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Iron in PDB 5chr: Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol

Protein crystallography data

The structure of Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol, PDB code: 5chr was solved by L.Carey, R.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.60 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.883, 67.192, 67.442, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 22

Iron Binding Sites:

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol (pdb code 5chr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol, PDB code: 5chr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5chr

Go back to Iron Binding Sites List in 5chr
Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:14.4
occ:1.00
FE A:HEM201 0.0 14.4 1.0
NA A:HEM201 2.0 11.1 1.0
NC A:HEM201 2.0 10.6 1.0
ND A:HEM201 2.1 13.5 1.0
NB A:HEM201 2.1 11.5 1.0
NE2 A:HIS89 2.3 14.1 1.0
O1 A:OXY205 2.5 14.7 0.5
C1A A:HEM201 3.0 16.4 1.0
C1C A:HEM201 3.0 16.0 1.0
C4C A:HEM201 3.1 11.5 1.0
C4A A:HEM201 3.1 11.6 1.0
C4D A:HEM201 3.1 20.7 1.0
C1D A:HEM201 3.1 14.3 1.0
C4B A:HEM201 3.1 14.1 1.0
C1B A:HEM201 3.1 13.7 1.0
CD2 A:HIS89 3.2 15.6 1.0
CE1 A:HIS89 3.3 16.6 1.0
CHA A:HEM201 3.4 16.3 1.0
CHC A:HEM201 3.4 14.4 1.0
CHD A:HEM201 3.4 12.3 1.0
CHB A:HEM201 3.5 11.4 1.0
O2 A:OXY205 3.7 19.8 0.5
C5 A:4NC204 4.1 17.0 0.5
C2A A:HEM201 4.2 14.9 1.0
C2C A:HEM201 4.3 13.9 1.0
C3A A:HEM201 4.3 11.9 1.0
C3C A:HEM201 4.3 12.2 1.0
C3D A:HEM201 4.3 15.8 1.0
C2D A:HEM201 4.3 11.6 1.0
C3B A:HEM201 4.4 14.3 1.0
O10 A:4NC204 4.4 16.0 0.5
C2B A:HEM201 4.4 10.6 1.0
CG2 A:VAL59 4.4 12.4 1.0
CG A:HIS89 4.4 16.3 1.0
ND1 A:HIS89 4.4 14.2 1.0
CE A:MET86 4.7 17.7 1.0
C6 A:4NC204 4.7 16.5 0.5
CG1 A:VAL59 4.9 15.2 1.0
NE2 A:HIS55 4.9 18.5 0.4
C4 A:4NC204 5.0 12.6 0.5

Iron binding site 2 out of 2 in 5chr

Go back to Iron Binding Sites List in 5chr
Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:14.6
occ:1.00
FE B:HEM201 0.0 14.6 1.0
NA B:HEM201 2.0 12.5 1.0
NC B:HEM201 2.0 11.2 1.0
NB B:HEM201 2.1 12.3 1.0
ND B:HEM201 2.1 16.3 1.0
NE2 B:HIS89 2.3 13.3 1.0
C1A B:HEM201 3.0 13.7 1.0
C4C B:HEM201 3.1 19.9 1.0
C1C B:HEM201 3.1 17.5 1.0
C4A B:HEM201 3.1 15.4 1.0
C4D B:HEM201 3.1 18.5 1.0
C1B B:HEM201 3.1 14.7 1.0
C4B B:HEM201 3.1 14.5 1.0
C1D B:HEM201 3.1 16.7 1.0
CD2 B:HIS89 3.2 14.8 1.0
CE1 B:HIS89 3.2 15.4 1.0
CHA B:HEM201 3.4 13.8 1.0
CHB B:HEM201 3.4 9.8 1.0
CHD B:HEM201 3.5 16.3 1.0
CHC B:HEM201 3.5 14.9 1.0
CG2 B:VAL59 4.1 13.1 1.0
C5 B:4NC202 4.2 20.9 1.0
C2A B:HEM201 4.3 15.6 1.0
C3C B:HEM201 4.3 21.2 1.0
C2C B:HEM201 4.3 14.2 1.0
C3A B:HEM201 4.3 12.2 1.0
C2B B:HEM201 4.3 12.8 1.0
C3B B:HEM201 4.3 12.8 1.0
ND1 B:HIS89 4.3 21.7 1.0
C3D B:HEM201 4.3 21.4 1.0
C2D B:HEM201 4.3 13.1 1.0
CG B:HIS89 4.4 22.0 1.0
O10 B:4NC202 4.6 24.8 1.0
C6 B:4NC202 4.8 20.1 1.0
CG1 B:VAL59 4.8 10.1 1.0
CE B:MET86 5.0 21.4 1.0

Reference:

N.L.Mccombs, J.D'antonio, D.A.Barrios, L.M.Carey, R.A.Ghiladi. Nonmicrobial Nitrophenol Degradation Via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin From Amphitrite Ornata. Biochemistry V. 55 2465 2016.
ISSN: ISSN 0006-2960
PubMed: 27070125
DOI: 10.1021/ACS.BIOCHEM.6B00143
Page generated: Sun Dec 13 15:57:50 2020

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