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Iron in PDB 2ybb: Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

Enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

All present enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876):
1.10.2.2; 1.6.5.3; 1.6.99.5; 1.9.3.1;

Other elements in 2ybb:

The structure of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Copper (Cu) 3 atoms
Calcium (Ca) 1 atom
Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 45;

Binding sites:

The binding sites of Iron atom in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) (pdb code 2ybb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 45 binding sites of Iron where determined in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876), PDB code: 2ybb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 45 in 2ybb

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Iron binding site 1 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe439

b:7.2
occ:1.00
FE1 1:SF4439 0.0 7.2 1.0
S4 1:SF4439 2.3 25.9 1.0
SG 1:CYS356 2.3 42.7 1.0
S2 1:SF4439 2.3 22.0 1.0
S3 1:SF4439 2.3 24.2 1.0
FE2 1:SF4439 2.7 0.7 1.0
FE3 1:SF4439 2.7 12.4 1.0
FE4 1:SF4439 2.8 0.7 1.0
CB 1:CYS356 3.1 33.6 1.0
N 1:CYS356 3.7 29.9 1.0
CB 1:PHE399 3.8 32.6 1.0
S1 1:SF4439 4.0 24.1 1.0
CA 1:CYS356 4.0 29.3 1.0
N 1:PHE399 4.1 33.2 1.0
CB 1:CYS359 4.1 30.9 1.0
N 1:CYS400 4.4 33.2 1.0
CA 1:PHE399 4.4 32.2 1.0
SG 1:CYS359 4.6 36.7 1.0
CB 1:LYS355 4.6 27.2 1.0
C 1:LYS355 4.7 27.2 1.0
SG 1:CYS400 4.7 23.1 1.0
SG 1:CYS353 4.8 36.2 1.0
CG 1:PHE399 4.8 31.9 1.0
CB 1:SER398 4.9 42.5 1.0
C 1:PHE399 4.9 34.5 1.0
CA 1:LYS355 4.9 27.0 1.0
N 1:LYS355 5.0 28.5 1.0

Iron binding site 2 out of 45 in 2ybb

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Iron binding site 2 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe439

b:0.7
occ:1.00
FE2 1:SF4439 0.0 0.7 1.0
S3 1:SF4439 2.2 24.2 1.0
SG 1:CYS400 2.3 23.1 1.0
S1 1:SF4439 2.3 24.1 1.0
S4 1:SF4439 2.3 25.9 1.0
FE4 1:SF4439 2.6 0.7 1.0
FE3 1:SF4439 2.7 12.4 1.0
FE1 1:SF4439 2.7 7.2 1.0
CB 1:CYS400 3.5 29.9 1.0
S2 1:SF4439 3.7 22.0 1.0
CB 1:LEU402 3.8 30.9 1.0
N 1:CYS400 4.0 33.2 1.0
O 1:CYS400 4.1 32.8 1.0
CA 1:CYS400 4.1 31.8 1.0
C 1:CYS400 4.3 33.8 1.0
N 1:LEU402 4.5 32.8 1.0
CG 1:PRO199 4.5 31.9 1.0
SG 1:CYS359 4.7 36.7 1.0
CA 1:LEU402 4.7 34.1 1.0
SG 1:CYS353 4.7 36.2 1.0
CG 1:LEU402 4.8 31.4 1.0
SG 1:CYS356 4.8 42.7 1.0
N 1:ALA403 4.8 36.4 1.0
CD1 1:ILE181 4.9 30.6 1.0
CD2 1:LEU402 4.9 33.0 1.0
CD1 1:LEU402 5.0 34.2 1.0

Iron binding site 3 out of 45 in 2ybb

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Iron binding site 3 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe439

b:12.4
occ:1.00
FE3 1:SF4439 0.0 12.4 1.0
SG 1:CYS353 2.3 36.2 1.0
S2 1:SF4439 2.3 22.0 1.0
S1 1:SF4439 2.3 24.1 1.0
S4 1:SF4439 2.3 25.9 1.0
FE2 1:SF4439 2.7 0.7 1.0
FE1 1:SF4439 2.7 7.2 1.0
FE4 1:SF4439 2.9 0.7 1.0
CB 1:CYS353 3.4 34.1 1.0
N 1:CYS353 3.7 31.0 1.0
S3 1:SF4439 3.9 24.2 1.0
CA 1:CYS353 4.0 30.9 1.0
N 1:LYS355 4.0 28.5 1.0
CB 1:LYS355 4.0 27.2 1.0
N 1:GLY354 4.1 33.3 1.0
C 1:CYS353 4.3 31.8 1.0
CA 1:LYS355 4.5 27.0 1.0
N 1:CYS356 4.6 29.9 1.0
SG 1:CYS400 4.6 23.1 1.0
OG 1:SER352 4.6 34.1 1.0
CD 1:PRO199 4.8 32.8 1.0
SG 1:CYS356 4.8 42.7 1.0
C 1:SER352 4.9 33.4 1.0
CG 1:PRO199 4.9 31.9 1.0
SG 1:CYS359 4.9 36.7 1.0
C 1:GLY354 4.9 30.3 1.0

Iron binding site 4 out of 45 in 2ybb

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Iron binding site 4 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe439

b:0.7
occ:1.00
FE4 1:SF4439 0.0 0.7 1.0
SG 1:CYS359 2.2 36.7 1.0
S1 1:SF4439 2.3 24.1 1.0
S3 1:SF4439 2.3 24.2 1.0
S2 1:SF4439 2.3 22.0 1.0
FE2 1:SF4439 2.6 0.7 1.0
FE1 1:SF4439 2.8 7.2 1.0
FE3 1:SF4439 2.9 12.4 1.0
CB 1:CYS359 3.0 30.9 1.0
OG 1:SER352 3.7 34.1 1.0
CD2 1:LEU402 3.9 33.0 1.0
S4 1:SF4439 3.9 25.9 1.0
CB 1:SER352 4.2 34.5 1.0
CB 1:LEU402 4.3 30.9 1.0
N 1:CYS353 4.4 31.0 1.0
CA 1:CYS359 4.4 34.3 1.0
CA 1:SER352 4.5 34.0 1.0
N 1:ALA403 4.6 36.4 1.0
CG 1:LEU402 4.6 31.4 1.0
SG 1:CYS400 4.6 23.1 1.0
SG 1:CYS356 4.8 42.7 1.0
CB 1:ALA403 4.8 37.6 1.0
CB 1:CYS356 4.9 33.6 1.0
SG 1:CYS353 4.9 36.2 1.0
CD1 1:LEU402 4.9 34.2 1.0
C 1:CYS359 5.0 36.5 1.0
C 1:SER352 5.0 33.4 1.0

Iron binding site 5 out of 45 in 2ybb

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Iron binding site 5 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe182

b:11.8
occ:1.00
FE1 2:FES182 0.0 11.8 1.0
S2 2:FES182 2.2 27.1 1.0
S1 2:FES182 2.2 33.4 1.0
SG 2:CYS83 2.3 34.9 1.0
SG 2:CYS88 2.3 36.9 1.0
FE2 2:FES182 3.0 20.4 1.0
CB 2:CYS88 3.2 41.8 1.0
CB 2:CYS83 3.4 38.1 1.0
N 2:CYS88 4.0 40.4 1.0
CA 2:CYS124 4.0 32.2 1.0
N 2:LEU125 4.2 34.6 1.0
CA 2:CYS88 4.2 41.1 1.0
O 2:THR85 4.6 43.8 1.0
SG 2:CYS124 4.6 37.5 1.0
C 2:CYS124 4.6 34.2 1.0
OG1 2:THR85 4.7 39.6 1.0
CB 2:VAL133 4.7 39.0 1.0
N 2:CYS124 4.7 35.2 1.0
CB 2:CYS124 4.8 33.6 1.0
CA 2:CYS83 4.8 37.7 1.0
SG 2:CYS128 4.8 34.6 1.0
CG2 2:VAL133 4.9 40.1 1.0
CA 2:CYS128 5.0 39.5 1.0

Iron binding site 6 out of 45 in 2ybb

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Iron binding site 6 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe182

b:20.4
occ:1.00
FE2 2:FES182 0.0 20.4 1.0
S1 2:FES182 2.2 33.4 1.0
S2 2:FES182 2.2 27.1 1.0
SG 2:CYS128 2.3 34.6 1.0
SG 2:CYS124 2.3 37.5 1.0
FE1 2:FES182 3.0 11.8 1.0
CB 2:CYS128 3.5 38.4 1.0
CB 2:CYS124 3.5 33.6 1.0
CA 2:CYS124 3.7 32.2 1.0
CA 2:CYS128 4.0 39.5 1.0
N 2:CYS128 4.1 37.5 1.0
N 2:GLY126 4.1 34.6 1.0
C 2:CYS124 4.2 34.2 1.0
N 2:LEU125 4.2 34.6 1.0
N 1:GLY99 4.2 38.8 1.0
N 2:SER127 4.4 39.3 1.0
CB 2:SER87 4.5 40.5 1.0
CA 2:GLY126 4.7 34.0 1.0
SG 2:CYS83 4.8 34.9 1.0
C 2:SER127 4.8 39.1 1.0
CA 1:PRO98 4.9 40.9 1.0
SG 2:CYS88 4.9 36.9 1.0
CA 1:GLY99 4.9 41.0 1.0
O 2:CYS124 5.0 35.6 1.0

Iron binding site 7 out of 45 in 2ybb

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Iron binding site 7 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe784

b:0.7
occ:1.00
FE1 3:SF4784 0.0 0.7 1.0
S3 3:SF4784 2.3 23.0 1.0
S2 3:SF4784 2.3 26.8 1.0
S4 3:SF4784 2.3 24.0 1.0
SG 3:CYS128 2.3 27.5 1.0
FE2 3:SF4784 2.6 6.7 1.0
FE4 3:SF4784 2.8 7.0 1.0
FE3 3:SF4784 2.8 9.5 1.0
CB 3:CYS128 3.5 25.9 1.0
S1 3:SF4784 3.9 36.3 1.0
CG 3:GLN131 4.0 25.8 1.0
CG1 3:VAL232 4.3 28.6 1.0
NE2 3:HIS115 4.4 29.9 1.0
N 3:GLN131 4.4 29.1 1.0
CB 3:GLN131 4.5 28.1 1.0
CB 3:LEU130 4.6 27.1 1.0
CB 3:LYS124 4.6 29.0 1.0
CD2 3:LEU130 4.7 26.6 1.0
SG 3:CYS119 4.7 29.6 1.0
SG 3:CYS122 4.8 31.1 1.0
CD 3:GLN131 4.8 29.1 1.0
CA 3:CYS128 4.9 27.3 1.0
CB 3:VAL232 4.9 28.2 1.0
CA 3:VAL232 4.9 27.3 1.0
CA 3:GLN131 4.9 28.2 1.0
N 3:GLY233 4.9 28.4 1.0
CG 3:LYS124 5.0 29.2 1.0

Iron binding site 8 out of 45 in 2ybb

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Iron binding site 8 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe784

b:6.7
occ:1.00
FE2 3:SF4784 0.0 6.7 1.0
S3 3:SF4784 2.3 23.0 1.0
S4 3:SF4784 2.3 24.0 1.0
SG 3:CYS119 2.3 29.6 1.0
S1 3:SF4784 2.3 36.3 1.0
FE1 3:SF4784 2.6 0.7 1.0
FE4 3:SF4784 2.8 7.0 1.0
FE3 3:SF4784 2.8 9.5 1.0
CB 3:CYS119 3.5 28.9 1.0
CA 3:CYS119 3.5 31.7 1.0
S2 3:SF4784 3.8 26.8 1.0
CG 3:GLN131 3.9 25.8 1.0
N 3:CYS119 4.0 31.3 1.0
NE2 3:GLN131 4.5 29.9 1.0
CD 3:GLN131 4.5 29.1 1.0
NE2 3:HIS115 4.6 29.9 1.0
SG 3:CYS128 4.7 27.5 1.0
SG 3:CYS122 4.8 31.1 1.0
C 3:CYS119 4.8 34.2 1.0
CD2 3:HIS115 5.0 33.7 1.0

Iron binding site 9 out of 45 in 2ybb

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Iron binding site 9 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe784

b:9.5
occ:1.00
FE3 3:SF4784 0.0 9.5 1.0
NE2 3:HIS115 2.1 29.9 1.0
S1 3:SF4784 2.3 36.3 1.0
S2 3:SF4784 2.3 26.8 1.0
S4 3:SF4784 2.3 24.0 1.0
FE4 3:SF4784 2.8 7.0 1.0
FE2 3:SF4784 2.8 6.7 1.0
FE1 3:SF4784 2.8 0.7 1.0
CD2 3:HIS115 3.0 33.7 1.0
CE1 3:HIS115 3.2 31.5 1.0
S3 3:SF4784 4.0 23.0 1.0
CG 3:HIS115 4.2 33.4 1.0
ND1 3:HIS115 4.2 30.9 1.0
CG 3:PRO116 4.4 33.6 1.0
CD2 3:LEU130 4.4 26.6 1.0
CG 3:ARG180 4.5 29.4 1.0
CG1 3:VAL232 4.7 28.6 1.0
SG 3:CYS119 4.7 29.6 1.0
CD 3:ARG180 4.8 28.8 1.0
SG 3:CYS122 4.9 31.1 1.0
CD 3:PRO116 4.9 33.2 1.0
SG 3:CYS128 4.9 27.5 1.0
CB 3:ARG180 5.0 28.9 1.0

Iron binding site 10 out of 45 in 2ybb

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Iron binding site 10 out of 45 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe784

b:7.0
occ:1.00
FE4 3:SF4784 0.0 7.0 1.0
S1 3:SF4784 2.3 36.3 1.0
S2 3:SF4784 2.3 26.8 1.0
SG 3:CYS122 2.3 31.1 1.0
S3 3:SF4784 2.3 23.0 1.0
FE2 3:SF4784 2.8 6.7 1.0
FE1 3:SF4784 2.8 0.7 1.0
FE3 3:SF4784 2.8 9.5 1.0
CB 3:CYS122 3.3 34.1 1.0
S4 3:SF4784 3.9 24.0 1.0
CB 3:LYS124 4.0 29.0 1.0
CD 3:ARG180 4.3 28.8 1.0
CA 3:CYS119 4.5 31.7 1.0
NE 3:ARG180 4.5 30.8 1.0
N 3:GLY233 4.7 28.4 1.0
SG 3:CYS128 4.8 27.5 1.0
N 3:CYS119 4.8 31.3 1.0
CA 3:CYS122 4.8 33.1 1.0
SG 3:CYS119 4.8 29.6 1.0
NE2 3:HIS115 4.8 29.9 1.0
CG 3:ARG180 4.9 29.4 1.0
CG 3:LYS124 5.0 29.2 1.0

Reference:

T.Althoff, D.J.Mills, J.-L.Popot, W.Kuehlbrandt. Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)IV(1). Embo J. V. 30 4652 2011.
ISSN: ISSN 0261-4189
PubMed: 21909073
DOI: 10.1038/EMBOJ.2011.324
Page generated: Sun Dec 13 14:57:50 2020

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