Iron in PDB 3o0f: Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution

The structure of Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution, PDB code: 3o0f was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.75 / 1.94
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	103.341, 103.341, 54.744, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 19.2

The structure of Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution (pdb code 3o0f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution, PDB code: 3o0f:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution


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 A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:27.3 occ:1.00 O A:HOH483 2.0 24.8 1.0 OE2 A:GLU74 2.2 25.5 1.0 NE2 A:HIS202 2.3 23.9 1.0 O2 A:PO4305 2.3 32.3 1.0 ND1 A:HIS85 2.4 33.0 1.0 CD A:GLU74 3.1 17.5 1.0 CE1 A:HIS202 3.2 23.6 1.0 CD2 A:HIS202 3.3 23.2 1.0 CG A:HIS85 3.3 26.9 1.0 CE1 A:HIS85 3.4 36.2 1.0 P A:PO4305 3.4 43.3 1.0 O A:HOH461 3.4 47.9 1.0 OE1 A:GLU74 3.4 19.7 1.0 O4 A:PO4305 3.4 31.3 1.0 FE A:FE304 3.5 26.6 1.0 CB A:HIS85 3.6 17.6 1.0 O1 A:PO4305 3.9 34.4 1.0 OD2 A:ASP260 4.3 26.4 1.0 ND1 A:HIS202 4.4 26.6 1.0 CG A:GLU74 4.4 13.4 1.0 O3' A:AMP301 4.4 30.9 1.0 CG A:HIS202 4.4 19.9 1.0 NE2 A:HIS85 4.5 39.9 1.0 CD2 A:HIS85 4.5 37.0 1.0 NE2 A:HIS17 4.5 12.9 1.0 CE1 A:HIS17 4.6 15.6 1.0 CE1 A:HIS49 4.7 14.1 1.0 O3 A:PO4305 4.7 33.5 1.0 CB A:ALA201 4.8 11.9 1.0 OD1 A:ASP260 4.9 18.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution


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 A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe304 b:26.6 occ:1.00 O4 A:PO4305 2.0 31.3 1.0 O A:HOH483 2.1 24.8 1.0 OE1 A:GLU74 2.2 19.7 1.0 NE2 A:HIS17 2.2 12.9 1.0 OD1 A:ASP260 2.3 18.1 1.0 NE2 A:HIS19 2.3 20.7 1.0 CD2 A:HIS17 3.0 15.3 1.0 CD A:GLU74 3.1 17.5 1.0 CG A:ASP260 3.1 18.9 1.0 CE1 A:HIS19 3.2 17.7 1.0 CE1 A:HIS17 3.2 15.6 1.0 CD2 A:HIS19 3.3 28.1 1.0 P A:PO4305 3.3 43.3 1.0 OE2 A:GLU74 3.3 25.5 1.0 OD2 A:ASP260 3.4 26.4 1.0 FE A:FE303 3.5 27.3 1.0 O2 A:PO4305 3.7 32.3 1.0 O1 A:PO4305 4.1 34.4 1.0 O3 A:PO4305 4.2 33.5 1.0 CG A:HIS17 4.2 16.2 1.0 CE1 A:HIS262 4.2 17.6 1.0 ND1 A:HIS17 4.3 16.7 1.0 ND1 A:HIS19 4.3 20.6 1.0 CG A:HIS19 4.4 13.1 1.0 ZN A:ZN302 4.4 25.3 1.0 CB A:ASP260 4.4 14.0 1.0 CG A:GLU74 4.4 13.4 1.0 CE1 A:HIS49 4.5 14.1 1.0 NE2 A:HIS49 4.6 14.6 1.0 NE2 A:HIS262 4.7 17.8 1.0 CA A:ASP260 4.7 12.2 1.0 CB A:GLU74 4.8 13.2 1.0 NE2 A:HIS202 4.9 23.9 1.0

G.W.Han, J.Ko, C.L.Farr, M.C.Deller, Q.Xu, H.J.Chiu, M.D.Miller, J.Sefcikova, S.Somarowthu, P.J.Beuning, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson, M.J.Ondrechen. Crystal Structure of A Metal-Dependent Phosphoesterase (YP_910028.1) From Bifidobacterium Adolescentis: Computational Prediction and Experimental Validation of Phosphoesterase Activity. Proteins V. 79 2146 2011.
ISSN: ISSN 0887-3585
PubMed: 21538547
DOI: 10.1002/PROT.23035