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Iron in PDB 1wtf: Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution, PDB code: 1wtf was solved by T.Shirakawa, Y.Takahashi, K.Wada, J.Hirota, T.Takao, D.Ohmori, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.84 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.461, 63.387, 56.857, 90.00, 95.06, 90.00
R / Rfree (%) 18.2 / 21.4

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution (pdb code 1wtf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution, PDB code: 1wtf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1wtf

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Iron binding site 1 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


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 Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:8.1
occ:1.00
 FE1 A:F3S1001 0.0 8.1 1.0
S3 A:F3S1001 2.2 8.2 1.0
S2 A:F3S1001 2.2 7.6 1.0
S1 A:F3S1001 2.3 8.9 1.0
SG A:CYS61 2.3 8.3 1.0
FE3 A:F3S1001 2.7 8.3 1.0
FE4 A:F3S1001 2.7 7.9 1.0
CB A:CYS61 3.4 9.1 1.0
OG1 A:THR63 3.8 9.2 1.0
S4 A:F3S1001 3.9 8.5 1.0
CA A:CYS61 3.9 9.0 1.0
CB A:CYS14 4.4 11.2 1.0
CD A:PRO62 4.4 10.4 1.0
CB A:SER65 4.5 9.1 1.0
C A:CYS61 4.6 7.8 1.0
N A:PRO62 4.6 8.4 1.0
CG1 A:ILE66 4.7 17.2 1.0
SG A:CYS14 4.7 12.7 1.0
SG A:CYS17 4.7 8.4 1.0
SG A:CYS11 4.9 8.0 1.0
OG A:SER65 4.9 10.2 1.0
N A:THR63 4.9 9.1 1.0
N A:SER65 4.9 7.6 1.0
CD1 A:ILE66 4.9 20.4 1.0
N A:CYS14 5.0 10.4 1.0

Iron binding site 2 out of 12 in 1wtf

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Iron binding site 2 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


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 Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:8.3
occ:1.00
 FE3 A:F3S1001 0.0 8.3 1.0
S3 A:F3S1001 2.1 8.2 1.0
S4 A:F3S1001 2.3 8.5 1.0
SG A:CYS11 2.3 8.0 1.0
S1 A:F3S1001 2.3 8.9 1.0
FE1 A:F3S1001 2.7 8.1 1.0
FE4 A:F3S1001 2.7 7.9 1.0
CB A:CYS11 3.4 4.6 1.0
CA A:CYS11 3.9 6.6 1.0
S2 A:F3S1001 3.9 7.6 1.0
N A:ALA13 4.0 8.1 1.0
N A:CYS14 4.1 10.4 1.0
CB A:ALA33 4.1 7.5 1.0
N A:ILE12 4.2 7.8 1.0
CA A:ALA13 4.4 8.4 1.0
C A:CYS11 4.4 6.2 1.0
N A:ALA33 4.7 7.7 1.0
SG A:CYS17 4.7 8.4 1.0
SG A:CYS61 4.7 8.3 1.0
C A:ALA13 4.7 10.5 1.0
CB A:SER65 4.8 9.1 1.0
OG1 A:THR63 4.8 9.2 1.0
N A:GLY15 4.9 11.5 1.0
C A:ILE12 4.9 8.0 1.0
CB A:CYS14 4.9 11.2 1.0

Iron binding site 3 out of 12 in 1wtf

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Iron binding site 3 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


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 Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:7.9
occ:1.00
 FE4 A:F3S1001 0.0 7.9 1.0
S3 A:F3S1001 2.2 8.2 1.0
SG A:CYS17 2.2 8.4 1.0
S4 A:F3S1001 2.3 8.5 1.0
S2 A:F3S1001 2.3 7.6 1.0
FE3 A:F3S1001 2.7 8.3 1.0
FE1 A:F3S1001 2.7 8.1 1.0
CB A:CYS17 3.3 6.9 1.0
CB A:ALA33 3.8 7.5 1.0
N A:CYS17 3.9 10.7 1.0
S1 A:F3S1001 4.0 8.9 1.0
CA A:CYS17 4.2 9.9 1.0
N A:GLY15 4.2 11.5 1.0
N A:ALA16 4.4 11.0 1.0
CD1 A:ILE66 4.6 20.4 1.0
CA A:GLY15 4.6 10.1 1.0
SG A:CYS11 4.7 8.0 1.0
CE2 A:TYR27 4.7 11.0 1.0
SG A:CYS61 4.8 8.3 1.0
C A:GLY15 4.8 11.6 1.0
CG1 A:ILE66 4.9 17.2 1.0
N A:CYS14 5.0 10.4 1.0

Iron binding site 4 out of 12 in 1wtf

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Iron binding site 4 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


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 Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:10.7
occ:1.00
 FE1 B:F3S1002 0.0 10.7 1.0
S3 B:F3S1002 2.2 9.3 1.0
S2 B:F3S1002 2.2 10.4 1.0
S1 B:F3S1002 2.3 9.7 1.0
SG B:CYS17 2.3 11.3 1.0
FE3 B:F3S1002 2.6 9.9 1.0
FE4 B:F3S1002 2.7 10.0 1.0
CB B:CYS17 3.3 11.9 1.0
N B:CYS17 3.8 12.7 1.0
S4 B:F3S1002 3.9 9.7 1.0
CB B:ALA33 3.9 9.2 1.0
CA B:CYS17 4.2 12.3 1.0
N B:GLY15 4.3 16.2 1.0
N B:ALA16 4.5 16.8 1.0
CD1 B:ILE66 4.6 13.9 1.0
O B:HOH1146 4.6 28.1 1.0
SG B:CYS11 4.7 9.9 1.0
CE2 B:TYR27 4.7 11.3 1.0
SG B:CYS61 4.7 11.4 1.0
CA B:GLY15 4.7 15.0 1.0
C B:GLY15 4.8 14.3 1.0
C B:ALA16 5.0 15.1 1.0

Iron binding site 5 out of 12 in 1wtf

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Iron binding site 5 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:9.9
occ:1.00
 FE3 B:F3S1002 0.0 9.9 1.0
S3 B:F3S1002 2.2 9.3 1.0
S1 B:F3S1002 2.3 9.7 1.0
S4 B:F3S1002 2.3 9.7 1.0
SG B:CYS61 2.3 11.4 1.0
FE1 B:F3S1002 2.6 10.7 1.0
FE4 B:F3S1002 2.7 10.0 1.0
CB B:CYS61 3.3 11.9 1.0
S2 B:F3S1002 3.8 10.4 1.0
OG1 B:THR63 3.8 11.8 1.0
CA B:CYS61 3.9 12.2 1.0
CD B:PRO62 4.2 15.6 1.0
CB B:SER65 4.5 11.2 1.0
C B:CYS61 4.5 11.8 1.0
N B:PRO62 4.5 10.7 1.0
CB B:CYS14 4.7 15.8 1.0
SG B:CYS17 4.8 11.3 1.0
SG B:CYS11 4.8 9.9 1.0
OG B:SER65 4.9 10.7 1.0
N B:THR63 4.9 9.7 1.0
SG B:CYS14 4.9 12.6 1.0
O B:HOH1146 4.9 28.1 1.0
CG1 B:ILE66 4.9 13.2 1.0
CD1 B:ILE66 4.9 13.9 1.0
N B:SER65 5.0 11.1 1.0

Iron binding site 6 out of 12 in 1wtf

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Iron binding site 6 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:10.0
occ:1.00
 FE4 B:F3S1002 0.0 10.0 1.0
S3 B:F3S1002 2.2 9.3 1.0
S2 B:F3S1002 2.3 10.4 1.0
SG B:CYS11 2.3 9.9 1.0
S4 B:F3S1002 2.3 9.7 1.0
FE3 B:F3S1002 2.7 9.9 1.0
FE1 B:F3S1002 2.7 10.7 1.0
CB B:CYS11 3.4 6.5 1.0
CA B:CYS11 3.8 8.7 1.0
S1 B:F3S1002 3.9 9.7 1.0
N B:ALA13 4.0 12.4 1.0
N B:ILE12 4.1 9.8 1.0
CB B:ALA33 4.1 9.2 1.0
N B:CYS14 4.2 11.9 1.0
C B:CYS11 4.2 9.4 1.0
CA B:ALA13 4.4 10.5 1.0
N B:ALA33 4.7 8.6 1.0
SG B:CYS61 4.7 11.4 1.0
SG B:CYS17 4.7 11.3 1.0
OG1 B:THR63 4.8 11.8 1.0
C B:ALA13 4.8 14.2 1.0
CB B:SER65 4.8 11.2 1.0
C B:ILE12 4.9 13.7 1.0

Iron binding site 7 out of 12 in 1wtf

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Iron binding site 7 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1003

b:9.4
occ:1.00
 FE1 C:F3S1003 0.0 9.4 1.0
S3 C:F3S1003 2.2 8.7 1.0
S2 C:F3S1003 2.2 8.7 1.0
S1 C:F3S1003 2.3 8.6 1.0
SG C:CYS61 2.3 9.5 1.0
FE3 C:F3S1003 2.7 8.4 1.0
FE4 C:F3S1003 2.7 8.7 1.0
CB C:CYS61 3.3 8.1 1.0
OG1 C:THR63 3.8 10.2 1.0
S4 C:F3S1003 3.9 9.3 1.0
CA C:CYS61 3.9 10.1 1.0
CD C:PRO62 4.3 12.0 1.0
CB C:SER65 4.4 12.0 1.0
CB C:CYS14 4.5 11.4 1.0
C C:CYS61 4.6 12.0 1.0
CG1 C:ILE66 4.6 11.5 1.0
N C:PRO62 4.6 11.8 1.0
SG C:CYS17 4.7 9.2 1.0
OG C:SER65 4.8 10.4 1.0
SG C:CYS11 4.9 7.8 1.0
N C:THR63 4.9 11.3 1.0
SG C:CYS14 5.0 16.9 1.0
N C:SER65 5.0 8.7 1.0

Iron binding site 8 out of 12 in 1wtf

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Iron binding site 8 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1003

b:8.4
occ:1.00
 FE3 C:F3S1003 0.0 8.4 1.0
S3 C:F3S1003 2.1 8.7 1.0
S4 C:F3S1003 2.3 9.3 1.0
SG C:CYS11 2.3 7.8 1.0
S1 C:F3S1003 2.3 8.6 1.0
FE1 C:F3S1003 2.7 9.4 1.0
FE4 C:F3S1003 2.7 8.7 1.0
CB C:CYS11 3.4 10.0 1.0
CA C:CYS11 3.8 9.7 1.0
S2 C:F3S1003 3.9 8.7 1.0
N C:ALA13 3.9 8.2 1.0
N C:ILE12 4.1 8.4 1.0
N C:CYS14 4.1 8.9 1.0
C C:CYS11 4.3 9.3 1.0
CA C:ALA13 4.3 7.9 1.0
CB C:ALA33 4.3 8.2 1.0
C C:ALA13 4.7 10.8 1.0
SG C:CYS17 4.7 9.2 1.0
SG C:CYS61 4.8 9.5 1.0
CB C:SER65 4.8 12.0 1.0
N C:ALA33 4.8 7.7 1.0
N C:GLY15 4.9 9.2 1.0
OG1 C:THR63 4.9 10.2 1.0
C C:ILE12 4.9 10.4 1.0

Iron binding site 9 out of 12 in 1wtf

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Iron binding site 9 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1003

b:8.7
occ:1.00
 FE4 C:F3S1003 0.0 8.7 1.0
S3 C:F3S1003 2.2 8.7 1.0
S4 C:F3S1003 2.2 9.3 1.0
S2 C:F3S1003 2.3 8.7 1.0
SG C:CYS17 2.3 9.2 1.0
FE3 C:F3S1003 2.7 8.4 1.0
FE1 C:F3S1003 2.7 9.4 1.0
CB C:CYS17 3.3 8.3 1.0
N C:CYS17 3.9 9.8 1.0
CB C:ALA33 3.9 8.2 1.0
S1 C:F3S1003 4.0 8.6 1.0
N C:GLY15 4.1 9.2 1.0
CA C:CYS17 4.2 8.9 1.0
CD1 C:ILE66 4.5 13.4 1.0
N C:ALA16 4.5 9.8 1.0
CA C:GLY15 4.5 9.8 1.0
CE2 C:TYR27 4.7 8.8 1.0
SG C:CYS11 4.7 7.8 1.0
SG C:CYS61 4.7 9.5 1.0
CG1 C:ILE66 4.8 11.5 1.0
C C:GLY15 4.8 10.8 1.0

Iron binding site 10 out of 12 in 1wtf

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Iron binding site 10 out of 12 in the Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Bacillus Thermoproteolyticus Ferredoxin Variants Containing Unexpected [3FE-4S] Cluster That Is Linked to Coenzyme A at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1004

b:10.1
occ:1.00
 FE1 D:F3S1004 0.0 10.1 1.0
S3 D:F3S1004 2.2 10.1 1.0
S1 D:F3S1004 2.2 10.3 1.0
S2 D:F3S1004 2.3 10.3 1.0
SG D:CYS11 2.3 10.1 1.0
FE3 D:F3S1004 2.7 10.6 1.0
FE4 D:F3S1004 2.7 10.6 1.0
CB D:CYS11 3.4 9.1 1.0
CA D:CYS11 3.8 7.7 1.0
N D:ALA13 3.8 9.7 1.0
S4 D:F3S1004 3.9 11.7 1.0
N D:ILE12 4.0 9.8 1.0
N D:CYS14 4.2 11.9 1.0
CB D:ALA33 4.2 9.4 1.0
CA D:ALA13 4.2 13.5 1.0
C D:CYS11 4.3 9.4 1.0
C D:ALA13 4.7 10.4 1.0
SG D:CYS17 4.7 10.2 1.0
CB D:SER65 4.7 13.8 1.0
N D:ALA33 4.8 9.9 1.0
C D:ILE12 4.8 13.6 1.0
OG1 D:THR63 4.8 11.7 1.0
SG D:CYS61 4.9 11.5 1.0

Reference:

T.Shirakawa, Y.Takahashi, K.Wada, J.Hirota, T.Takao, D.Ohmori, K.Fukuyama. Identification of Variant Molecules of Bacillus Thermoproteolyticus Ferredoxin: Crystal Structure Reveals Bound Coenzyme A and An Unexpected [3FE-4S] Cluster Associated with A Canonical [4FE-4S] Ligand Motif Biochemistry V. 44 12402 2005.
ISSN: ISSN 0006-2960
PubMed: 16156653
DOI: 10.1021/BI0508441
Page generated: Sat Aug 3 16:36:17 2024

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