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Iron in PDB 2gmj: Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase

Enzymatic activity of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase

All present enzymatic activity of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase:
1.5.5.1;

Protein crystallography data

The structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase, PDB code: 2gmj was solved by J.Zhang, F.E.Frerman, J.-J.P.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.75 / 2.60
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 154.839, 154.839, 130.199, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 25.5

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase (pdb code 2gmj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase, PDB code: 2gmj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2gmj

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Iron binding site 1 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:8.7
occ:1.00
 FE1 A:SF4610 0.0 8.7 1.0
S4 A:SF4610 2.3 7.1 1.0
S3 A:SF4610 2.3 6.7 1.0
S2 A:SF4610 2.3 8.0 1.0
SG A:CYS559 2.7 12.4 1.0
FE2 A:SF4610 2.7 8.3 1.0
FE3 A:SF4610 2.7 6.8 1.0
FE4 A:SF4610 2.8 9.3 1.0
CB A:CYS559 2.9 9.0 1.0
N A:CYS559 3.6 11.7 1.0
S1 A:SF4610 3.8 10.1 1.0
CA A:CYS559 3.9 11.4 1.0
CD1 A:LEU504 4.0 17.3 1.0
CE1 A:TYR533 4.4 10.4 1.0
OH A:TYR533 4.4 9.6 1.0
N A:THR558 4.6 9.7 1.0
C A:THR558 4.8 11.8 1.0
CD1 A:TRP570 4.8 18.0 1.0
C A:LYS557 4.8 10.0 1.0
CZ A:TYR533 4.9 9.1 1.0
C A:CYS559 4.9 11.8 1.0
N A:LYS557 4.9 11.8 1.0
CG A:LEU504 4.9 17.5 1.0
SG A:CYS528 5.0 12.3 1.0
N A:ASP560 5.0 12.8 1.0
SG A:CYS556 5.0 14.9 1.0

Iron binding site 2 out of 8 in 2gmj

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Iron binding site 2 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:8.3
occ:1.00
 FE2 A:SF4610 0.0 8.3 1.0
S3 A:SF4610 2.3 6.7 1.0
S4 A:SF4610 2.3 7.1 1.0
S1 A:SF4610 2.3 10.1 1.0
SG A:CYS528 2.5 12.3 1.0
FE1 A:SF4610 2.7 8.7 1.0
FE3 A:SF4610 2.8 6.8 1.0
FE4 A:SF4610 2.9 9.3 1.0
CB A:CYS528 3.4 15.0 1.0
S2 A:SF4610 3.9 8.0 1.0
CA A:CYS528 4.1 14.5 1.0
CD A:PRO529 4.2 15.1 1.0
CG2 A:VAL532 4.3 18.7 1.0
CB A:VAL532 4.4 18.1 1.0
N A:PRO529 4.5 14.8 1.0
C A:CYS528 4.6 15.3 1.0
N A:ALA530 4.7 15.7 1.0
CE1 A:TYR533 4.8 10.4 1.0
CB A:ALA530 4.8 14.2 1.0
SG A:CYS556 5.0 14.9 1.0

Iron binding site 3 out of 8 in 2gmj

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Iron binding site 3 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:6.8
occ:1.00
 FE3 A:SF4610 0.0 6.8 1.0
S4 A:SF4610 2.2 7.1 1.0
S2 A:SF4610 2.3 8.0 1.0
S1 A:SF4610 2.3 10.1 1.0
SG A:CYS553 2.5 16.2 1.0
FE1 A:SF4610 2.7 8.7 1.0
FE4 A:SF4610 2.8 9.3 1.0
FE2 A:SF4610 2.8 8.3 1.0
CB A:CYS553 3.5 16.5 1.0
S3 A:SF4610 3.8 6.7 1.0
CA A:CYS553 3.9 14.3 1.0
CD1 A:LEU504 4.1 17.3 1.0
N A:HIS555 4.2 9.6 1.0
N A:VAL554 4.2 12.1 1.0
NE1 A:TRP570 4.2 17.8 1.0
CD1 A:TRP570 4.4 18.0 1.0
C A:CYS553 4.4 13.5 1.0
CA A:HIS555 4.6 10.2 1.0
N A:CYS556 4.6 12.1 1.0
CG A:LEU504 4.7 17.5 1.0
CD2 A:LEU504 4.8 18.1 1.0
CG2 A:VAL532 4.9 18.7 1.0
SG A:CYS559 5.0 12.4 1.0

Iron binding site 4 out of 8 in 2gmj

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Iron binding site 4 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:9.3
occ:1.00
 FE4 A:SF4610 0.0 9.3 1.0
S2 A:SF4610 2.2 8.0 1.0
S3 A:SF4610 2.2 6.7 1.0
S1 A:SF4610 2.2 10.1 1.0
SG A:CYS556 2.5 14.9 1.0
FE3 A:SF4610 2.8 6.8 1.0
FE1 A:SF4610 2.8 8.7 1.0
FE2 A:SF4610 2.9 8.3 1.0
N A:CYS556 3.5 12.1 1.0
N A:LYS557 3.6 11.8 1.0
CB A:CYS556 3.7 14.7 1.0
S4 A:SF4610 3.9 7.1 1.0
N A:THR558 3.9 9.7 1.0
CA A:CYS556 3.9 13.1 1.0
C A:CYS556 4.1 13.3 1.0
CD A:PRO529 4.2 15.1 1.0
CA A:LYS557 4.4 10.0 1.0
CB A:THR558 4.5 10.2 1.0
C A:LYS557 4.5 10.0 1.0
N A:CYS559 4.6 11.7 1.0
C A:HIS555 4.6 11.5 1.0
CG A:PRO529 4.6 15.4 1.0
OG1 A:THR558 4.6 11.5 1.0
CA A:THR558 4.7 11.1 1.0
N A:HIS555 4.9 9.6 1.0
SG A:CYS553 4.9 16.2 1.0
CG2 A:VAL554 4.9 5.4 1.0
SG A:CYS528 4.9 12.3 1.0
CA A:HIS555 5.0 10.2 1.0

Iron binding site 5 out of 8 in 2gmj

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Iron binding site 5 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe612

b:51.5
occ:1.00
 FE1 B:SF4612 0.0 51.5 1.0
S4 B:SF4612 2.3 53.6 1.0
S3 B:SF4612 2.3 54.3 1.0
S2 B:SF4612 2.3 54.8 1.0
SG B:CYS559 2.4 65.3 1.0
FE4 B:SF4612 2.7 53.7 1.0
FE2 B:SF4612 2.8 53.7 1.0
FE3 B:SF4612 2.8 54.0 1.0
CB B:CYS559 3.3 60.1 1.0
S1 B:SF4612 3.9 53.2 1.0
N B:CYS559 4.0 59.4 1.0
CE1 B:TYR533 4.3 62.9 1.0
CA B:CYS559 4.3 59.1 1.0
OH B:TYR533 4.4 62.8 1.0
CD2 B:LEU504 4.5 62.0 1.0
SG B:CYS528 4.6 54.1 1.0
SG B:CYS553 4.7 63.4 1.0
CG B:LEU504 4.8 61.6 1.0
N B:THR558 4.8 58.7 1.0
CD1 B:LEU504 4.8 61.7 1.0
CZ B:TYR533 4.8 62.9 1.0
CD1 B:TRP570 4.9 60.1 1.0
SG B:CYS556 5.0 63.4 1.0

Iron binding site 6 out of 8 in 2gmj

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Iron binding site 6 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe612

b:53.7
occ:1.00
 FE2 B:SF4612 0.0 53.7 1.0
S3 B:SF4612 2.3 54.3 1.0
S4 B:SF4612 2.3 53.6 1.0
S1 B:SF4612 2.4 53.2 1.0
SG B:CYS528 2.4 54.1 1.0
FE4 B:SF4612 2.8 53.7 1.0
FE1 B:SF4612 2.8 51.5 1.0
FE3 B:SF4612 2.9 54.0 1.0
CB B:CYS528 3.7 58.4 1.0
S2 B:SF4612 3.9 54.8 1.0
CA B:CYS528 3.9 58.5 1.0
CD B:PRO529 4.0 58.9 1.0
CG2 B:VAL532 4.1 64.7 1.0
CB B:VAL532 4.2 64.7 1.0
N B:PRO529 4.3 59.6 1.0
C B:CYS528 4.4 59.2 1.0
N B:ALA530 4.4 60.8 1.0
CB B:ALA530 4.6 61.2 1.0
CG B:PRO529 4.6 58.7 1.0
CE1 B:TYR533 4.6 62.9 1.0
CA B:CYS553 4.7 63.5 1.0
SG B:CYS556 4.9 63.4 1.0
CA B:ALA530 4.9 61.2 1.0
CG1 B:VAL532 5.0 65.0 1.0
SG B:CYS559 5.0 65.3 1.0

Iron binding site 7 out of 8 in 2gmj

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Iron binding site 7 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe612

b:54.0
occ:1.00
 FE3 B:SF4612 0.0 54.0 1.0
S4 B:SF4612 2.2 53.6 1.0
S2 B:SF4612 2.3 54.8 1.0
S1 B:SF4612 2.3 53.2 1.0
SG B:CYS553 2.5 63.4 1.0
FE4 B:SF4612 2.7 53.7 1.0
FE1 B:SF4612 2.8 51.5 1.0
FE2 B:SF4612 2.9 53.7 1.0
CB B:CYS553 3.2 63.3 1.0
CA B:CYS553 3.3 63.5 1.0
N B:VAL554 3.6 63.9 1.0
C B:CYS553 3.9 63.6 1.0
N B:HIS555 3.9 64.0 1.0
S3 B:SF4612 3.9 54.3 1.0
N B:CYS556 4.4 62.2 1.0
CA B:HIS555 4.5 64.2 1.0
NE1 B:TRP570 4.6 60.5 1.0
N B:CYS553 4.6 64.3 1.0
C B:VAL554 4.7 63.6 1.0
CA B:VAL554 4.7 63.5 1.0
CD1 B:TRP570 4.8 60.1 1.0
CG2 B:VAL532 4.8 64.7 1.0
SG B:CYS556 4.8 63.4 1.0
SG B:CYS559 4.9 65.3 1.0
CD1 B:LEU504 4.9 61.7 1.0
O B:CYS553 4.9 62.9 1.0
C B:HIS555 5.0 63.4 1.0
CD2 B:LEU504 5.0 62.0 1.0

Iron binding site 8 out of 8 in 2gmj

Go back to Iron Binding Sites List in 2gmj
Iron binding site 8 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe612

b:53.7
occ:1.00
 FE4 B:SF4612 0.0 53.7 1.0
S1 B:SF4612 2.2 53.2 1.0
S2 B:SF4612 2.2 54.8 1.0
S3 B:SF4612 2.2 54.3 1.0
SG B:CYS556 2.4 63.4 1.0
FE3 B:SF4612 2.7 54.0 1.0
FE1 B:SF4612 2.7 51.5 1.0
FE2 B:SF4612 2.8 53.7 1.0
S4 B:SF4612 3.8 53.6 1.0
N B:CYS556 3.8 62.2 1.0
CB B:CYS556 3.8 61.8 1.0
N B:LYS557 3.9 60.1 1.0
CD B:PRO529 4.0 58.9 1.0
N B:THR558 4.1 58.7 1.0
CG B:PRO529 4.1 58.7 1.0
CA B:CYS556 4.1 61.3 1.0
C B:CYS556 4.4 60.5 1.0
CB B:THR558 4.5 59.5 1.0
SG B:CYS559 4.6 65.3 1.0
N B:CYS559 4.7 59.4 1.0
CG2 B:VAL554 4.8 62.5 1.0
CA B:THR558 4.8 59.1 1.0
CA B:LYS557 4.8 59.3 1.0
OG1 B:THR558 4.9 60.4 1.0
C B:HIS555 4.9 63.4 1.0
SG B:CYS528 4.9 54.1 1.0
N B:HIS555 4.9 64.0 1.0
C B:LYS557 4.9 59.2 1.0
N B:VAL554 5.0 63.9 1.0

Reference:

J.Zhang, F.E.Frerman, J.J.Kim. Structure of Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase and Electron Transfer to the Mitochondrial Ubiquinone Pool. Proc.Natl.Acad.Sci.Usa V. 103 16212 2006.
ISSN: ISSN 0027-8424
PubMed: 17050691
DOI: 10.1073/PNAS.0604567103
Page generated: Sun Dec 13 14:45:27 2020

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