Iron in PDB 4mlm: Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1

The structure of Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1, PDB code: 4mlm 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)	19.80 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.670, 76.040, 60.700, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.8

The structure of Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1 (pdb code 4mlm). 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 Phnz From Uncultured Bacterium HF130_AEPN_1, PDB code: 4mlm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1


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 Phnz From Uncultured Bacterium HF130_AEPN_1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.6 occ:1.00 OD2 A:ASP59 2.1 13.1 1.0 O A:HOH301 2.1 11.5 1.0 NE2 A:HIS34 2.1 11.0 1.0 OD1 A:ASP161 2.2 13.6 1.0 OH A:TYR24 2.2 15.5 1.0 NE2 A:HIS58 2.2 13.5 1.0 CG A:ASP161 3.0 15.4 1.0 CE1 A:HIS34 3.0 13.6 1.0 CG A:ASP59 3.0 10.2 1.0 CD2 A:HIS34 3.1 13.0 1.0 CZ A:TYR24 3.1 19.7 1.0 CD2 A:HIS58 3.1 10.6 1.0 CE1 A:HIS58 3.1 11.4 1.0 OD2 A:ASP161 3.3 15.7 1.0 OD1 A:ASP59 3.5 12.2 1.0 CE1 A:TYR24 3.7 16.7 1.0 FE A:FE202 3.8 11.9 1.0 O11 A:TLA203 3.9 13.4 1.0 CE2 A:TYR24 4.0 16.5 1.0 O A:HOH331 4.0 25.1 1.0 ND1 A:HIS34 4.1 12.1 1.0 CG A:HIS34 4.2 13.3 1.0 ND1 A:HIS58 4.2 15.2 1.0 CG A:HIS58 4.3 13.3 1.0 CB A:ASP161 4.3 9.8 1.0 CB A:ASP59 4.3 9.6 1.0 C1 A:TLA203 4.5 16.1 1.0 CA A:ASP161 4.7 9.9 1.0 NE2 A:HIS104 4.8 10.9 1.0 O2 A:TLA203 4.8 13.7 1.0 H2 A:TLA203 4.8 17.0 1.0 O A:ASP161 4.9 13.0 1.0 CD1 A:TYR24 4.9 18.1 1.0 C2 A:TLA203 5.0 14.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1


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 Phnz From Uncultured Bacterium HF130_AEPN_1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:11.9 occ:1.00 O2 A:TLA203 2.0 13.7 1.0 OD1 A:ASP59 2.1 12.2 1.0 O11 A:TLA203 2.1 13.4 1.0 O A:HOH301 2.2 11.5 1.0 NE2 A:HIS104 2.2 10.9 1.0 NE2 A:HIS80 2.2 11.8 1.0 HA A:TLA203 2.7 16.4 1.0 C1 A:TLA203 2.9 16.1 1.0 C2 A:TLA203 3.0 14.2 1.0 CG A:ASP59 3.1 10.2 1.0 CE1 A:HIS104 3.1 10.6 1.0 CE1 A:HIS80 3.2 13.9 1.0 CD2 A:HIS80 3.2 10.8 1.0 CD2 A:HIS104 3.2 10.7 1.0 OD2 A:ASP59 3.5 13.1 1.0 H2 A:TLA203 3.5 17.0 1.0 FE A:FE201 3.8 12.6 1.0 CD2 A:HIS58 3.9 10.6 1.0 NE2 A:HIS62 4.0 14.1 1.0 C3 A:TLA203 4.1 16.4 1.0 O1 A:TLA203 4.1 15.5 1.0 O3 A:TLA203 4.2 15.6 1.0 OH A:TYR24 4.2 15.5 1.0 ND1 A:HIS104 4.3 11.3 1.0 ND1 A:HIS80 4.3 11.7 1.0 OD2 A:ASP161 4.3 15.7 1.0 CG A:HIS80 4.3 11.7 1.0 CG A:HIS104 4.4 11.4 1.0 NE2 A:HIS58 4.4 13.5 1.0 CB A:ASP59 4.4 9.6 1.0 NH1 A:ARG158 4.7 14.6 1.0 CE1 A:HIS62 4.7 11.4 1.0 O A:HIS58 4.7 11.6 1.0 C4 A:TLA203 4.7 15.4 1.0 CA A:ASP59 4.8 10.1 1.0 HB A:TLA203 4.8 18.6 1.0 CD2 A:HIS62 4.9 13.2 1.0 H3 A:TLA203 4.9 19.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1


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 Phnz From Uncultured Bacterium HF130_AEPN_1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:14.1 occ:1.00 OD2 B:ASP59 2.1 13.2 1.0 OD1 B:ASP161 2.1 15.7 1.0 O B:HOH301 2.1 11.8 1.0 NE2 B:HIS34 2.1 14.7 1.0 NE2 B:HIS58 2.2 15.7 1.0 OH B:TYR24 2.2 15.9 1.0 CG B:ASP161 3.0 17.4 1.0 CG B:ASP59 3.0 13.9 1.0 CD2 B:HIS34 3.1 14.4 1.0 CE1 B:HIS34 3.1 14.6 1.0 CD2 B:HIS58 3.1 12.0 1.0 CZ B:TYR24 3.1 20.4 1.0 CE1 B:HIS58 3.2 14.8 1.0 OD2 B:ASP161 3.4 17.9 1.0 OD1 B:ASP59 3.5 10.5 1.0 CE2 B:TYR24 3.7 20.5 1.0 FE B:FE203 3.7 11.7 1.0 O41 B:TLA204 3.9 12.1 1.0 O B:HOH365 4.0 29.0 1.0 CE1 B:TYR24 4.1 15.7 1.0 ND1 B:HIS34 4.2 16.6 1.0 CB B:ASP161 4.2 15.7 1.0 CG B:HIS34 4.2 16.1 1.0 ND1 B:HIS58 4.3 14.4 1.0 CG B:HIS58 4.3 12.1 1.0 CB B:ASP59 4.3 9.9 1.0 HB B:TLA204 4.4 19.1 1.0 C4 B:TLA204 4.4 14.5 1.0 CA B:ASP161 4.7 16.3 1.0 H3 B:TLA204 4.7 13.9 1.0 NE2 B:HIS104 4.8 10.9 1.0 O B:ASP161 4.9 17.7 1.0 O3 B:TLA204 4.9 15.9 1.0 C3 B:TLA204 4.9 11.6 1.0 CD2 B:TYR24 5.0 19.6 1.0 CD2 B:HIS104 5.0 12.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Phnz From Uncultured Bacterium HF130_AEPN_1


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 Phnz From Uncultured Bacterium HF130_AEPN_1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:11.7 occ:1.00 HB B:TLA204 1.2 19.1 1.0 O3 B:TLA204 2.1 15.9 1.0 OD1 B:ASP59 2.1 10.5 1.0 O B:HOH301 2.1 11.8 1.0 O41 B:TLA204 2.1 12.1 1.0 NE2 B:HIS104 2.2 10.9 1.0 NE2 B:HIS80 2.2 12.3 1.0 C4 B:TLA204 2.8 14.5 1.0 C3 B:TLA204 2.8 11.6 1.0 CG B:ASP59 3.1 13.9 1.0 CE1 B:HIS80 3.1 13.2 1.0 CD2 B:HIS104 3.2 12.5 1.0 CE1 B:HIS104 3.2 12.6 1.0 CD2 B:HIS80 3.2 9.1 1.0 H3 B:TLA204 3.3 13.9 1.0 OD2 B:ASP59 3.5 13.2 1.0 FE B:FE202 3.7 14.1 1.0 CD2 B:HIS58 4.0 12.0 1.0 NE2 B:HIS62 4.0 14.8 1.0 O4 B:TLA204 4.0 14.1 1.0 C2 B:TLA204 4.1 13.5 1.0 OH B:TYR24 4.2 15.9 1.0 O2 B:TLA204 4.3 14.9 1.0 ND1 B:HIS80 4.3 10.8 1.0 ND1 B:HIS104 4.3 11.0 1.0 CG B:HIS104 4.3 10.7 1.0 OD2 B:ASP161 4.3 17.9 1.0 CG B:HIS80 4.3 10.0 1.0 NE2 B:HIS58 4.4 15.7 1.0 CB B:ASP59 4.4 9.9 1.0 CE1 B:HIS62 4.7 12.6 1.0 O B:HIS58 4.7 11.6 1.0 NH1 B:ARG158 4.7 15.6 1.0 C1 B:TLA204 4.7 17.3 1.0 CA B:ASP59 4.8 12.2 1.0 H2 B:TLA204 4.8 16.2 1.0 CD2 B:HIS62 4.8 15.6 1.0 OD1 B:ASP161 5.0 15.7 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