Iron in PDB 3e0f: Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 2.40 A Resolution

The structure of Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 2.40 A Resolution, PDB code: 3e0f 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)	29.58 / 2.40
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	102.460, 102.460, 54.170, 90.00, 90.00, 120.00
R / Rfree (%)	14.9 / 20.7

The structure of Crystal Structure of A Putative Metal-Dependent Phosphoesterase (BAD_1165) From Bifidobacterium Adolescentis Atcc 15703 at 2.40 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 2.40 A Resolution (pdb code 3e0f). 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 2.40 A Resolution, PDB code: 3e0f:
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 2.40 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 2.40 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:28.2 occ:1.00 O2 A:PO4304 2.0 32.5 1.0 OE2 A:GLU74 2.0 35.7 1.0 ND1 A:HIS85 2.2 45.1 1.0 NE2 A:HIS202 2.5 28.1 1.0 CE1 A:HIS85 3.0 41.5 1.0 CD A:GLU74 3.1 24.9 1.0 P A:PO4304 3.1 30.3 1.0 CG A:HIS85 3.2 39.7 1.0 CD2 A:HIS202 3.4 28.0 1.0 O4 A:PO4304 3.4 38.2 1.0 CE1 A:HIS202 3.5 32.3 1.0 FE A:FE303 3.5 29.0 1.0 OE1 A:GLU74 3.5 30.0 1.0 CB A:HIS85 3.6 30.7 1.0 O1 A:PO4304 3.6 34.0 1.0 NE2 A:HIS85 4.2 34.5 1.0 CD2 A:HIS85 4.3 37.2 1.0 OD2 A:ASP260 4.3 28.7 1.0 CG A:GLU74 4.4 28.2 1.0 O3 A:PO4304 4.4 31.7 1.0 NE2 A:HIS17 4.5 19.8 1.0 CG A:HIS202 4.6 31.4 1.0 ND1 A:HIS202 4.6 41.2 1.0 CE1 A:HIS17 4.6 23.8 1.0 CE1 A:HIS49 4.7 22.2 1.0 OD1 A:ASP260 4.9 30.3 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 2.40 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 2.40 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:29.0 occ:1.00 O4 A:PO4304 2.0 38.2 1.0 OE1 A:GLU74 2.1 30.0 1.0 NE2 A:HIS17 2.2 19.8 1.0 NE2 A:HIS19 2.3 24.7 1.0 OD1 A:ASP260 2.4 30.3 1.0 CD A:GLU74 3.0 24.9 1.0 CE1 A:HIS19 3.1 28.2 1.0 CD2 A:HIS17 3.1 20.0 1.0 CG A:ASP260 3.1 24.4 1.0 CE1 A:HIS17 3.2 23.8 1.0 P A:PO4304 3.3 30.3 1.0 OE2 A:GLU74 3.3 35.7 1.0 OD2 A:ASP260 3.3 28.7 1.0 CD2 A:HIS19 3.4 26.8 1.0 FE A:FE302 3.5 28.2 1.0 O2 A:PO4304 3.6 32.5 1.0 O1 A:PO4304 3.7 34.0 1.0 CE1 A:HIS262 4.2 18.4 1.0 ND1 A:HIS17 4.2 17.9 1.0 CG A:HIS17 4.2 23.2 1.0 ND1 A:HIS19 4.3 26.6 1.0 CG A:GLU74 4.4 28.2 1.0 ZN A:ZN301 4.4 39.2 1.0 CB A:ASP260 4.4 26.6 1.0 CG A:HIS19 4.4 19.3 1.0 CE1 A:HIS49 4.5 22.2 1.0 O3 A:PO4304 4.5 31.7 1.0 NE2 A:HIS262 4.6 21.3 1.0 CA A:ASP260 4.7 24.3 1.0 CB A:GLU74 4.8 24.1 1.0 NE2 A:HIS49 4.8 21.9 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