Iron in PDB 3bfj: Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase

All present enzymatic activity of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase:
1.1.1.202;

The structure of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase, PDB code: 3bfj was solved by D.Marcal, F.J.Enguita, M.A.Carrondo, Structural Proteomics In Europe(Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.937, 226.611, 232.627, 90.00, 92.91, 90.00
R / Rfree (%)	20.3 / 25.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase (pdb code 3bfj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase, PDB code: 3bfj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1388 b:41.7 occ:1.00 NE2 A:HIS267 2.0 42.1 1.0 O A:HOH1424 2.3 41.0 1.0 NE2 A:HIS202 2.4 44.1 1.0 OD1 A:ASP198 2.4 42.6 1.0 O A:HOH1418 2.5 32.9 1.0 NE2 A:HIS281 2.5 48.5 1.0 CE1 A:HIS267 3.0 41.8 1.0 CD2 A:HIS267 3.0 42.2 1.0 CE1 A:HIS202 3.1 43.8 1.0 CG A:ASP198 3.2 44.0 1.0 CD2 A:HIS281 3.2 48.6 1.0 OD2 A:ASP198 3.2 44.0 1.0 CD2 A:HIS202 3.4 44.2 1.0 CE1 A:HIS281 3.6 48.9 1.0 OD1 A:ASN285 3.7 48.7 1.0 ND1 A:HIS267 4.1 41.6 1.0 CG A:HIS267 4.2 42.1 1.0 ND1 A:HIS202 4.2 44.2 1.0 CG A:HIS202 4.4 44.7 1.0 CG A:HIS281 4.4 48.9 1.0 ND1 A:HIS281 4.6 48.9 1.0 CB A:ASP198 4.7 44.4 1.0 CG A:ASN285 4.7 47.6 1.0 O A:ASP198 4.8 44.7 1.0

Iron binding site 2 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1388 b:40.1 occ:1.00 NE2 B:HIS267 2.2 44.1 1.0 NE2 B:HIS281 2.2 50.1 1.0 NE2 B:HIS202 2.3 42.1 1.0 OD1 B:ASP198 2.4 45.0 1.0 O B:HOH1433 2.5 38.2 1.0 CD2 B:HIS267 3.1 43.8 1.0 CE1 B:HIS202 3.1 42.2 1.0 CD2 B:HIS281 3.2 50.0 1.0 CG B:ASP198 3.2 45.5 1.0 CE1 B:HIS281 3.2 49.7 1.0 OD2 B:ASP198 3.2 46.3 1.0 CE1 B:HIS267 3.2 43.6 1.0 CD2 B:HIS202 3.3 41.9 1.0 OD1 B:ASN285 3.9 50.0 1.0 ND1 B:HIS202 4.2 42.5 1.0 CG B:HIS267 4.3 43.8 1.0 ND1 B:HIS281 4.3 49.8 1.0 CG B:HIS281 4.3 49.7 1.0 ND1 B:HIS267 4.3 43.8 1.0 CG B:HIS202 4.4 42.8 1.0 CB B:ASP198 4.7 44.6 1.0 O B:ASP198 4.8 44.6 1.0 CG B:ASN285 4.9 48.9 1.0

Iron binding site 3 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1388 b:43.2 occ:1.00 NE2 C:HIS267 2.1 42.1 1.0 O C:HOH1415 2.2 30.1 1.0 NE2 C:HIS202 2.2 43.7 1.0 NE2 C:HIS281 2.3 48.6 1.0 OD1 C:ASP198 2.4 45.0 1.0 CD2 C:HIS267 3.0 42.2 1.0 CE1 C:HIS202 3.1 43.5 1.0 CD2 C:HIS281 3.1 49.0 1.0 CE1 C:HIS267 3.1 42.6 1.0 CD2 C:HIS202 3.2 43.9 1.0 CG C:ASP198 3.3 45.5 1.0 CE1 C:HIS281 3.4 49.0 1.0 OD2 C:ASP198 3.5 46.5 1.0 OD1 C:ASN285 3.7 47.1 1.0 CG C:HIS267 4.2 41.9 1.0 ND1 C:HIS267 4.2 42.5 1.0 ND1 C:HIS202 4.2 44.1 1.0 CG C:HIS202 4.3 44.1 1.0 CG C:HIS281 4.4 49.5 1.0 ND1 C:HIS281 4.5 49.6 1.0 O C:ASP198 4.7 44.9 1.0 CB C:ASP198 4.7 45.2 1.0 CG C:ASN285 4.8 46.0 1.0 CD1 C:LEU263 4.9 42.3 1.0

Iron binding site 4 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1388 b:38.9 occ:1.00 O D:HOH1437 2.0 25.9 1.0 O D:HOH1436 2.1 34.4 1.0 NE2 D:HIS267 2.2 43.2 1.0 NE2 D:HIS281 2.3 49.4 1.0 OD1 D:ASP198 2.3 45.8 1.0 NE2 D:HIS202 2.3 42.8 1.0 CD2 D:HIS281 3.1 49.3 1.0 CG D:ASP198 3.1 45.8 1.0 CD2 D:HIS267 3.2 43.1 1.0 OD2 D:ASP198 3.2 47.1 1.0 CE1 D:HIS202 3.2 42.9 1.0 CE1 D:HIS267 3.3 43.4 1.0 CD2 D:HIS202 3.3 42.8 1.0 CE1 D:HIS281 3.4 49.1 1.0 OD1 D:ASN285 3.7 49.1 1.0 CG D:HIS281 4.3 49.5 1.0 ND1 D:HIS202 4.3 43.1 1.0 CG D:HIS267 4.3 43.4 1.0 ND1 D:HIS267 4.4 43.1 1.0 ND1 D:HIS281 4.4 49.3 1.0 CG D:HIS202 4.4 43.9 1.0 CB D:ASP198 4.6 45.5 1.0 O D:ASP198 4.7 45.3 1.0 CG D:ASN285 4.8 47.9 1.0 O D:GLY145 4.9 46.3 1.0

Iron binding site 5 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1388 b:30.9 occ:1.00 O E:HOH1464 1.9 26.7 1.0 NE2 E:HIS267 2.2 42.2 1.0 O E:HOH1407 2.2 23.1 1.0 OD1 E:ASP198 2.3 47.2 1.0 NE2 E:HIS202 2.3 38.4 1.0 NE2 E:HIS281 2.3 48.4 1.0 CD2 E:HIS267 3.1 42.7 1.0 CE1 E:HIS202 3.2 39.5 1.0 CG E:ASP198 3.2 46.8 1.0 CE1 E:HIS267 3.2 42.5 1.0 CD2 E:HIS281 3.2 48.1 1.0 CD2 E:HIS202 3.3 40.3 1.0 CE1 E:HIS281 3.3 48.0 1.0 OD2 E:ASP198 3.4 47.2 1.0 OD1 E:ASN285 3.7 47.6 1.0 ND1 E:HIS202 4.3 41.1 1.0 CG E:HIS267 4.3 42.6 1.0 ND1 E:HIS267 4.3 42.0 1.0 CG E:HIS202 4.3 42.4 1.0 ND1 E:HIS281 4.4 47.9 1.0 CG E:HIS281 4.4 47.8 1.0 CB E:ASP198 4.6 46.0 1.0 O E:ASP198 4.7 45.8 1.0 CG E:ASN285 4.9 46.1 1.0

Iron binding site 6 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1388 b:51.1 occ:1.00 O F:HOH1407 2.2 42.6 1.0 NE2 F:HIS281 2.3 49.0 1.0 NE2 F:HIS267 2.3 44.3 1.0 OD1 F:ASP198 2.3 44.9 1.0 NE2 F:HIS202 2.3 43.6 1.0 CE1 F:HIS202 3.1 43.5 1.0 CD2 F:HIS281 3.1 48.2 1.0 CG F:ASP198 3.2 45.3 1.0 CD2 F:HIS267 3.2 43.3 1.0 OD2 F:ASP198 3.2 44.8 1.0 CE1 F:HIS267 3.3 44.3 1.0 CE1 F:HIS281 3.3 48.5 1.0 CD2 F:HIS202 3.4 44.1 1.0 OD1 F:ASN285 4.0 48.4 1.0 ND1 F:HIS202 4.2 44.0 1.0 CG F:HIS281 4.3 48.5 1.0 CG F:HIS202 4.3 44.7 1.0 ND1 F:HIS267 4.3 43.7 1.0 CG F:HIS267 4.4 43.4 1.0 ND1 F:HIS281 4.4 48.7 1.0 O F:ASP198 4.6 45.3 1.0 CB F:ASP198 4.6 45.4 1.0

Iron binding site 7 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe1388 b:43.6 occ:1.00 O G:HOH1429 2.1 41.9 1.0 NE2 G:HIS281 2.1 49.4 1.0 NE2 G:HIS202 2.2 41.7 1.0 NE2 G:HIS267 2.2 43.5 1.0 OD1 G:ASP198 2.4 46.8 1.0 CD2 G:HIS281 3.1 49.6 1.0 CE1 G:HIS202 3.1 42.4 1.0 CE1 G:HIS281 3.1 49.5 1.0 CD2 G:HIS267 3.1 43.1 1.0 CD2 G:HIS202 3.2 42.0 1.0 CE1 G:HIS267 3.2 43.2 1.0 CG G:ASP198 3.3 46.1 1.0 OD2 G:ASP198 3.6 46.3 1.0 OD1 G:ASN285 4.0 49.7 1.0 ND1 G:HIS202 4.2 42.8 1.0 ND1 G:HIS281 4.2 49.4 1.0 CG G:HIS281 4.2 49.6 1.0 CG G:HIS202 4.3 43.2 1.0 CG G:HIS267 4.3 43.0 1.0 ND1 G:HIS267 4.3 43.0 1.0 CB G:ASP198 4.7 45.6 1.0 O G:ASP198 4.8 45.5 1.0 CG G:ASN285 4.9 48.7 1.0

Iron binding site 8 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe1388 b:31.2 occ:1.00 O H:HOH1451 2.2 38.5 1.0 NE2 H:HIS267 2.2 43.0 1.0 NE2 H:HIS202 2.3 41.4 1.0 OD1 H:ASP198 2.3 46.7 1.0 NE2 H:HIS281 2.3 47.7 1.0 CG H:ASP198 3.1 46.3 1.0 CD2 H:HIS267 3.2 43.0 1.0 CE1 H:HIS202 3.2 41.5 1.0 CD2 H:HIS281 3.2 47.6 1.0 CE1 H:HIS267 3.2 42.7 1.0 OD2 H:ASP198 3.2 45.5 1.0 CD2 H:HIS202 3.3 41.7 1.0 CE1 H:HIS281 3.3 46.2 1.0 OD1 H:ASN285 4.0 49.8 1.0 ND1 H:HIS202 4.3 42.8 1.0 ND1 H:HIS267 4.3 43.2 1.0 CG H:HIS267 4.4 43.1 1.0 CG H:HIS202 4.4 42.8 1.0 CG H:HIS281 4.4 47.5 1.0 ND1 H:HIS281 4.4 47.1 1.0 CB H:ASP198 4.6 45.3 1.0 O H:ASP198 4.8 45.7 1.0 CD1 H:LEU263 5.0 41.4 1.0

Iron binding site 9 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe1388 b:36.9 occ:1.00 O I:HOH1439 2.1 46.5 1.0 O I:HOH1394 2.2 28.2 1.0 OD1 I:ASP198 2.3 42.8 1.0 NE2 I:HIS267 2.3 41.1 1.0 NE2 I:HIS281 2.3 48.8 1.0 NE2 I:HIS202 2.4 41.8 1.0 CD2 I:HIS267 3.2 41.2 1.0 CD2 I:HIS281 3.2 49.2 1.0 CD2 I:HIS202 3.2 41.9 1.0 CG I:ASP198 3.3 44.0 1.0 CE1 I:HIS281 3.4 48.8 1.0 CE1 I:HIS267 3.4 41.7 1.0 CE1 I:HIS202 3.4 42.1 1.0 OD2 I:ASP198 3.5 44.3 1.0 OD1 I:ASN285 3.8 50.3 1.0 CG I:HIS267 4.4 40.9 1.0 CG I:HIS281 4.4 49.4 1.0 CG I:HIS202 4.4 43.2 1.0 ND1 I:HIS281 4.4 49.6 1.0 ND1 I:HIS267 4.4 41.1 1.0 ND1 I:HIS202 4.5 42.3 1.0 CB I:ASP198 4.7 44.1 1.0 O I:ASP198 4.8 44.0 1.0 CG I:ASN285 4.9 48.0 1.0

Iron binding site 10 out of 20 in the Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure Analysis of 1,3-Propanediol Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe1388 b:43.1 occ:1.00 NE2 J:HIS202 2.2 43.7 1.0 NE2 J:HIS281 2.3 51.5 1.0 NE2 J:HIS267 2.4 44.8 1.0 OD1 J:ASP198 2.4 44.7 1.0 O J:HOH1419 2.5 38.8 1.0 CE1 J:HIS202 3.1 43.7 1.0 CE1 J:HIS281 3.2 52.2 1.0 CD2 J:HIS202 3.2 43.8 1.0 CD2 J:HIS267 3.2 44.6 1.0 CD2 J:HIS281 3.3 51.4 1.0 CG J:ASP198 3.3 45.0 1.0 CE1 J:HIS267 3.4 44.6 1.0 OD2 J:ASP198 3.5 44.7 1.0 OD1 J:ASN285 4.1 48.4 1.0 ND1 J:HIS202 4.2 44.2 1.0 ND1 J:HIS281 4.3 52.2 1.0 CG J:HIS202 4.3 43.9 1.0 CG J:HIS281 4.4 51.5 1.0 CG J:HIS267 4.4 44.2 1.0 ND1 J:HIS267 4.5 44.1 1.0 CB J:ASP198 4.7 44.7 1.0 O J:ASP198 4.8 44.6 1.0

D.Marcal, A.T.Rego, M.A.Carrondo, F.J.Enguita. 1,3-Propanediol Dehydrogenase From Klebsiella Pneumoniae: Decameric Quaternary Structure and Possible Subunit Cooperativity J.Bacteriol. V. 191 1143 2009.
ISSN: ISSN 0021-9193
PubMed: 19011020
DOI: 10.1128/JB.01077-08