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

The structure of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus, PDB code: 3tmc 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)	13.67 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.100, 49.401, 78.372, 73.17, 75.90, 67.34
R / Rfree (%)	20.9 / 23.5

The binding sites of Iron atom in the BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus (pdb code 3tmc). 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: 3tmc:
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:5.7 occ:1.00 O A:HOH315 2.0 4.8 1.0 OD1 A:ASP184 2.1 4.4 1.0 O3 A:PO4311 2.1 3.9 1.0 OE2 A:GLU238 2.2 3.8 1.0 NE2 A:HIS212 2.2 6.2 1.0 NE2 A:HIS237 2.2 5.7 1.0 CD2 A:HIS237 3.0 4.7 1.0 CE1 A:HIS212 3.1 5.6 1.0 CG A:ASP184 3.1 3.4 1.0 P A:PO4311 3.2 6.7 1.0 CD A:GLU238 3.2 4.3 1.0 CD2 A:HIS212 3.3 4.9 1.0 CE1 A:HIS237 3.3 4.6 1.0 FE A:FE310 3.4 5.2 1.0 OD2 A:ASP184 3.4 4.2 1.0 O1 A:PO4311 3.4 9.5 1.0 O2 A:PO4311 3.6 7.3 1.0 CG A:GLU238 3.8 2.6 1.0 NE2 A:HIS187 3.9 5.7 1.0 CD2 A:HIS183 4.0 4.1 1.0 ND1 A:HIS212 4.2 6.1 1.0 CG A:HIS237 4.2 6.4 1.0 NE2 A:HIS183 4.3 3.6 1.0 OE1 A:GLU238 4.3 8.2 1.0 ND1 A:HIS237 4.3 6.1 1.0 CG A:HIS212 4.3 6.3 1.0 CD2 A:HIS187 4.4 6.4 1.0 ND2 A:ASN265 4.4 6.8 1.0 CB A:ASP184 4.4 3.9 1.0 O4 A:PO4311 4.5 10.4 1.0 OD1 A:ASN265 4.7 5.5 1.0 CG A:ASN265 4.8 4.7 1.0 CA A:ASP184 4.8 5.3 1.0 CZ2 A:TRP209 5.0 7.4 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:5.2 occ:1.00 O A:HOH315 1.9 4.8 1.0 O2 A:PO4311 2.0 7.3 1.0 OD1 A:ASN265 2.2 5.5 1.0 NE2 A:HIS150 2.2 3.7 1.0 OD2 A:ASP184 2.2 4.2 1.0 NE2 A:HIS183 2.2 3.6 1.0 CG A:ASN265 3.0 4.7 1.0 CG A:ASP184 3.0 3.4 1.0 CD2 A:HIS150 3.1 5.5 1.0 CE1 A:HIS150 3.1 4.1 1.0 CD2 A:HIS183 3.1 4.1 1.0 P A:PO4311 3.2 6.7 1.0 CE1 A:HIS183 3.3 4.6 1.0 OD1 A:ASP184 3.3 4.4 1.0 FE A:FE309 3.4 5.7 1.0 O3 A:PO4311 3.5 3.9 1.0 ND2 A:ASN265 3.5 6.8 1.0 O1 A:PO4311 3.7 9.5 1.0 ND1 A:HIS150 4.2 2.8 1.0 CB A:ASN265 4.3 2.6 1.0 CG A:HIS150 4.3 3.6 1.0 CG A:HIS183 4.3 4.2 1.0 ND1 A:HIS183 4.3 4.0 1.0 CB A:ASP184 4.4 3.9 1.0 OE2 A:GLU238 4.4 3.8 1.0 O4 A:PO4311 4.5 10.4 1.0 NE2 A:HIS237 4.6 5.7 1.0 CD2 A:HIS237 4.7 4.7 1.0 CE2 A:PHE273 4.9 9.8 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:6.3 occ:1.00 O B:HOH412 1.9 3.8 1.0 OD1 B:ASP184 2.1 4.4 1.0 O4 B:PO4311 2.1 5.2 1.0 OE2 B:GLU238 2.2 4.2 1.0 NE2 B:HIS212 2.2 6.8 1.0 NE2 B:HIS237 2.2 5.5 1.0 CD2 B:HIS237 3.0 3.8 1.0 CE1 B:HIS212 3.1 5.8 1.0 CG B:ASP184 3.1 5.5 1.0 P B:PO4311 3.2 6.5 1.0 CD2 B:HIS212 3.2 5.4 1.0 CD B:GLU238 3.3 4.1 1.0 CE1 B:HIS237 3.3 6.4 1.0 FE B:FE310 3.4 5.5 1.0 O2 B:PO4311 3.4 9.4 1.0 OD2 B:ASP184 3.4 3.1 1.0 O1 B:PO4311 3.6 6.3 1.0 CG B:GLU238 3.8 2.1 1.0 CD2 B:HIS183 3.9 0.7 1.0 NE2 B:HIS187 4.0 5.6 1.0 NE2 B:HIS183 4.2 4.6 1.0 ND1 B:HIS212 4.2 5.6 1.0 CG B:HIS237 4.2 4.0 1.0 OE1 B:GLU238 4.3 8.6 1.0 CG B:HIS212 4.3 5.7 1.0 ND1 B:HIS237 4.3 6.9 1.0 ND2 B:ASN265 4.4 9.3 1.0 CD2 B:HIS187 4.4 5.1 1.0 CB B:ASP184 4.5 5.1 1.0 O3 B:PO4311 4.5 11.4 1.0 OD1 B:ASN265 4.7 5.5 1.0 CG B:ASN265 4.8 5.4 1.0 CA B:ASP184 4.8 2.6 1.0 CZ2 B:TRP209 5.0 9.9 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:5.5 occ:1.00 O B:HOH412 1.9 3.8 1.0 O1 B:PO4311 2.0 6.3 1.0 OD1 B:ASN265 2.1 5.5 1.0 NE2 B:HIS150 2.1 4.5 1.0 OD2 B:ASP184 2.2 3.1 1.0 NE2 B:HIS183 2.3 4.6 1.0 CG B:ASN265 3.0 5.4 1.0 CG B:ASP184 3.1 5.5 1.0 CD2 B:HIS150 3.1 5.6 1.0 CE1 B:HIS150 3.1 3.6 1.0 P B:PO4311 3.1 6.5 1.0 CD2 B:HIS183 3.2 0.7 1.0 CE1 B:HIS183 3.3 7.5 1.0 FE B:FE309 3.4 6.3 1.0 OD1 B:ASP184 3.4 4.4 1.0 O4 B:PO4311 3.4 5.2 1.0 ND2 B:ASN265 3.5 9.3 1.0 O2 B:PO4311 3.7 9.4 1.0 CB B:ASN265 4.2 0.3 1.0 ND1 B:HIS150 4.2 4.7 1.0 CG B:HIS150 4.3 3.9 1.0 CG B:HIS183 4.3 4.3 1.0 ND1 B:HIS183 4.4 6.3 1.0 CB B:ASP184 4.4 5.1 1.0 O3 B:PO4311 4.4 11.4 1.0 OE2 B:GLU238 4.5 4.2 1.0 NE2 B:HIS237 4.6 5.5 1.0 CD2 B:HIS237 4.7 3.8 1.0 CE2 B:PHE273 4.9 7.6 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