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Iron in PDB 1dur: Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus

Protein crystallography data

The structure of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus, PDB code: 1dur was solved by E.T.Adman, L.C.Sieker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.520, 37.750, 39.370, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus (pdb code 1dur). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus, PDB code: 1dur:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1dur

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Iron binding site 1 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe56

b:8.9
occ:1.00
 FE1 A:SF456 0.0 8.9 1.0
S2 A:SF456 2.2 7.4 1.0
S4 A:SF456 2.2 6.2 1.0
S3 A:SF456 2.2 7.0 1.0
SG A:CYS8 2.3 5.7 1.0
FE4 A:SF456 2.7 7.2 1.0
FE2 A:SF456 2.7 10.2 1.0
FE3 A:SF456 2.7 8.1 1.0
CB A:CYS8 3.4 6.3 1.0
CA A:CYS8 3.8 8.2 1.0
S1 A:SF456 3.8 8.1 1.0
N A:ALA10 4.0 9.0 1.0
N A:ILE9 4.1 7.9 1.0
C A:CYS8 4.3 8.2 1.0
CA A:ALA10 4.4 9.0 1.0
CG2 A:ILE4 4.5 5.1 1.0
CB A:TYR29 4.5 8.9 1.0
N A:CYS11 4.6 10.8 1.0
SG A:CYS46 4.7 7.4 1.0
SG A:CYS14 4.7 6.5 1.0
CB A:ALA50 4.7 7.0 1.0
CG A:TYR29 4.8 10.1 1.0
SG A:CYS11 4.8 13.2 1.0
CD1 A:TYR29 4.8 10.8 1.0
N A:TYR29 4.9 9.2 1.0
C A:ILE9 5.0 8.9 1.0

Iron binding site 2 out of 8 in 1dur

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Iron binding site 2 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe56

b:10.2
occ:1.00
 FE2 A:SF456 0.0 10.2 1.0
SG A:CYS11 2.2 13.2 1.0
S4 A:SF456 2.2 6.2 1.0
S1 A:SF456 2.2 8.1 1.0
S3 A:SF456 2.2 7.0 1.0
FE3 A:SF456 2.6 8.1 1.0
FE1 A:SF456 2.7 8.9 1.0
FE4 A:SF456 2.7 7.2 1.0
N A:CYS11 3.6 10.8 1.0
CB A:CYS11 3.6 10.1 1.0
S2 A:SF456 3.8 7.4 1.0
N A:GLY12 3.8 11.9 1.0
CA A:CYS11 4.0 11.8 1.0
N A:ALA13 4.2 10.1 1.0
CD A:PRO47 4.3 10.5 1.0
C A:CYS11 4.3 11.3 1.0
SG A:CYS46 4.4 7.4 1.0
C A:ALA10 4.6 9.9 1.0
SG A:CYS14 4.6 6.5 1.0
N A:ALA10 4.7 9.0 1.0
CB A:ALA13 4.7 10.3 1.0
CA A:GLY12 4.7 10.8 1.0
CG A:PRO47 4.7 11.7 1.0
SG A:CYS8 4.7 5.7 1.0
CA A:ALA10 4.8 9.0 1.0
N A:CYS14 4.8 7.9 1.0
C A:GLY12 4.9 10.9 1.0
CG1 A:ILE9 4.9 8.6 1.0
CA A:ALA13 5.0 9.2 1.0

Iron binding site 3 out of 8 in 1dur

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Iron binding site 3 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe56

b:8.1
occ:1.00
 FE3 A:SF456 0.0 8.1 1.0
S1 A:SF456 2.2 8.1 1.0
SG A:CYS46 2.2 7.4 1.0
S4 A:SF456 2.2 6.2 1.0
S2 A:SF456 2.3 7.4 1.0
FE2 A:SF456 2.6 10.2 1.0
FE4 A:SF456 2.7 7.2 1.0
FE1 A:SF456 2.7 8.9 1.0
CB A:CYS46 3.1 8.9 1.0
S3 A:SF456 3.7 7.0 1.0
CA A:CYS46 3.8 8.7 1.0
CD A:PRO47 4.2 10.5 1.0
CB A:ALA50 4.3 7.0 1.0
SG A:CYS11 4.4 13.2 1.0
CG2 A:VAL48 4.4 12.4 1.0
CD A:PRO51 4.4 6.4 1.0
CG A:PRO51 4.5 6.0 1.0
C A:CYS46 4.6 10.0 1.0
N A:PRO47 4.6 10.3 1.0
SG A:CYS14 4.8 6.5 1.0
SG A:CYS8 4.9 5.7 1.0
N A:ALA50 4.9 7.9 1.0
CG A:PRO47 4.9 11.7 1.0
N A:CYS46 5.0 9.9 1.0

Iron binding site 4 out of 8 in 1dur

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Iron binding site 4 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe56

b:7.2
occ:1.00
 FE4 A:SF456 0.0 7.2 1.0
S3 A:SF456 2.2 7.0 1.0
S1 A:SF456 2.2 8.1 1.0
S2 A:SF456 2.2 7.4 1.0
SG A:CYS14 2.2 6.5 1.0
FE1 A:SF456 2.7 8.9 1.0
FE3 A:SF456 2.7 8.1 1.0
FE2 A:SF456 2.7 10.2 1.0
CB A:CYS14 3.2 8.4 1.0
S4 A:SF456 3.8 6.2 1.0
N A:CYS14 3.9 7.9 1.0
CA A:CYS14 4.2 8.1 1.0
CD1 A:ILE4 4.6 5.3 1.0
SG A:CYS11 4.6 13.2 1.0
CB A:TYR29 4.6 8.9 1.0
SG A:CYS8 4.7 5.7 1.0
CG A:TYR29 4.7 10.1 1.0
SG A:CYS46 4.7 7.4 1.0
N A:ALA13 4.8 10.1 1.0
CD2 A:TYR29 4.8 11.1 1.0
N A:GLY12 4.9 11.9 1.0

Iron binding site 5 out of 8 in 1dur

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Iron binding site 5 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe57

b:8.7
occ:1.00
 FE1 A:SF457 0.0 8.7 1.0
S4 A:SF457 2.2 8.3 1.0
S2 A:SF457 2.2 8.8 1.0
SG A:CYS36 2.2 9.2 1.0
S3 A:SF457 2.3 7.9 1.0
FE4 A:SF457 2.7 8.7 1.0
FE3 A:SF457 2.7 9.6 1.0
FE2 A:SF457 2.7 9.6 1.0
CB A:CYS36 3.4 10.8 1.0
CA A:CYS36 3.8 10.8 1.0
S1 A:SF457 3.8 8.4 1.0
N A:ILE37 4.0 11.3 1.0
SG A:CYS22 4.1 11.3 1.0
N A:ASP38 4.2 11.4 1.0
C A:CYS36 4.3 11.0 1.0
CB A:TYR2 4.7 6.8 1.0
SG A:CYS42 4.7 9.4 1.0
SG A:CYS18 4.7 8.3 1.0
CG2 A:ILE31 4.8 9.8 1.0
CA A:ASP38 4.8 11.5 1.0
CD1 A:ILE31 4.8 7.3 1.0
N A:CYS39 4.9 9.6 1.0
SG A:CYS39 4.9 10.8 1.0

Iron binding site 6 out of 8 in 1dur

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Iron binding site 6 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe57

b:9.6
occ:1.00
 FE2 A:SF457 0.0 9.6 1.0
S1 A:SF457 2.1 8.4 1.0
S4 A:SF457 2.2 8.3 1.0
S3 A:SF457 2.2 7.9 1.0
SG A:CYS39 2.3 10.8 1.0
FE3 A:SF457 2.6 9.6 1.0
FE4 A:SF457 2.6 8.7 1.0
FE1 A:SF457 2.7 8.7 1.0
CB A:CYS39 3.6 10.2 1.0
N A:CYS39 3.8 9.6 1.0
S2 A:SF457 3.8 8.8 1.0
N A:GLY40 3.9 11.2 1.0
CA A:CYS39 4.1 10.8 1.0
N A:SER41 4.3 11.4 1.0
CD A:PRO19 4.3 10.7 1.0
C A:CYS39 4.3 11.1 1.0
SG A:CYS18 4.5 8.3 1.0
SG A:CYS42 4.5 9.4 1.0
CG A:PRO19 4.6 10.2 1.0
CG1 A:ILE37 4.6 11.0 1.0
SG A:CYS36 4.7 9.2 1.0
CA A:GLY40 4.7 11.6 1.0
N A:ASP38 4.8 11.4 1.0
CB A:SER41 4.8 13.2 1.0
C A:ASP38 4.8 10.5 1.0
N A:CYS42 4.8 9.4 1.0
C A:GLY40 4.9 11.3 1.0

Iron binding site 7 out of 8 in 1dur

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Iron binding site 7 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe57

b:9.6
occ:1.00
 FE3 A:SF457 0.0 9.6 1.0
SG A:CYS18 2.2 8.3 1.0
S2 A:SF457 2.2 8.8 1.0
S4 A:SF457 2.3 8.3 1.0
S1 A:SF457 2.3 8.4 1.0
FE2 A:SF457 2.6 9.6 1.0
FE1 A:SF457 2.7 8.7 1.0
FE4 A:SF457 2.7 8.7 1.0
CB A:CYS18 3.4 10.1 1.0
SG A:CYS22 3.6 11.3 1.0
S3 A:SF457 3.8 7.9 1.0
CA A:CYS18 4.0 10.7 1.0
CD1 A:ILE23 4.4 8.5 1.0
CD A:PRO19 4.5 10.7 1.0
CG1 A:ILE23 4.5 10.6 1.0
SG A:CYS39 4.6 10.8 1.0
C A:CYS18 4.7 11.6 1.0
CG2 A:VAL20 4.8 11.8 1.0
SG A:CYS42 4.8 9.4 1.0
SG A:CYS36 4.8 9.2 1.0
N A:PRO19 4.9 11.2 1.0

Iron binding site 8 out of 8 in 1dur

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Iron binding site 8 out of 8 in the Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Replacement For 1FDX 2(4FE4S) Ferredoxin From (Now) Peptostreptococcus Asaccharolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe57

b:8.7
occ:1.00
 FE4 A:SF457 0.0 8.7 1.0
S3 A:SF457 2.1 7.9 1.0
S1 A:SF457 2.2 8.4 1.0
SG A:CYS42 2.2 9.4 1.0
S2 A:SF457 2.3 8.8 1.0
FE2 A:SF457 2.6 9.6 1.0
FE1 A:SF457 2.7 8.7 1.0
FE3 A:SF457 2.7 9.6 1.0
CB A:CYS42 3.2 7.9 1.0
S4 A:SF457 3.8 8.3 1.0
N A:CYS42 3.9 9.4 1.0
CA A:CYS42 4.2 9.1 1.0
CD1 A:ILE31 4.5 7.3 1.0
CD1 A:ILE23 4.5 8.5 1.0
SG A:CYS36 4.6 9.2 1.0
SG A:CYS39 4.7 10.8 1.0
CB A:TYR2 4.7 6.8 1.0
SG A:CYS18 4.8 8.3 1.0
N A:SER41 4.8 11.4 1.0
CG A:TYR2 4.8 7.8 1.0
N A:GLY40 4.8 11.2 1.0
CD2 A:TYR2 5.0 8.1 1.0

Reference:

E.T.Adman, L.C.Sieker. The 2[4FE-4S] Ferredoxins To Be Published.
Page generated: Sat Aug 3 03:59:39 2024

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