Iron in PDB 5v5q: Dehaloperoxidase B L9I Mutant

The structure of Dehaloperoxidase B L9I Mutant, PDB code: 5v5q was solved by L.M.Carey, R.A.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.81 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.818, 67.658, 67.554, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.9

The binding sites of Iron atom in the Dehaloperoxidase B L9I Mutant (pdb code 5v5q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Dehaloperoxidase B L9I Mutant, PDB code: 5v5q:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Dehaloperoxidase B L9I Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dehaloperoxidase B L9I Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.5 occ:0.45 FE A:HEM201 0.0 22.5 0.5 FE A:HEM201 0.0 22.6 0.6 NC A:HEM201 2.0 22.6 0.6 NC A:HEM201 2.0 22.6 0.5 ND A:HEM201 2.0 25.5 0.5 ND A:HEM201 2.0 25.5 0.6 NA A:HEM201 2.1 21.4 0.5 NB A:HEM201 2.1 19.2 0.6 NA A:HEM201 2.1 21.4 0.6 NB A:HEM201 2.1 19.1 0.5 O1 A:OXY203 2.4 18.4 1.0 NE2 A:HIS89 2.5 29.6 1.0 C4C A:HEM201 3.0 20.8 0.6 C4C A:HEM201 3.0 20.8 0.5 C1C A:HEM201 3.0 22.7 0.6 C1C A:HEM201 3.0 22.6 0.5 C1D A:HEM201 3.0 20.9 0.5 C1D A:HEM201 3.0 20.8 0.5 C4D A:HEM201 3.1 22.7 0.5 C1A A:HEM201 3.1 21.7 0.5 C4D A:HEM201 3.1 22.7 0.6 C4A A:HEM201 3.1 18.9 0.5 C4B A:HEM201 3.1 19.9 0.6 C1B A:HEM201 3.1 17.0 0.6 C4A A:HEM201 3.1 18.9 0.6 C1B A:HEM201 3.1 17.1 0.5 C4B A:HEM201 3.1 19.9 0.5 C1A A:HEM201 3.1 21.7 0.6 CD2 A:HIS89 3.3 31.4 1.0 CHD A:HEM201 3.4 22.2 0.6 CHD A:HEM201 3.4 22.2 0.5 CHC A:HEM201 3.4 22.2 0.6 CHC A:HEM201 3.4 22.2 0.5 CHA A:HEM201 3.4 21.3 0.5 CHB A:HEM201 3.5 14.8 0.6 CHB A:HEM201 3.5 14.8 0.5 CHA A:HEM201 3.5 21.2 0.6 CE1 A:HIS89 3.5 23.8 1.0 O2 A:OXY203 3.6 23.6 1.0 C3C A:HEM201 4.2 24.3 0.6 C2C A:HEM201 4.2 21.6 0.6 C3C A:HEM201 4.2 24.3 0.5 C2C A:HEM201 4.2 21.6 0.5 C2D A:HEM201 4.3 22.6 0.5 C3D A:HEM201 4.3 23.9 0.5 C2D A:HEM201 4.3 22.6 0.6 C3D A:HEM201 4.3 23.9 0.6 C2A A:HEM201 4.3 20.1 0.5 C3A A:HEM201 4.3 23.6 0.5 C2B A:HEM201 4.3 18.9 0.6 C3B A:HEM201 4.3 18.9 0.6 C3A A:HEM201 4.3 23.7 0.6 C2B A:HEM201 4.4 18.9 0.5 C2A A:HEM201 4.4 20.2 0.6 C3B A:HEM201 4.4 18.9 0.5 CG2 A:VAL59 4.4 18.7 1.0 CE1 A:HIS55 4.5 22.0 1.0 CG A:HIS89 4.5 27.1 1.0 ND1 A:HIS89 4.5 24.4 1.0 CE A:MET86 4.8 23.7 1.0

Iron binding site 2 out of 3 in the Dehaloperoxidase B L9I Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dehaloperoxidase B L9I Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.6 occ:0.55 FE A:HEM201 0.0 22.6 0.6 FE A:HEM201 0.0 22.5 0.5 NC A:HEM201 2.0 22.6 0.6 ND A:HEM201 2.0 25.5 0.5 ND A:HEM201 2.0 25.5 0.6 NA A:HEM201 2.0 21.4 0.5 NC A:HEM201 2.0 22.6 0.5 NA A:HEM201 2.1 21.4 0.6 NB A:HEM201 2.1 19.2 0.6 NB A:HEM201 2.1 19.1 0.5 O1 A:OXY203 2.4 18.4 1.0 NE2 A:HIS89 2.5 29.6 1.0 C4C A:HEM201 3.0 20.8 0.6 C4C A:HEM201 3.0 20.8 0.5 C4D A:HEM201 3.0 22.7 0.5 C1D A:HEM201 3.0 20.9 0.5 C1D A:HEM201 3.0 20.8 0.5 C1A A:HEM201 3.0 21.7 0.5 C1C A:HEM201 3.0 22.7 0.6 C4D A:HEM201 3.1 22.7 0.6 C4A A:HEM201 3.1 18.9 0.5 C1C A:HEM201 3.1 22.6 0.5 C4A A:HEM201 3.1 18.9 0.6 C1A A:HEM201 3.1 21.7 0.6 C1B A:HEM201 3.1 17.0 0.6 C1B A:HEM201 3.1 17.1 0.5 C4B A:HEM201 3.1 19.9 0.6 C4B A:HEM201 3.2 19.9 0.5 CD2 A:HIS89 3.3 31.4 1.0 CHD A:HEM201 3.4 22.2 0.6 CHD A:HEM201 3.4 22.2 0.5 CHA A:HEM201 3.4 21.3 0.5 CHA A:HEM201 3.4 21.2 0.6 CHB A:HEM201 3.5 14.8 0.6 CHC A:HEM201 3.5 22.2 0.6 CHB A:HEM201 3.5 14.8 0.5 CHC A:HEM201 3.5 22.2 0.5 CE1 A:HIS89 3.5 23.8 1.0 O2 A:OXY203 3.6 23.6 1.0 C3C A:HEM201 4.2 24.3 0.6 C2C A:HEM201 4.2 21.6 0.6 C3C A:HEM201 4.2 24.3 0.5 C3D A:HEM201 4.2 23.9 0.5 C2D A:HEM201 4.3 22.6 0.5 C2C A:HEM201 4.3 21.6 0.5 C2D A:HEM201 4.3 22.6 0.6 C2A A:HEM201 4.3 20.1 0.5 C3D A:HEM201 4.3 23.9 0.6 C3A A:HEM201 4.3 23.6 0.5 C3A A:HEM201 4.3 23.7 0.6 C2A A:HEM201 4.3 20.2 0.6 C2B A:HEM201 4.3 18.9 0.6 C2B A:HEM201 4.4 18.9 0.5 C3B A:HEM201 4.4 18.9 0.6 CG2 A:VAL59 4.4 18.7 1.0 C3B A:HEM201 4.4 18.9 0.5 CE1 A:HIS55 4.4 22.0 1.0 CG A:HIS89 4.5 27.1 1.0 ND1 A:HIS89 4.5 24.4 1.0 CE A:MET86 4.7 23.7 1.0

Iron binding site 3 out of 3 in the Dehaloperoxidase B L9I Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dehaloperoxidase B L9I Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:22.5 occ:1.00 FE B:HEM201 0.0 22.5 1.0 NA B:HEM201 2.0 13.5 1.0 NB B:HEM201 2.0 17.5 1.0 NC B:HEM201 2.0 25.4 1.0 ND B:HEM201 2.1 18.5 1.0 NE2 B:HIS89 2.4 20.1 1.0 O1 B:OXY203 2.4 15.1 1.0 C4B B:HEM201 3.0 15.2 1.0 C4C B:HEM201 3.0 19.4 1.0 C1C B:HEM201 3.0 20.0 1.0 C4A B:HEM201 3.1 22.9 1.0 C1B B:HEM201 3.1 20.0 1.0 C1D B:HEM201 3.1 11.5 1.0 C1A B:HEM201 3.1 19.9 1.0 C4D B:HEM201 3.1 19.2 1.0 CD2 B:HIS89 3.2 31.3 1.0 CHC B:HEM201 3.4 14.3 1.0 CHD B:HEM201 3.4 21.7 1.0 CHB B:HEM201 3.4 15.6 1.0 CE1 B:HIS89 3.5 23.1 1.0 CHA B:HEM201 3.5 18.9 1.0 O2 B:OXY203 3.6 27.2 1.0 C3C B:HEM201 4.3 20.8 1.0 C2C B:HEM201 4.3 18.0 1.0 C3A B:HEM201 4.3 15.3 1.0 C2B B:HEM201 4.3 16.7 1.0 C3B B:HEM201 4.3 18.1 1.0 C2A B:HEM201 4.3 17.5 1.0 C2D B:HEM201 4.3 29.2 1.0 C3D B:HEM201 4.3 24.2 1.0 CG2 B:VAL59 4.4 18.3 1.0 CG B:HIS89 4.4 27.6 1.0 ND1 B:HIS89 4.5 23.5 1.0 CE1 B:HIS55 4.7 18.6 1.0 CE B:MET86 4.9 21.0 1.0

L.M.Carey, R.Gavenko, D.A.Svistunenko, R.A.Ghiladi. How Nature Tunes Isoenzyme Activity in the Multifunctional Catalytic Globin Dehaloperoxidase From Amphitrite Ornata. Biochim Biophys Acta V.1866 230 2018PROTEINS Proteom.
ISSN: ISSN 1570-9639
PubMed: 29128676
DOI: 10.1016/J.BBAPAP.2017.11.004