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Iron in PDB 1d4e: Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate

Enzymatic activity of Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate

All present enzymatic activity of Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate:
1.3.99.1;

Protein crystallography data

The structure of Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate, PDB code: 1d4e was solved by D.Leys, A.S.Tsapin, T.E.Meyer, M.A.Cusanovich, J.J.Van Beeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.080, 73.080, 216.200, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 31.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate (pdb code 1d4e). 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 the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate, PDB code: 1d4e:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1d4e

Go back to Iron Binding Sites List in 1d4e
Iron binding site 1 out of 4 in the Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate


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 the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:33.3
occ:1.00
 FE A:HEM601 0.0 33.3 1.0
NE2 A:HIS63 1.9 17.9 1.0
ND A:HEM601 2.0 35.0 1.0
NA A:HEM601 2.0 38.6 1.0
NB A:HEM601 2.0 36.0 1.0
NC A:HEM601 2.0 32.4 1.0
NE2 A:HIS88 2.0 23.5 1.0
CE1 A:HIS63 2.6 20.1 1.0
CE1 A:HIS88 2.8 23.5 1.0
C4D A:HEM601 3.0 36.1 1.0
C1D A:HEM601 3.0 35.2 1.0
C1B A:HEM601 3.0 37.0 1.0
C1A A:HEM601 3.0 39.9 1.0
C1C A:HEM601 3.0 31.8 1.0
C4A A:HEM601 3.0 39.4 1.0
C4C A:HEM601 3.1 29.6 1.0
C4B A:HEM601 3.1 35.5 1.0
CD2 A:HIS63 3.1 20.1 1.0
CD2 A:HIS88 3.2 24.8 1.0
CHA A:HEM601 3.3 38.1 1.0
CHC A:HEM601 3.4 33.1 1.0
CHB A:HEM601 3.4 37.9 1.0
CHD A:HEM601 3.4 32.0 1.0
ND1 A:HIS63 3.8 21.4 1.0
ND1 A:HIS88 4.0 25.0 1.0
CG A:HIS63 4.1 21.1 1.0
C3D A:HEM601 4.2 35.8 1.0
C2D A:HEM601 4.2 34.8 1.0
CG A:HIS88 4.2 25.5 1.0
C3C A:HEM601 4.2 29.2 1.0
C2A A:HEM601 4.2 41.1 1.0
C3A A:HEM601 4.3 40.4 1.0
C3B A:HEM601 4.3 35.6 1.0
C2C A:HEM601 4.3 30.6 1.0
C2B A:HEM601 4.3 37.2 1.0

Iron binding site 2 out of 4 in 1d4e

Go back to Iron Binding Sites List in 1d4e
Iron binding site 2 out of 4 in the Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate


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 the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:20.7
occ:1.00
 FE A:HEM602 0.0 20.7 1.0
NE2 A:HIS60 1.9 20.7 1.0
NC A:HEM602 2.0 23.3 1.0
ND A:HEM602 2.0 24.5 1.0
NB A:HEM602 2.0 19.8 1.0
NA A:HEM602 2.0 23.3 1.0
NE2 A:HIS74 2.1 23.1 1.0
CD2 A:HIS60 2.8 23.3 1.0
CD2 A:HIS74 2.9 23.7 1.0
C4B A:HEM602 3.0 18.9 1.0
C4D A:HEM602 3.0 27.9 1.0
C1C A:HEM602 3.0 22.4 1.0
C1D A:HEM602 3.0 25.4 1.0
CE1 A:HIS60 3.0 22.4 1.0
C4C A:HEM602 3.0 23.7 1.0
C1B A:HEM602 3.0 19.8 1.0
C1A A:HEM602 3.1 22.7 1.0
C4A A:HEM602 3.1 22.9 1.0
CE1 A:HIS74 3.2 25.3 1.0
CHD A:HEM602 3.4 25.4 1.0
CHC A:HEM602 3.4 19.9 1.0
CHA A:HEM602 3.4 25.5 1.0
CHB A:HEM602 3.4 21.8 1.0
CG A:HIS60 4.0 24.9 1.0
ND1 A:HIS60 4.1 24.2 1.0
CG A:HIS74 4.1 23.8 1.0
ND1 A:HIS74 4.2 25.5 1.0
C2D A:HEM602 4.2 27.7 1.0
C3B A:HEM602 4.2 18.2 1.0
C2C A:HEM602 4.2 22.7 1.0
C3D A:HEM602 4.2 29.9 1.0
C3C A:HEM602 4.2 22.5 1.0
C2B A:HEM602 4.3 19.0 1.0
C2A A:HEM602 4.3 22.8 1.0
C3A A:HEM602 4.3 23.4 1.0

Iron binding site 3 out of 4 in 1d4e

Go back to Iron Binding Sites List in 1d4e
Iron binding site 3 out of 4 in the Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate


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 the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:43.4
occ:1.00
 FE A:HEM603 0.0 43.4 1.0
NE2 A:HIS19 1.9 28.1 1.0
NE2 A:HIS77 2.0 31.4 1.0
ND A:HEM603 2.0 44.6 1.0
NA A:HEM603 2.0 47.6 1.0
NC A:HEM603 2.0 44.3 1.0
NB A:HEM603 2.0 48.0 1.0
CE1 A:HIS19 2.8 30.7 1.0
CD2 A:HIS19 2.9 30.2 1.0
CE1 A:HIS77 2.9 33.9 1.0
CD2 A:HIS77 3.0 33.3 1.0
C4A A:HEM603 3.0 49.7 1.0
C4D A:HEM603 3.0 44.5 1.0
C1D A:HEM603 3.0 43.2 1.0
C4C A:HEM603 3.0 42.6 1.0
C1A A:HEM603 3.0 48.0 1.0
C1B A:HEM603 3.0 49.4 1.0
C1C A:HEM603 3.1 44.2 1.0
C4B A:HEM603 3.1 48.7 1.0
CHD A:HEM603 3.4 43.2 1.0
CHA A:HEM603 3.4 46.4 1.0
CHB A:HEM603 3.4 50.1 1.0
CHC A:HEM603 3.5 46.3 1.0
ND1 A:HIS19 3.9 32.1 1.0
CG A:HIS19 4.0 31.2 1.0
ND1 A:HIS77 4.1 33.6 1.0
CG A:HIS77 4.1 34.2 1.0
C3A A:HEM603 4.2 50.0 1.0
C2A A:HEM603 4.2 50.8 1.0
C3D A:HEM603 4.2 43.3 1.0
C2D A:HEM603 4.2 42.4 1.0
C3C A:HEM603 4.2 41.8 1.0
C2C A:HEM603 4.3 43.2 1.0
C3B A:HEM603 4.3 50.7 1.0
C2B A:HEM603 4.3 51.0 1.0

Iron binding site 4 out of 4 in 1d4e

Go back to Iron Binding Sites List in 1d4e
Iron binding site 4 out of 4 in the Crystal Structure of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate


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 the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 Complexed with Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:28.0
occ:1.00
 FE A:HEM604 0.0 28.0 1.0
NA A:HEM604 2.0 29.2 1.0
NC A:HEM604 2.0 27.3 1.0
NB A:HEM604 2.0 28.1 1.0
NE2 A:HIS9 2.0 34.5 1.0
ND A:HEM604 2.0 30.1 1.0
NE2 A:HIS42 2.1 15.8 1.0
CE1 A:HIS9 2.7 35.5 1.0
C1A A:HEM604 3.0 30.4 1.0
C4C A:HEM604 3.0 28.3 1.0
C1C A:HEM604 3.0 27.2 1.0
C4A A:HEM604 3.0 30.1 1.0
C1B A:HEM604 3.0 27.1 1.0
CE1 A:HIS42 3.0 16.4 1.0
C4B A:HEM604 3.1 27.2 1.0
C4D A:HEM604 3.1 30.9 1.0
C1D A:HEM604 3.1 30.1 1.0
CD2 A:HIS42 3.2 17.0 1.0
CD2 A:HIS9 3.2 37.3 1.0
CHB A:HEM604 3.3 28.8 1.0
CHD A:HEM604 3.4 30.3 1.0
CHA A:HEM604 3.4 30.6 1.0
CHC A:HEM604 3.4 27.3 1.0
ND1 A:HIS9 3.9 37.8 1.0
CG A:HIS9 4.2 40.2 1.0
ND1 A:HIS42 4.2 16.6 1.0
C3C A:HEM604 4.2 27.7 1.0
C2C A:HEM604 4.2 27.6 1.0
C2A A:HEM604 4.2 32.3 1.0
C2B A:HEM604 4.2 26.0 1.0
C3A A:HEM604 4.2 31.4 1.0
C3B A:HEM604 4.2 25.7 1.0
CG A:HIS42 4.3 17.4 1.0
C2D A:HEM604 4.3 30.2 1.0
C3D A:HEM604 4.3 30.1 1.0

Reference:

D.Leys, A.S.Tsapin, K.H.Nealson, T.E.Meyer, M.A.Cusanovich, J.J.Van Beeumen. Structure and Mechanism of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Mr-1. Nat.Struct.Biol. V. 6 1113 1999.
ISSN: ISSN 1072-8368
PubMed: 10581551
DOI: 10.1038/70051
Page generated: Sun Dec 13 14:10:07 2020

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