Iron in PDB 3tmb: BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus

The structure of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus, PDB code: 3tmb was solved by A.L.Lovering, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.168, 45.451, 98.005, 90.00, 113.29, 90.00
R / Rfree (%)	19.4 / 21.9

The binding sites of Iron atom in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus (pdb code 3tmb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus, PDB code: 3tmb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe309 b:15.6 occ:1.00 O A:HOH312 1.9 14.0 1.0 O2 A:PO4311 2.1 15.2 1.0 OD2 A:ASP184 2.1 11.5 1.0 OD1 A:ASN265 2.2 15.0 1.0 NE2 A:HIS150 2.2 13.8 1.0 NE2 A:HIS183 2.3 10.4 1.0 CG A:ASP184 3.0 11.7 1.0 CG A:ASN265 3.0 17.1 1.0 CD2 A:HIS150 3.1 10.9 1.0 CD2 A:HIS183 3.1 12.1 1.0 P A:PO4311 3.2 17.3 1.0 CE1 A:HIS150 3.2 15.1 1.0 FE A:FE310 3.3 15.1 1.0 CE1 A:HIS183 3.3 14.8 1.0 OD1 A:ASP184 3.4 12.3 1.0 O1 A:PO4311 3.4 15.2 1.0 ND2 A:ASN265 3.5 14.8 1.0 O4 A:PO4311 3.8 28.9 1.0 CB A:ASN265 4.3 12.9 1.0 CG A:HIS150 4.3 13.0 1.0 ND1 A:HIS150 4.3 10.7 1.0 CG A:HIS183 4.3 14.0 1.0 CB A:ASP184 4.3 10.8 1.0 ND1 A:HIS183 4.4 11.7 1.0 O3 A:PO4311 4.4 25.1 1.0 OE2 A:GLU238 4.4 12.7 1.0 NE2 A:HIS237 4.5 12.7 1.0 CD2 A:HIS237 4.6 12.4 1.0 CE2 A:PHE273 4.8 18.6 1.0 CG2 A:VAL154 5.0 13.1 1.0

Iron binding site 2 out of 4 in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe310 b:15.1 occ:1.00 O A:HOH312 1.9 14.0 1.0 O1 A:PO4311 2.1 15.2 1.0 OD1 A:ASP184 2.1 12.3 1.0 OE2 A:GLU238 2.1 12.7 1.0 NE2 A:HIS237 2.2 12.7 1.0 NE2 A:HIS212 2.2 13.1 1.0 CD2 A:HIS237 3.1 12.4 1.0 CG A:ASP184 3.1 11.7 1.0 CE1 A:HIS212 3.1 14.0 1.0 CD A:GLU238 3.2 16.1 1.0 P A:PO4311 3.2 17.3 1.0 CE1 A:HIS237 3.2 12.7 1.0 CD2 A:HIS212 3.3 13.3 1.0 FE A:FE309 3.3 15.6 1.0 OD2 A:ASP184 3.4 11.5 1.0 O4 A:PO4311 3.6 28.9 1.0 O2 A:PO4311 3.6 15.2 1.0 CG A:GLU238 3.8 12.6 1.0 CD2 A:HIS183 3.9 12.1 1.0 NE2 A:HIS187 4.1 13.7 1.0 OE1 A:GLU238 4.2 15.2 1.0 ND1 A:HIS212 4.2 10.9 1.0 CG A:HIS237 4.3 14.3 1.0 NE2 A:HIS183 4.3 10.4 1.0 ND1 A:HIS237 4.3 14.7 1.0 CG A:HIS212 4.4 12.9 1.0 ND2 A:ASN265 4.4 14.8 1.0 CB A:ASP184 4.4 10.8 1.0 CD2 A:HIS187 4.5 17.0 1.0 O3 A:PO4311 4.5 25.1 1.0 OD1 A:ASN265 4.7 15.0 1.0 CA A:ASP184 4.8 13.2 1.0 CG A:ASN265 4.8 17.1 1.0

Iron binding site 3 out of 4 in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe309 b:23.9 occ:1.00 O B:HOH349 2.0 19.6 1.0 O3 B:PO4311 2.1 20.2 1.0 OD1 B:ASP184 2.1 20.4 1.0 OE2 B:GLU238 2.1 26.4 1.0 NE2 B:HIS212 2.2 27.4 1.0 NE2 B:HIS237 2.2 22.5 1.0 CE1 B:HIS212 3.0 31.2 1.0 CD2 B:HIS237 3.1 18.3 1.0 CG B:ASP184 3.1 24.3 1.0 P B:PO4311 3.2 25.1 1.0 CD2 B:HIS212 3.2 29.0 1.0 CD B:GLU238 3.2 23.9 1.0 CE1 B:HIS237 3.3 20.7 1.0 FE B:FE310 3.3 22.1 1.0 OD2 B:ASP184 3.4 25.7 1.0 O4 B:PO4311 3.5 30.7 1.0 O1 B:PO4311 3.6 23.7 1.0 CG B:GLU238 3.8 23.3 1.0 NE2 B:HIS187 4.0 32.0 1.0 CD2 B:HIS183 4.0 18.2 1.0 ND1 B:HIS212 4.2 33.4 1.0 CG B:HIS237 4.3 19.9 1.0 NE2 B:HIS183 4.3 20.1 1.0 OE1 B:GLU238 4.3 24.5 1.0 CG B:HIS212 4.3 30.5 1.0 CD2 B:HIS187 4.4 31.4 1.0 ND2 B:ASN265 4.4 23.7 1.0 ND1 B:HIS237 4.4 19.7 1.0 CB B:ASP184 4.5 23.6 1.0 O2 B:PO4311 4.5 33.3 1.0 OD1 B:ASN265 4.6 19.1 1.0 CA B:ASP184 4.8 20.9 1.0 CG B:ASN265 4.8 22.3 1.0 CZ2 B:TRP209 5.0 34.4 1.0

Iron binding site 4 out of 4 in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe310 b:22.1 occ:1.00 O B:HOH349 1.9 19.6 1.0 O1 B:PO4311 2.1 23.7 1.0 OD1 B:ASN265 2.1 19.1 1.0 OD2 B:ASP184 2.1 25.7 1.0 NE2 B:HIS150 2.2 19.5 1.0 NE2 B:HIS183 2.3 20.1 1.0 CG B:ASP184 3.0 24.3 1.0 CG B:ASN265 3.0 22.3 1.0 CD2 B:HIS183 3.1 18.2 1.0 CD2 B:HIS150 3.1 19.8 1.0 P B:PO4311 3.2 25.1 1.0 CE1 B:HIS150 3.3 21.1 1.0 CE1 B:HIS183 3.3 18.8 1.0 FE B:FE309 3.3 23.9 1.0 O3 B:PO4311 3.4 20.2 1.0 OD1 B:ASP184 3.4 20.4 1.0 ND2 B:ASN265 3.5 23.7 1.0 O4 B:PO4311 3.8 30.7 1.0 CB B:ASN265 4.2 18.9 1.0 CB B:ASP184 4.3 23.6 1.0 CG B:HIS150 4.3 18.4 1.0 CG B:HIS183 4.3 18.9 1.0 ND1 B:HIS150 4.3 20.1 1.0 ND1 B:HIS183 4.4 20.1 1.0 OE2 B:GLU238 4.4 26.4 1.0 O2 B:PO4311 4.4 33.3 1.0 NE2 B:HIS237 4.6 22.5 1.0 CD2 B:HIS237 4.6 18.3 1.0 CE2 B:PHE273 4.8 29.1 1.0

A.L.Lovering, M.J.Capeness, C.Lambert, L.Hobley, R.E.Sockett. The Structure of An Unconventional Hd-Gyp Protein From Bdellovibrio Reveals the Roles of Conserved Residues in This Class of Cyclic-Di-Gmp Phosphodiesterases. Mbio V. 2 2011.
ISSN: ESSN 2150-7511
PubMed: 21990613
DOI: 10.1128/MBIO.00163-11