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Iron in PDB 3qnr: Dypb From Rhodococcus Jostii RHA1, Crystal Form 1

Protein crystallography data

The structure of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1, PDB code: 3qnr was solved by R.Singh, J.N.Roberts, J.C.Grigg, L.D.Eltis, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.41 / 2.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.379, 132.379, 160.211, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 21.8

Iron Binding Sites:

The binding sites of Iron atom in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 (pdb code 3qnr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1, PDB code: 3qnr:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3qnr

Go back to Iron Binding Sites List in 3qnr
Iron binding site 1 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:29.7
occ:1.00
FE A:HEM400 0.0 29.7 1.0
NA A:HEM400 2.0 27.1 1.0
NC A:HEM400 2.0 27.9 1.0
NB A:HEM400 2.0 29.2 1.0
NE2 A:HIS226 2.0 27.1 1.0
ND A:HEM400 2.1 27.1 1.0
O A:HOH518 2.2 41.2 1.0
CE1 A:HIS226 2.9 28.9 1.0
C4C A:HEM400 3.0 29.1 1.0
C1C A:HEM400 3.0 29.5 1.0
C1A A:HEM400 3.0 26.9 1.0
C4A A:HEM400 3.0 27.4 1.0
C4B A:HEM400 3.0 30.3 1.0
C1B A:HEM400 3.1 29.3 1.0
C4D A:HEM400 3.1 27.5 1.0
C1D A:HEM400 3.1 29.0 1.0
CD2 A:HIS226 3.1 27.7 1.0
CHA A:HEM400 3.4 25.6 1.0
CHC A:HEM400 3.4 29.1 1.0
CHD A:HEM400 3.4 29.2 1.0
CHB A:HEM400 3.4 26.1 1.0
ND1 A:HIS226 4.1 30.3 1.0
NH1 A:ARG244 4.1 33.6 1.0
CG A:HIS226 4.2 30.9 1.0
C3C A:HEM400 4.2 29.1 1.0
C2C A:HEM400 4.2 28.7 1.0
C3A A:HEM400 4.3 25.8 1.0
C2A A:HEM400 4.3 25.6 1.0
C3B A:HEM400 4.3 30.9 1.0
C2B A:HEM400 4.3 30.2 1.0
OD1 A:ASN230 4.3 36.5 1.0
C2D A:HEM400 4.3 26.7 1.0
C3D A:HEM400 4.3 27.9 1.0
CD A:ARG244 4.7 31.1 1.0
ND2 A:ASN246 4.8 38.7 1.0
CZ A:ARG244 4.9 31.6 1.0

Iron binding site 2 out of 3 in 3qnr

Go back to Iron Binding Sites List in 3qnr
Iron binding site 2 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:33.0
occ:1.00
FE B:HEM400 0.0 33.0 1.0
NB B:HEM400 1.9 30.9 1.0
NC B:HEM400 2.0 30.7 1.0
ND B:HEM400 2.0 30.0 1.0
NA B:HEM400 2.1 29.4 1.0
NE2 B:HIS226 2.1 38.8 1.0
O B:HOH394 2.3 44.1 1.0
C1B B:HEM400 3.0 32.5 1.0
C1D B:HEM400 3.0 32.3 1.0
C4C B:HEM400 3.0 29.9 1.0
C4B B:HEM400 3.0 32.5 1.0
C4A B:HEM400 3.0 29.9 1.0
CD2 B:HIS226 3.1 35.8 1.0
C1C B:HEM400 3.1 29.2 1.0
C4D B:HEM400 3.1 31.4 1.0
C1A B:HEM400 3.1 30.1 1.0
CE1 B:HIS226 3.2 37.4 1.0
CHD B:HEM400 3.3 30.5 1.0
CHB B:HEM400 3.4 30.5 1.0
CHC B:HEM400 3.4 30.7 1.0
CHA B:HEM400 3.5 31.2 1.0
NH1 B:ARG244 4.0 32.8 1.0
C2B B:HEM400 4.2 30.7 1.0
C3B B:HEM400 4.2 30.9 1.0
CG B:HIS226 4.2 37.8 1.0
C2D B:HEM400 4.2 30.2 1.0
C3C B:HEM400 4.2 28.6 1.0
ND1 B:HIS226 4.2 36.6 1.0
C2C B:HEM400 4.3 28.9 1.0
C3D B:HEM400 4.3 30.8 1.0
C3A B:HEM400 4.3 30.9 1.0
C2A B:HEM400 4.3 30.9 1.0
OD1 B:ASN230 4.5 37.7 1.0
CD B:ARG244 4.6 32.0 1.0
ND2 B:ASN246 4.7 41.3 1.0
CZ B:ARG244 4.8 33.3 1.0

Iron binding site 3 out of 3 in 3qnr

Go back to Iron Binding Sites List in 3qnr
Iron binding site 3 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:41.0
occ:1.00
FE C:HEM400 0.0 41.0 1.0
NB C:HEM400 2.0 37.2 1.0
ND C:HEM400 2.0 36.8 1.0
NE2 C:HIS226 2.0 44.9 1.0
NA C:HEM400 2.1 37.4 1.0
NC C:HEM400 2.1 40.5 1.0
O C:HOH456 2.1 58.6 1.0
CE1 C:HIS226 2.8 45.8 1.0
C4B C:HEM400 3.0 39.1 1.0
C1B C:HEM400 3.0 37.6 1.0
C1D C:HEM400 3.1 39.9 1.0
C4A C:HEM400 3.1 34.4 1.0
C1A C:HEM400 3.1 35.0 1.0
C4D C:HEM400 3.1 38.7 1.0
C4C C:HEM400 3.1 40.4 1.0
C1C C:HEM400 3.1 39.0 1.0
CD2 C:HIS226 3.2 46.3 1.0
CHB C:HEM400 3.4 35.9 1.0
CHA C:HEM400 3.4 36.5 1.0
CHD C:HEM400 3.4 40.3 1.0
CHC C:HEM400 3.4 39.5 1.0
ND1 C:HIS226 4.0 46.1 1.0
NH1 C:ARG244 4.1 42.2 1.0
CG C:HIS226 4.2 46.3 1.0
C3B C:HEM400 4.2 36.7 1.0
C2B C:HEM400 4.2 35.1 1.0
C3A C:HEM400 4.3 34.2 1.0
C2A C:HEM400 4.3 34.9 1.0
C2D C:HEM400 4.3 38.8 1.0
C3D C:HEM400 4.3 37.1 1.0
C3C C:HEM400 4.3 40.8 1.0
C2C C:HEM400 4.4 41.3 1.0
OD1 C:ASN230 4.4 50.5 1.0
CD C:ARG244 4.6 42.0 1.0
ND2 C:ASN246 4.7 44.7 1.0
CZ C:ARG244 4.8 42.5 1.0

Reference:

J.N.Roberts, R.Singh, J.C.Grigg, M.E.Murphy, T.D.Bugg, L.D.Eltis. Characterization of Dye-Decolorizing Peroxidases From Rhodococcus Jostii RHA1. Biochemistry V. 50 5108 2011.
ISSN: ISSN 0006-2960
PubMed: 21534572
DOI: 10.1021/BI200427H
Page generated: Sun Aug 4 18:52:34 2024

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