Iron in PDB 5v2d: Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase

The structure of Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase, PDB code: 5v2d was solved by P.C.Loewen, M.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	96.397, 104.673, 104.709, 90.00, 94.79, 90.00
R / Rfree (%)	16.1 / 19.3

The binding sites of Iron atom in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase (pdb code 5v2d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase, PDB code: 5v2d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase


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 Pseudomonas Brassicacearum Lignostilbene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:21.8 occ:1.00 O A:HOH780 2.1 26.5 1.0 NE2 A:HIS219 2.1 24.3 1.0 NE2 A:HIS284 2.1 25.7 1.0 NE2 A:HIS475 2.1 22.0 1.0 NE2 A:HIS168 2.1 22.2 1.0 CD2 A:HIS284 3.0 25.0 1.0 CE1 A:HIS219 3.0 24.7 1.0 CD2 A:HIS219 3.0 22.8 1.0 CD2 A:HIS475 3.1 22.0 1.0 CE1 A:HIS168 3.1 23.0 1.0 CE1 A:HIS284 3.1 28.4 1.0 CE1 A:HIS475 3.1 22.8 1.0 CD2 A:HIS168 3.2 22.6 1.0 O A:HOH850 4.1 39.5 1.0 ND1 A:HIS219 4.1 23.2 1.0 CG A:HIS284 4.2 25.3 1.0 ND1 A:HIS284 4.2 26.1 1.0 CG A:HIS219 4.2 23.1 1.0 ND1 A:HIS475 4.2 23.1 1.0 CG A:HIS475 4.2 22.5 1.0 ND1 A:HIS168 4.2 22.7 1.0 CG A:HIS168 4.3 22.6 1.0 CG2 A:THR122 4.5 23.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase


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 Pseudomonas Brassicacearum Lignostilbene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:21.5 occ:1.00 NE2 B:HIS284 2.1 23.7 1.0 O B:HOH812 2.1 29.3 1.0 NE2 B:HIS219 2.1 23.9 1.0 NE2 B:HIS168 2.1 24.5 1.0 NE2 B:HIS475 2.1 23.6 1.0 CD2 B:HIS284 3.0 25.3 1.0 CD2 B:HIS219 3.0 22.2 1.0 CD2 B:HIS475 3.1 22.5 1.0 CE1 B:HIS284 3.1 26.7 1.0 CE1 B:HIS168 3.1 24.9 1.0 CE1 B:HIS219 3.1 23.6 1.0 CE1 B:HIS475 3.1 22.1 1.0 CD2 B:HIS168 3.2 24.2 1.0 CG B:HIS284 4.1 26.0 1.0 ND1 B:HIS284 4.1 27.3 1.0 ND1 B:HIS219 4.2 22.3 1.0 CG B:HIS475 4.2 22.0 1.0 ND1 B:HIS475 4.2 23.0 1.0 CG B:HIS219 4.2 23.1 1.0 ND1 B:HIS168 4.2 23.0 1.0 CG B:HIS168 4.3 23.5 1.0 CG2 B:THR122 4.4 23.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe500 b:24.1 occ:1.00 NE2 C:HIS284 2.1 26.8 1.0 NE2 C:HIS219 2.1 24.4 1.0 O C:HOH765 2.1 25.1 1.0 NE2 C:HIS168 2.1 26.1 1.0 NE2 C:HIS475 2.1 24.4 1.0 CD2 C:HIS284 3.0 25.7 1.0 CD2 C:HIS475 3.1 23.7 1.0 CE1 C:HIS284 3.1 29.5 1.0 CE1 C:HIS168 3.1 26.5 1.0 CE1 C:HIS219 3.1 24.8 1.0 CD2 C:HIS219 3.1 24.9 1.0 CE1 C:HIS475 3.1 25.9 1.0 CD2 C:HIS168 3.2 25.2 1.0 CG C:HIS284 4.1 27.6 1.0 ND1 C:HIS284 4.1 28.7 1.0 ND1 C:HIS219 4.2 23.9 1.0 CG C:HIS475 4.2 25.3 1.0 ND1 C:HIS475 4.2 24.7 1.0 CG C:HIS219 4.2 24.2 1.0 ND1 C:HIS168 4.2 24.3 1.0 CG C:HIS168 4.3 24.7 1.0 CG2 C:THR122 4.4 26.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Pseudomonas Brassicacearum Lignostilbene Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe500 b:21.2 occ:1.00 NE2 D:HIS219 2.0 23.0 1.0 O D:HOH774 2.1 28.0 1.0 NE2 D:HIS284 2.1 23.2 1.0 NE2 D:HIS168 2.1 24.7 1.0 NE2 D:HIS475 2.1 22.2 1.0 CD2 D:HIS284 3.0 24.4 1.0 CD2 D:HIS219 3.0 23.8 1.0 CE1 D:HIS219 3.0 25.6 1.0 CE1 D:HIS168 3.0 26.5 1.0 CD2 D:HIS475 3.1 21.8 1.0 CE1 D:HIS284 3.1 26.0 1.0 CE1 D:HIS475 3.1 24.3 1.0 CD2 D:HIS168 3.1 26.4 1.0 ND1 D:HIS219 4.1 24.6 1.0 CG D:HIS284 4.2 24.5 1.0 CG D:HIS219 4.2 24.6 1.0 ND1 D:HIS284 4.2 26.4 1.0 ND1 D:HIS168 4.2 26.9 1.0 CG D:HIS475 4.2 22.9 1.0 ND1 D:HIS475 4.2 21.7 1.0 CG D:HIS168 4.3 25.7 1.0 O D:HOH852 4.3 36.5 1.0 CG2 D:THR122 4.4 22.4 1.0

P.C.Loewen, J.Switala, J.P.Wells, F.Huang, A.T.Zara, J.S.Allingham, M.C.Loewen. Structure and Function of A Lignostilbene-Alpha , Beta-Dioxygenase Orthologue From Pseudomonas Brassicacearum. Bmc Biochem. V. 19 8 2018.
ISSN: ESSN 1471-2091
PubMed: 30115012
DOI: 10.1186/S12858-018-0098-4