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Iron in PDB 1d4d: Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1

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

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

Protein crystallography data

The structure of Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1, PDB code: 1d4d 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) 8.50 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.863, 72.863, 216.469, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 30.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 (pdb code 1d4d). 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 Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1, PDB code: 1d4d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1d4d

Go back to Iron Binding Sites List in 1d4d
Iron binding site 1 out of 4 in the Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1


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

b:32.5
occ:1.00
FE A:HEM601 0.0 32.5 1.0
NE2 A:HIS88 1.9 24.5 1.0
NE2 A:HIS63 1.9 22.0 1.0
ND A:HEM601 2.0 37.0 1.0
NC A:HEM601 2.0 35.6 1.0
NB A:HEM601 2.0 36.7 1.0
NA A:HEM601 2.0 38.8 1.0
CE1 A:HIS88 2.7 24.7 1.0
CE1 A:HIS63 2.7 23.7 1.0
C4D A:HEM601 3.0 38.1 1.0
C1D A:HEM601 3.0 36.4 1.0
C1C A:HEM601 3.0 35.3 1.0
C4A A:HEM601 3.0 39.6 1.0
C4C A:HEM601 3.0 35.5 1.0
C1B A:HEM601 3.0 36.8 1.0
C4B A:HEM601 3.1 35.5 1.0
C1A A:HEM601 3.1 39.8 1.0
CD2 A:HIS63 3.1 23.7 1.0
CD2 A:HIS88 3.1 25.4 1.0
CHD A:HEM601 3.4 36.1 1.0
CHA A:HEM601 3.4 38.9 1.0
CHB A:HEM601 3.4 38.2 1.0
CHC A:HEM601 3.4 34.8 1.0
ND1 A:HIS88 3.9 25.0 1.0
ND1 A:HIS63 3.9 24.1 1.0
CG A:HIS88 4.1 25.1 1.0
CG A:HIS63 4.1 24.4 1.0
C3C A:HEM601 4.2 35.5 1.0
C3D A:HEM601 4.2 38.0 1.0
C2D A:HEM601 4.2 37.7 1.0
C2C A:HEM601 4.2 35.1 1.0
C3B A:HEM601 4.3 35.5 1.0
C2B A:HEM601 4.3 37.0 1.0
C3A A:HEM601 4.3 41.4 1.0
C2A A:HEM601 4.3 41.4 1.0

Iron binding site 2 out of 4 in 1d4d

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Iron binding site 2 out of 4 in the Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1


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

b:22.9
occ:1.00
FE A:HEM602 0.0 22.9 1.0
ND A:HEM602 2.0 25.0 1.0
NC A:HEM602 2.0 23.3 1.0
NA A:HEM602 2.0 23.3 1.0
NB A:HEM602 2.0 22.8 1.0
NE2 A:HIS60 2.0 23.3 1.0
NE2 A:HIS74 2.0 22.1 1.0
CD2 A:HIS74 2.8 24.1 1.0
CD2 A:HIS60 2.9 25.6 1.0
C4D A:HEM602 3.0 25.8 1.0
C1D A:HEM602 3.0 24.7 1.0
C1C A:HEM602 3.0 22.8 1.0
C1B A:HEM602 3.0 21.9 1.0
C4C A:HEM602 3.0 24.4 1.0
C4B A:HEM602 3.0 21.8 1.0
C1A A:HEM602 3.1 22.9 1.0
C4A A:HEM602 3.1 22.7 1.0
CE1 A:HIS60 3.1 24.4 1.0
CE1 A:HIS74 3.2 23.9 1.0
CHA A:HEM602 3.4 24.0 1.0
CHD A:HEM602 3.4 24.2 1.0
CHC A:HEM602 3.4 21.4 1.0
CHB A:HEM602 3.4 21.1 1.0
CG A:HIS74 4.1 23.9 1.0
CG A:HIS60 4.1 27.0 1.0
ND1 A:HIS60 4.2 26.3 1.0
ND1 A:HIS74 4.2 23.3 1.0
C3D A:HEM602 4.2 27.2 1.0
C2D A:HEM602 4.2 25.8 1.0
C3B A:HEM602 4.2 22.2 1.0
C3C A:HEM602 4.2 23.4 1.0
C2C A:HEM602 4.3 23.2 1.0
C2B A:HEM602 4.3 21.6 1.0
C2A A:HEM602 4.3 22.9 1.0
C3A A:HEM602 4.3 22.1 1.0

Iron binding site 3 out of 4 in 1d4d

Go back to Iron Binding Sites List in 1d4d
Iron binding site 3 out of 4 in the Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1


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

b:47.7
occ:1.00
FE A:HEM603 0.0 47.7 1.0
NE2 A:HIS19 1.9 32.9 1.0
NE2 A:HIS77 2.0 35.3 1.0
ND A:HEM603 2.0 49.3 1.0
NA A:HEM603 2.0 52.5 1.0
NB A:HEM603 2.0 51.9 1.0
NC A:HEM603 2.0 48.5 1.0
CD2 A:HIS19 2.9 35.0 1.0
CE1 A:HIS19 2.9 35.4 1.0
CE1 A:HIS77 2.9 35.5 1.0
C4A A:HEM603 3.0 54.1 1.0
CD2 A:HIS77 3.0 36.8 1.0
C1A A:HEM603 3.0 52.8 1.0
C4D A:HEM603 3.0 49.0 1.0
C4C A:HEM603 3.0 47.4 1.0
C1D A:HEM603 3.0 48.1 1.0
C1B A:HEM603 3.0 52.9 1.0
C1C A:HEM603 3.1 48.0 1.0
C4B A:HEM603 3.1 52.6 1.0
CHA A:HEM603 3.4 51.5 1.0
CHD A:HEM603 3.4 48.0 1.0
CHB A:HEM603 3.4 53.6 1.0
CHC A:HEM603 3.5 50.1 1.0
CG A:HIS19 4.0 36.4 1.0
ND1 A:HIS19 4.0 36.1 1.0
ND1 A:HIS77 4.0 35.6 1.0
CG A:HIS77 4.1 36.8 1.0
C3A A:HEM603 4.2 55.0 1.0
C2A A:HEM603 4.2 55.1 1.0
C3D A:HEM603 4.2 48.4 1.0
C2D A:HEM603 4.2 47.4 1.0
C3C A:HEM603 4.3 46.5 1.0
C2C A:HEM603 4.3 47.5 1.0
C2B A:HEM603 4.3 53.8 1.0
C3B A:HEM603 4.3 54.1 1.0

Iron binding site 4 out of 4 in 1d4d

Go back to Iron Binding Sites List in 1d4d
Iron binding site 4 out of 4 in the Crystal Structure of the Succinate Complexed Form of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1


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

b:28.2
occ:1.00
FE A:HEM604 0.0 28.2 1.0
NA A:HEM604 2.0 31.4 1.0
NC A:HEM604 2.0 28.6 1.0
NB A:HEM604 2.0 30.4 1.0
ND A:HEM604 2.0 31.8 1.0
NE2 A:HIS9 2.0 43.1 1.0
NE2 A:HIS42 2.1 21.8 1.0
CE1 A:HIS9 2.7 43.3 1.0
CE1 A:HIS42 3.0 22.9 1.0
C1A A:HEM604 3.0 33.0 1.0
C1C A:HEM604 3.0 28.2 1.0
C4A A:HEM604 3.0 31.7 1.0
C4C A:HEM604 3.0 29.4 1.0
C1B A:HEM604 3.1 30.2 1.0
C1D A:HEM604 3.1 30.3 1.0
C4D A:HEM604 3.1 32.6 1.0
C4B A:HEM604 3.1 28.7 1.0
CD2 A:HIS42 3.2 21.9 1.0
CD2 A:HIS9 3.2 44.8 1.0
CHA A:HEM604 3.4 32.4 1.0
CHB A:HEM604 3.4 31.6 1.0
CHC A:HEM604 3.4 29.1 1.0
CHD A:HEM604 3.4 30.7 1.0
ND1 A:HIS9 4.0 44.5 1.0
ND1 A:HIS42 4.1 22.6 1.0
CG A:HIS9 4.2 46.5 1.0
C2C A:HEM604 4.2 28.8 1.0
C2A A:HEM604 4.2 34.3 1.0
C3C A:HEM604 4.2 28.7 1.0
C3A A:HEM604 4.2 32.4 1.0
CG A:HIS42 4.2 22.0 1.0
C2B A:HEM604 4.3 30.8 1.0
C3B A:HEM604 4.3 29.7 1.0
C2D A:HEM604 4.3 31.7 1.0
C3D A:HEM604 4.3 32.6 1.0
CD2 A:LEU5 5.0 43.3 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: Wed Jul 16 13:10:27 2025

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