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

The structure of BD1817, A Hdg"Y"P Protein From Bdellovibrio Bacteriovorus, PDB code: 3tmd 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)	43.74 / 2.64
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.010, 101.010, 94.500, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 25.1

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

Iron binding site 1 out of 2 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:Fe901 b:64.5 occ:1.00 O A:HOH309 2.0 37.9 1.0 O2 A:PO4903 2.1 77.0 1.0 NE2 A:HIS150 2.1 67.3 1.0 OD1 A:ASN265 2.3 71.9 1.0 OD2 A:ASP184 2.3 67.2 1.0 NE2 A:HIS183 2.5 54.5 1.0 CE1 A:HIS150 2.9 68.6 1.0 CD2 A:HIS150 3.2 65.7 1.0 CG A:ASP184 3.2 68.4 1.0 CG A:ASN265 3.3 71.2 1.0 P A:PO4903 3.3 77.0 1.0 CE1 A:HIS183 3.3 57.0 1.0 O4 A:PO4903 3.5 77.0 1.0 FE A:FE902 3.5 69.1 1.0 CD2 A:HIS183 3.6 54.4 1.0 OD1 A:ASP184 3.6 67.9 1.0 ND2 A:ASN265 3.7 67.3 1.0 O3 A:PO4903 4.0 77.0 1.0 ND1 A:HIS150 4.1 65.0 1.0 CG A:HIS150 4.2 66.2 1.0 OE2 A:GLU238 4.4 73.3 1.0 O1 A:PO4903 4.4 77.0 1.0 CB A:ASP184 4.4 67.4 1.0 ND1 A:HIS183 4.5 55.1 1.0 CB A:ASN265 4.5 68.2 1.0 CE2 A:PHE273 4.6 68.2 1.0 CG A:HIS183 4.7 54.9 1.0 NE2 A:HIS237 4.8 67.3 1.0 CD2 A:HIS237 4.9 65.6 1.0

Iron binding site 2 out of 2 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:Fe902 b:69.1 occ:1.00 O A:HOH309 1.9 37.9 1.0 O4 A:PO4903 2.1 77.0 1.0 OE2 A:GLU238 2.1 73.3 1.0 NE2 A:HIS212 2.3 60.3 1.0 NE2 A:HIS237 2.3 67.3 1.0 OD1 A:ASP184 2.3 67.9 1.0 CE1 A:HIS212 3.0 64.1 1.0 CD2 A:HIS237 3.2 65.6 1.0 CD A:GLU238 3.2 73.1 1.0 CG A:ASP184 3.3 68.4 1.0 P A:PO4903 3.3 77.0 1.0 CE1 A:HIS237 3.4 66.9 1.0 CD2 A:HIS212 3.4 61.8 1.0 OD2 A:ASP184 3.4 67.2 1.0 FE A:FE901 3.5 64.5 1.0 O2 A:PO4903 3.7 77.0 1.0 O3 A:PO4903 3.8 77.0 1.0 CG A:GLU238 3.8 71.0 1.0 NE2 A:HIS187 4.0 76.8 1.0 ND1 A:HIS212 4.2 59.9 1.0 CD2 A:HIS187 4.2 80.1 1.0 CD2 A:HIS183 4.3 54.4 1.0 OE1 A:GLU238 4.3 73.6 1.0 NE2 A:HIS183 4.3 54.5 1.0 CG A:HIS237 4.4 69.2 1.0 CG A:HIS212 4.4 60.8 1.0 ND1 A:HIS237 4.4 69.8 1.0 O1 A:PO4903 4.5 77.0 1.0 ND2 A:ASN265 4.5 67.3 1.0 CB A:ASP184 4.7 67.4 1.0 OD1 A:ASN265 4.8 71.9 1.0 CG A:ASN265 4.9 71.2 1.0 CE1 A:HIS187 5.0 77.9 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