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Iron in PDB 2gmh: Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone

Enzymatic activity of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone

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

Protein crystallography data

The structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone, PDB code: 2gmh 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) 29.67 / 2.50
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 154.322, 154.322, 128.536, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.4

Other elements in 2gmh:

The structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone (pdb code 2gmh). 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 in Complexed with Ubiquinone, PDB code: 2gmh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2gmh

Go back to Iron Binding Sites List in 2gmh
Iron binding site 1 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:19.3
occ:1.00
 FE1 A:SF4610 0.0 19.3 1.0
S2 A:SF4610 2.3 19.4 1.0
S4 A:SF4610 2.3 19.3 1.0
S3 A:SF4610 2.3 16.7 1.0
SG A:CYS553 2.3 23.1 1.0
FE4 A:SF4610 2.7 22.5 1.0
FE2 A:SF4610 2.7 18.0 1.0
FE3 A:SF4610 2.8 22.7 1.0
CB A:CYS553 3.4 26.8 1.0
CA A:CYS553 3.7 26.1 1.0
S1 A:SF4610 3.9 18.0 1.0
N A:VAL554 3.9 23.1 1.0
N A:HIS555 4.0 19.4 1.0
CD1 A:LEU504 4.2 29.6 1.0
C A:CYS553 4.2 26.5 1.0
NE1 A:TRP570 4.4 22.5 1.0
CG2 A:VAL532 4.4 25.6 1.0
CA A:HIS555 4.5 21.6 1.0
N A:CYS556 4.6 19.7 1.0
CD1 A:TRP570 4.7 21.2 1.0
SG A:CYS528 4.8 20.5 1.0
SG A:CYS556 4.8 22.3 1.0
SG A:CYS559 4.9 20.5 1.0
CG A:LEU504 4.9 32.3 1.0
C A:VAL554 4.9 20.1 1.0
N A:CYS553 4.9 24.6 1.0
CD2 A:LEU504 4.9 30.0 1.0
CA A:VAL554 5.0 21.0 1.0

Iron binding site 2 out of 8 in 2gmh

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


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:18.0
occ:1.00
 FE2 A:SF4610 0.0 18.0 1.0
SG A:CYS528 2.2 20.5 1.0
S1 A:SF4610 2.3 18.0 1.0
S4 A:SF4610 2.3 19.3 1.0
S3 A:SF4610 2.3 16.7 1.0
FE4 A:SF4610 2.7 22.5 1.0
FE1 A:SF4610 2.7 19.3 1.0
FE3 A:SF4610 2.8 22.7 1.0
CB A:CYS528 3.4 23.7 1.0
S2 A:SF4610 3.8 19.4 1.0
CD A:PRO529 3.9 24.2 1.0
CA A:CYS528 4.0 25.8 1.0
CG2 A:VAL532 4.0 25.6 1.0
CB A:VAL532 4.2 23.4 1.0
N A:PRO529 4.5 26.0 1.0
C A:CYS528 4.5 25.4 1.0
CB A:ALA530 4.6 16.8 1.0
CE1 A:TYR533 4.6 17.8 1.0
N A:ALA530 4.6 22.3 1.0
SG A:CYS556 4.7 22.3 1.0
CG A:PRO529 4.7 21.8 1.0
SG A:CYS559 4.7 20.5 1.0
SG A:CYS553 5.0 23.1 1.0

Iron binding site 3 out of 8 in 2gmh

Go back to Iron Binding Sites List in 2gmh
Iron binding site 3 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:22.7
occ:1.00
 FE3 A:SF4610 0.0 22.7 1.0
S4 A:SF4610 2.2 19.3 1.0
SG A:CYS556 2.2 22.3 1.0
S2 A:SF4610 2.3 19.4 1.0
S1 A:SF4610 2.3 18.0 1.0
FE4 A:SF4610 2.7 22.5 1.0
FE2 A:SF4610 2.8 18.0 1.0
FE1 A:SF4610 2.8 19.3 1.0
N A:CYS556 3.6 19.7 1.0
CB A:CYS556 3.6 20.7 1.0
N A:LYS557 3.8 18.6 1.0
S3 A:SF4610 3.9 16.7 1.0
CD A:PRO529 3.9 24.2 1.0
CA A:CYS556 4.0 21.6 1.0
N A:THR558 4.0 20.4 1.0
CG A:PRO529 4.2 21.8 1.0
C A:CYS556 4.4 20.5 1.0
CB A:THR558 4.5 17.4 1.0
C A:HIS555 4.6 20.8 1.0
CA A:LYS557 4.7 17.8 1.0
SG A:CYS528 4.7 20.5 1.0
CG2 A:VAL554 4.7 19.1 1.0
N A:HIS555 4.7 19.4 1.0
SG A:CYS559 4.7 20.5 1.0
N A:CYS559 4.7 21.6 1.0
OG1 A:THR558 4.8 21.5 1.0
SG A:CYS553 4.8 23.1 1.0
C A:LYS557 4.8 20.7 1.0
CA A:THR558 4.8 19.9 1.0
CA A:HIS555 4.9 21.6 1.0

Iron binding site 4 out of 8 in 2gmh

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


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe610

b:22.5
occ:1.00
 FE4 A:SF4610 0.0 22.5 1.0
S2 A:SF4610 2.2 19.4 1.0
S1 A:SF4610 2.2 18.0 1.0
S3 A:SF4610 2.2 16.7 1.0
SG A:CYS559 2.3 20.5 1.0
FE3 A:SF4610 2.7 22.7 1.0
FE1 A:SF4610 2.7 19.3 1.0
FE2 A:SF4610 2.7 18.0 1.0
CB A:CYS559 3.3 19.6 1.0
S4 A:SF4610 3.8 19.3 1.0
N A:CYS559 3.8 21.6 1.0
CD1 A:LEU504 3.9 29.6 1.0
CA A:CYS559 4.2 21.7 1.0
OH A:TYR533 4.3 21.3 1.0
CE1 A:TYR533 4.4 17.8 1.0
CD1 A:TRP570 4.6 21.2 1.0
SG A:CYS556 4.6 22.3 1.0
N A:THR558 4.6 20.4 1.0
SG A:CYS553 4.7 23.1 1.0
SG A:CYS528 4.7 20.5 1.0
CG A:LEU504 4.8 32.3 1.0
CZ A:TYR533 4.8 22.5 1.0
C A:THR558 5.0 21.3 1.0
N A:LYS557 5.0 18.6 1.0

Iron binding site 5 out of 8 in 2gmh

Go back to Iron Binding Sites List in 2gmh
Iron binding site 5 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe613

b:59.8
occ:1.00
 FE1 B:SF4613 0.0 59.8 1.0
S2 B:SF4613 2.3 57.4 1.0
S4 B:SF4613 2.3 58.4 1.0
S3 B:SF4613 2.3 59.0 1.0
SG B:CYS553 2.5 69.5 1.0
FE4 B:SF4613 2.7 59.3 1.0
FE3 B:SF4613 2.8 59.8 1.0
FE2 B:SF4613 2.8 59.2 1.0
CB B:CYS553 3.1 67.7 1.0
CA B:CYS553 3.3 67.6 1.0
N B:VAL554 3.7 66.4 1.0
S1 B:SF4613 3.9 56.0 1.0
C B:CYS553 3.9 67.2 1.0
N B:HIS555 4.1 64.4 1.0
CG2 B:VAL532 4.4 67.4 1.0
N B:CYS553 4.5 67.6 1.0
N B:CYS556 4.6 61.9 1.0
NE1 B:TRP570 4.7 53.5 1.0
CA B:HIS555 4.7 63.9 1.0
CD1 B:LEU504 4.8 66.5 1.0
CD1 B:TRP570 4.8 54.4 1.0
SG B:CYS528 4.8 53.4 1.0
SG B:CYS556 4.9 66.8 1.0
CA B:VAL554 4.9 65.8 1.0
SG B:CYS559 4.9 52.2 1.0
C B:VAL554 4.9 65.3 1.0
O B:CYS553 4.9 67.6 1.0

Iron binding site 6 out of 8 in 2gmh

Go back to Iron Binding Sites List in 2gmh
Iron binding site 6 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe613

b:59.2
occ:1.00
 FE2 B:SF4613 0.0 59.2 1.0
SG B:CYS528 2.3 53.4 1.0
S1 B:SF4613 2.3 56.0 1.0
S3 B:SF4613 2.3 59.0 1.0
S4 B:SF4613 2.3 58.4 1.0
FE4 B:SF4613 2.7 59.3 1.0
FE1 B:SF4613 2.8 59.8 1.0
FE3 B:SF4613 2.8 59.8 1.0
CB B:CYS528 3.6 57.3 1.0
CD B:PRO529 3.7 59.0 1.0
S2 B:SF4613 3.9 57.4 1.0
CG2 B:VAL532 4.0 67.4 1.0
CA B:CYS528 4.1 57.6 1.0
CE1 B:TYR533 4.3 69.8 1.0
CB B:VAL532 4.4 68.3 1.0
CG B:PRO529 4.5 59.5 1.0
N B:PRO529 4.5 58.9 1.0
CB B:ALA530 4.6 63.7 1.0
N B:ALA530 4.6 63.9 1.0
C B:CYS528 4.6 58.1 1.0
SG B:CYS559 4.7 52.2 1.0
SG B:CYS556 4.7 66.8 1.0
CA B:CYS553 4.9 67.6 1.0
CD1 B:TYR533 4.9 69.8 1.0

Iron binding site 7 out of 8 in 2gmh

Go back to Iron Binding Sites List in 2gmh
Iron binding site 7 out of 8 in the Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed with Ubiquinone


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe613

b:59.8
occ:1.00
 FE3 B:SF4613 0.0 59.8 1.0
S4 B:SF4613 2.2 58.4 1.0
SG B:CYS556 2.3 66.8 1.0
S2 B:SF4613 2.3 57.4 1.0
S1 B:SF4613 2.3 56.0 1.0
FE4 B:SF4613 2.7 59.3 1.0
FE1 B:SF4613 2.8 59.8 1.0
FE2 B:SF4613 2.8 59.2 1.0
CB B:CYS556 3.6 61.7 1.0
N B:CYS556 3.7 61.9 1.0
S3 B:SF4613 3.9 59.0 1.0
CD B:PRO529 3.9 59.0 1.0
CG B:PRO529 3.9 59.5 1.0
N B:LYS557 3.9 60.0 1.0
CA B:CYS556 4.0 61.5 1.0
N B:THR558 4.2 56.6 1.0
C B:CYS556 4.3 60.2 1.0
CB B:THR558 4.4 54.4 1.0
OG1 B:THR558 4.6 54.3 1.0
SG B:CYS559 4.7 52.2 1.0
SG B:CYS528 4.7 53.4 1.0
N B:CYS559 4.8 55.9 1.0
C B:HIS555 4.8 62.6 1.0
CG2 B:VAL554 4.8 66.5 1.0
N B:HIS555 4.8 64.4 1.0
CA B:THR558 4.9 55.8 1.0
CA B:LYS557 4.9 58.7 1.0
N B:VAL554 4.9 66.4 1.0
SG B:CYS553 4.9 69.5 1.0
C B:LYS557 5.0 57.5 1.0

Iron binding site 8 out of 8 in 2gmh

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


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 in Complexed with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe613

b:59.3
occ:1.00
 FE4 B:SF4613 0.0 59.3 1.0
S1 B:SF4613 2.2 56.0 1.0
S2 B:SF4613 2.2 57.4 1.0
S3 B:SF4613 2.2 59.0 1.0
SG B:CYS559 2.3 52.2 1.0
FE3 B:SF4613 2.7 59.8 1.0
FE1 B:SF4613 2.7 59.8 1.0
FE2 B:SF4613 2.7 59.2 1.0
CB B:CYS559 3.4 54.2 1.0
S4 B:SF4613 3.8 58.4 1.0
N B:CYS559 3.9 55.9 1.0
OH B:TYR533 4.1 68.8 1.0
CD1 B:LEU504 4.2 66.5 1.0
CA B:CYS559 4.3 54.8 1.0
CE1 B:TYR533 4.5 69.8 1.0
CD1 B:TRP570 4.6 54.4 1.0
N B:THR558 4.7 56.6 1.0
SG B:CYS556 4.7 66.8 1.0
SG B:CYS528 4.8 53.4 1.0
SG B:CYS553 4.8 69.5 1.0
CZ B:TYR533 4.8 69.4 1.0
N B:LYS557 4.9 60.0 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: Sat Aug 3 22:34:58 2024

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