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Iron in PDB 3lb3: Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin

Protein crystallography data

The structure of Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin, PDB code: 3lb3 was solved by V.S.De Serrano, S.Franzen, M.K.Thompson, M.F.Davis, F.P.Nicoletti, B.D.Howes, G.Smulevich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.201, 67.210, 68.724, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Other elements in 3lb3:

The structure of Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin (pdb code 3lb3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin, PDB code: 3lb3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3lb3

Go back to Iron Binding Sites List in 3lb3
Iron binding site 1 out of 2 in the Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe139

b:18.6
occ:1.00
FE A:HEM139 0.0 18.6 1.0
NC A:HEM139 2.0 16.6 1.0
ND A:HEM139 2.1 18.1 1.0
NA A:HEM139 2.1 16.6 1.0
NB A:HEM139 2.1 16.6 1.0
NE2 A:HIS89 2.1 20.5 1.0
C4C A:HEM139 3.0 17.3 1.0
C1A A:HEM139 3.1 18.5 1.0
C1C A:HEM139 3.1 15.3 1.0
C1D A:HEM139 3.1 18.4 1.0
C4D A:HEM139 3.1 18.9 1.0
CE1 A:HIS89 3.1 22.4 1.0
C4B A:HEM139 3.1 15.5 1.0
CD2 A:HIS89 3.1 23.4 1.0
C1B A:HEM139 3.1 15.3 1.0
C4A A:HEM139 3.1 17.2 1.0
CHD A:HEM139 3.4 18.1 1.0
CHA A:HEM139 3.4 17.6 1.0
CHC A:HEM139 3.5 18.2 1.0
CHB A:HEM139 3.5 16.6 1.0
C5 A:4CH191 4.0 84.8 1.0
CL9 A:4CH191 4.2 85.4 1.0
ND1 A:HIS89 4.2 22.7 1.0
CG A:HIS89 4.3 23.4 1.0
C3C A:HEM139 4.3 17.9 1.0
C2C A:HEM139 4.3 15.2 1.0
C2A A:HEM139 4.3 18.9 1.0
CG2 A:VAL59 4.3 15.2 1.0
C2D A:HEM139 4.3 19.4 1.0
C3D A:HEM139 4.3 19.6 1.0
C3A A:HEM139 4.3 17.4 1.0
C2B A:HEM139 4.3 15.6 1.0
C3B A:HEM139 4.3 15.7 1.0
C4 A:4CH191 4.6 84.3 1.0
CE A:MET86 4.8 25.6 1.0
CG1 A:VAL59 4.9 16.1 1.0

Iron binding site 2 out of 2 in 3lb3

Go back to Iron Binding Sites List in 3lb3
Iron binding site 2 out of 2 in the Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Two-Site Competitive Inhibition in Dehaloperoxidase-Hemoglobin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe139

b:17.6
occ:1.00
FE B:HEM139 0.0 17.6 1.0
NB B:HEM139 2.1 17.1 1.0
NC B:HEM139 2.1 17.6 1.0
ND B:HEM139 2.1 18.5 1.0
NA B:HEM139 2.1 17.2 1.0
NE2 B:HIS89 2.1 19.5 1.0
C4C B:HEM139 3.1 18.0 1.0
CE1 B:HIS89 3.1 19.6 1.0
C4B B:HEM139 3.1 17.3 1.0
C1D B:HEM139 3.1 19.4 1.0
C1B B:HEM139 3.1 17.6 1.0
C4A B:HEM139 3.1 16.9 1.0
C4D B:HEM139 3.1 20.0 1.0
C1C B:HEM139 3.1 18.1 1.0
C1A B:HEM139 3.1 18.7 1.0
CD2 B:HIS89 3.2 18.6 1.0
CHD B:HEM139 3.4 18.6 1.0
CHB B:HEM139 3.4 18.4 1.0
CHC B:HEM139 3.5 18.1 1.0
CHA B:HEM139 3.5 15.6 1.0
C3 B:4CH192 3.7 51.8 1.0
ND1 B:HIS89 4.2 19.5 1.0
C2 B:4CH192 4.2 50.9 1.0
CG2 B:VAL59 4.3 14.9 1.0
CG B:HIS89 4.3 19.6 1.0
C3B B:HEM139 4.3 17.9 1.0
C2B B:HEM139 4.3 16.8 1.0
C3C B:HEM139 4.3 18.6 1.0
C2D B:HEM139 4.3 18.6 1.0
C3D B:HEM139 4.3 19.7 1.0
C3A B:HEM139 4.3 15.3 1.0
C2C B:HEM139 4.3 17.5 1.0
C2A B:HEM139 4.3 18.3 1.0
CE B:MET86 4.6 18.8 1.0
C4 B:4CH192 4.6 50.5 0.9
CG1 B:VAL59 4.9 14.7 1.0
CL9 B:4CH192 4.9 53.0 1.0

Reference:

M.K.Thompson, M.F.Davis, V.De Serrano, F.P.Nicoletti, B.D.Howes, G.Smulevich, S.Franzen. Internal Binding of Halogenated Phenols in Dehaloperoxidase-Hemoglobin Inhibits Peroxidase Function. Biophys.J. V. 99 1586 2010.
ISSN: ISSN 0006-3495
PubMed: 20816071
DOI: 10.1016/J.BPJ.2010.05.041
Page generated: Sun Dec 13 15:11:10 2020

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