP161 3.9 74.3 1.0 CD2 E:HIS58 4.0 43.0 1.0 NE2 E:HIS62 4.2 43.1 1.0 ND1 E:HIS80 4.2 74.3 1.0 CG E:HIS104 4.3 45.7 1.0 ND1 E:HIS104 4.3 44.0 1.0 OAB E:ODV203 4.4 53.7 1.0 CG E:HIS80 4.4 70.2 1.0 CB E:ASP59 4.4 53.1 1.0 CAF E:ODV203 4.4 23.0 1.0 NE2 E:HIS58 4.5 43.0 1.0 CG2 E:VAL105 4.5 52.3 1.0 O E:HIS58 4.7 64.2 1.0 CA E:ASP59 4.7 54.3 1.0 CD2 E:HIS62 4.8 44.7 1.0 CE1 E:HIS62 4.9 55.2 1.0 CZ E:ARG158 4.9 46.2 1.0

Iron binding site 8 out of 8 in the X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of 2-Amino-1-Hydroxyethylphosphonate-Bound Phnz within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe202 b:48.3 occ:1.00 OD1 E:ASP161 2.0 79.3 1.0 OD2 E:ASP59 2.0 50.1 1.0 OD2 E:ASP161 2.1 74.3 1.0 NE2 E:HIS58 2.2 43.0 1.0 NE2 E:HIS34 2.2 69.9 1.0 CG E:ASP161 2.3 74.7 1.0 CG E:ASP59 3.0 54.9 1.0 CE1 E:HIS34 3.1 74.1 1.0 CD2 E:HIS58 3.1 43.0 1.0 CE1 E:HIS58 3.2 46.5 1.0 CD2 E:HIS34 3.4 67.9 1.0 OD1 E:ASP59 3.5 60.9 1.0 FE E:FE201 3.7 48.0 1.0 CB E:ASP161 3.8 70.4 1.0 OAC E:ODV203 4.0 18.6 1.0 CB E:ASP59 4.2 53.1 1.0 ND1 E:HIS34 4.2 74.9 1.0 CG E:HIS58 4.3 48.2 1.0 CAG E:ODV203 4.3 19.9 1.0 ND1 E:HIS58 4.3 49.2 1.0 CG E:HIS34 4.4 69.2 1.0 NH1 E:ARG158 4.5 48.2 1.0 OE2 E:GLU27 4.6 87.5 1.0 O E:ASP161 4.6 74.3 1.0 CA E:ASP161 4.6 71.0 1.0 OAD E:ODV203 4.8 51.2 1.0 C E:ASP161 4.9 71.2 1.0 NE2 E:HIS104 4.9 39.9 1.0 CD2 E:HIS104 5.0 41.1 1.0

B.Worsdorfer, M.Lingaraju, N.H.Yennawar, A.K.Boal, C.Krebs, J.M.Bollinger, M.E.Pandelia. Organophosphonate-Degrading Phnz Reveals An Emerging Family of Hd Domain Mixed-Valent Diiron Oxygenases. Proc.Natl.Acad.Sci.Usa V. 110 18874 2013.
ISSN: ISSN 0027-8424
PubMed: 24198335
DOI: 10.1073/PNAS.1315927110