Iron in PDB 6yj4: Structure of Yarrowia Lipolytica Complex I at 2.7 A

Enzymatic activity of Structure of Yarrowia Lipolytica Complex I at 2.7 A

All present enzymatic activity of Structure of Yarrowia Lipolytica Complex I at 2.7 A:
1.6.5.3; 1.6.99.3; 7.1.1.2;

Other elements in 6yj4:

The structure of Structure of Yarrowia Lipolytica Complex I at 2.7 A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Structure of Yarrowia Lipolytica Complex I at 2.7 A (pdb code 6yj4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Structure of Yarrowia Lipolytica Complex I at 2.7 A, PDB code: 6yj4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6yj4

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Iron binding site 1 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:41.2
occ:1.00
 FE1 B:SF4301 0.0 41.2 1.0
SG B:CYS150 2.2 37.7 1.0
S4 B:SF4301 2.3 41.2 1.0
S2 B:SF4301 2.3 41.2 1.0
S3 B:SF4301 2.3 41.2 1.0
FE3 B:SF4301 2.7 41.2 1.0
FE4 B:SF4301 2.7 41.2 1.0
FE2 B:SF4301 2.7 41.2 1.0
CB B:CYS150 2.8 37.7 1.0
N B:CYS150 3.7 37.7 1.0
CA B:CYS150 3.8 37.7 1.0
S1 B:SF4301 3.9 41.2 1.0
CQ2 D:2MR121 3.9 38.7 1.0
SG B:CYS180 4.6 36.0 1.0
N B:THR122 4.8 40.3 1.0
SG B:CYS86 4.9 39.1 1.0
C B:SER149 4.9 35.6 1.0
N B:SER149 5.0 35.6 1.0
SG B:CYS85 5.0 40.7 1.0

Iron binding site 2 out of 28 in 6yj4

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Iron binding site 2 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:41.2
occ:1.00
 FE2 B:SF4301 0.0 41.2 1.0
SG B:CYS86 2.3 39.1 1.0
S1 B:SF4301 2.3 41.2 1.0
S4 B:SF4301 2.3 41.2 1.0
S3 B:SF4301 2.3 41.2 1.0
FE3 B:SF4301 2.7 41.2 1.0
FE4 B:SF4301 2.7 41.2 1.0
FE1 B:SF4301 2.7 41.2 1.0
CB B:CYS86 3.8 39.1 1.0
S2 B:SF4301 3.9 41.2 1.0
N B:CYS86 4.2 39.1 1.0
CA B:GLY148 4.2 37.0 1.0
SG B:CYS85 4.2 40.7 1.0
CA B:CYS86 4.5 39.1 1.0
N B:SER149 4.7 35.6 1.0
CA B:PRO181 4.7 37.1 1.0
CB B:CYS150 4.8 37.7 1.0
CA B:CYS180 4.8 36.0 1.0
CD B:PRO182 4.8 37.1 1.0
C B:GLY148 4.9 37.0 1.0
SG B:CYS180 4.9 36.0 1.0
N B:CYS150 4.9 37.7 1.0
SG B:CYS150 4.9 37.7 1.0
O B:GLY179 4.9 35.0 1.0
C B:CYS85 4.9 40.7 1.0
O B:MET147 4.9 38.9 1.0

Iron binding site 3 out of 28 in 6yj4

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Iron binding site 3 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:41.2
occ:1.00
 FE3 B:SF4301 0.0 41.2 1.0
S4 B:SF4301 2.3 41.2 1.0
S2 B:SF4301 2.3 41.2 1.0
S1 B:SF4301 2.3 41.2 1.0
SG B:CYS85 2.3 40.7 1.0
FE2 B:SF4301 2.7 41.2 1.0
FE1 B:SF4301 2.7 41.2 1.0
FE4 B:SF4301 2.7 41.2 1.0
CQ2 D:2MR121 3.6 38.7 1.0
CB B:CYS85 3.9 40.7 1.0
S3 B:SF4301 3.9 41.2 1.0
NE2 D:HIS226 4.1 37.2 1.0
N B:CYS85 4.4 40.7 1.0
NH2 D:2MR121 4.5 38.7 1.0
CA B:CYS85 4.5 40.7 1.0
SG B:CYS86 4.6 39.1 1.0
SG B:CYS180 4.6 36.0 1.0
N B:CYS86 4.6 39.1 1.0
SG B:CYS150 4.7 37.7 1.0
C B:CYS85 4.7 40.7 1.0
CD2 D:HIS226 4.7 37.2 1.0
CG D:ARG141 4.8 36.0 1.0
NE D:ARG141 4.9 36.0 1.0
CD D:ARG141 4.9 36.0 1.0
CB B:ALA84 5.0 41.3 1.0

Iron binding site 4 out of 28 in 6yj4

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Iron binding site 4 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:41.2
occ:1.00
 FE4 B:SF4301 0.0 41.2 1.0
SG B:CYS180 2.2 36.0 1.0
S1 B:SF4301 2.3 41.2 1.0
S2 B:SF4301 2.3 41.2 1.0
S3 B:SF4301 2.3 41.2 1.0
FE3 B:SF4301 2.7 41.2 1.0
FE1 B:SF4301 2.7 41.2 1.0
FE2 B:SF4301 2.7 41.2 1.0
CB B:CYS180 3.2 36.0 1.0
CA B:CYS180 3.3 36.0 1.0
C B:CYS180 3.9 36.0 1.0
S4 B:SF4301 3.9 41.2 1.0
NE D:ARG141 4.3 36.0 1.0
O B:CYS180 4.3 36.0 1.0
N B:PRO181 4.4 37.1 1.0
O B:GLY179 4.5 35.0 1.0
SG B:CYS85 4.5 40.7 1.0
SG B:CYS150 4.6 37.7 1.0
N B:CYS180 4.6 36.0 1.0
CA B:PRO181 4.7 37.1 1.0
CD2 D:HIS226 4.7 37.2 1.0
SG B:CYS86 4.8 39.1 1.0
NE2 D:HIS226 4.8 37.2 1.0
N B:SER149 5.0 35.6 1.0
C B:GLY179 5.0 35.0 1.0

Iron binding site 5 out of 28 in 6yj4

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Iron binding site 5 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:66.3
occ:1.00
 FE1 E:FES301 0.0 66.3 1.0
S2 E:FES301 2.2 66.3 1.0
S1 E:FES301 2.2 66.3 1.0
SG E:CYS132 2.3 64.8 1.0
SG E:CYS127 2.3 64.8 1.0
FE2 E:FES301 2.7 66.3 1.0
CB E:CYS127 3.1 64.8 1.0
OG1 E:THR129 3.2 61.7 1.0
CB E:CYS132 3.4 64.8 1.0
CG E:MET177 3.9 68.2 1.0
N E:CYS132 4.2 64.8 1.0
CA E:CYS168 4.4 62.0 1.0
CA E:CYS132 4.4 64.8 1.0
SG E:CYS172 4.5 66.0 1.0
CA E:CYS127 4.5 64.8 1.0
CB E:CYS168 4.6 62.0 1.0
SD E:MET177 4.6 68.2 1.0
CB E:THR129 4.6 61.7 1.0
C E:CYS127 4.7 64.8 1.0
SG E:CYS168 4.7 62.0 1.0
CA E:CYS172 4.8 66.0 1.0
O E:CYS127 4.9 64.8 1.0
N E:LEU169 4.9 64.0 1.0
N E:THR129 4.9 61.7 1.0
CE E:MET177 4.9 68.2 1.0
CB E:CYS172 5.0 66.0 1.0

Iron binding site 6 out of 28 in 6yj4

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Iron binding site 6 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:66.3
occ:1.00
 FE2 E:FES301 0.0 66.3 1.0
SG E:CYS172 2.2 66.0 1.0
S1 E:FES301 2.2 66.3 1.0
S2 E:FES301 2.2 66.3 1.0
SG E:CYS168 2.3 62.0 1.0
FE1 E:FES301 2.7 66.3 1.0
CB E:CYS168 2.9 62.0 1.0
CA E:CYS168 3.4 62.0 1.0
CB E:CYS172 3.5 66.0 1.0
OG1 E:THR129 3.8 61.7 1.0
CA E:CYS172 3.9 66.0 1.0
N E:LEU169 4.0 64.0 1.0
SG E:CYS127 4.0 64.8 1.0
C E:CYS168 4.1 62.0 1.0
N E:CYS172 4.1 66.0 1.0
N E:GLY170 4.3 64.1 1.0
N E:ALA171 4.5 65.8 1.0
N F:GLY125 4.5 63.4 1.0
SG E:CYS132 4.6 64.8 1.0
N E:CYS168 4.7 62.0 1.0
C E:ALA171 4.8 65.8 1.0
CA F:PRO124 4.9 60.4 1.0
CA E:GLY170 4.9 64.1 1.0

Iron binding site 7 out of 28 in 6yj4

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Iron binding site 7 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:48.2
occ:1.00
 FE1 F:SF4502 0.0 48.2 1.0
SG F:CYS381 2.2 47.7 1.0
S3 F:SF4502 2.3 48.2 1.0
S4 F:SF4502 2.3 48.2 1.0
S2 F:SF4502 2.3 48.2 1.0
FE3 F:SF4502 2.7 48.2 1.0
FE2 F:SF4502 2.7 48.2 1.0
FE4 F:SF4502 2.7 48.2 1.0
CB F:CYS381 3.3 47.7 1.0
N F:CYS381 3.7 47.7 1.0
S1 F:SF4502 3.9 48.2 1.0
CA F:CYS381 3.9 47.7 1.0
N F:GLY382 4.0 46.4 1.0
N F:GLN383 4.0 44.9 1.0
CB F:GLN383 4.1 44.9 1.0
CD F:PRO225 4.2 48.9 1.0
C F:CYS381 4.3 47.7 1.0
OE1 F:GLN383 4.5 44.9 1.0
OG F:SER380 4.5 48.4 1.0
CA F:GLN383 4.6 44.9 1.0
N F:CYS384 4.6 43.9 1.0
CG F:PRO225 4.6 48.9 1.0
SG F:CYS427 4.7 48.3 1.0
SG F:CYS384 4.8 43.9 1.0
C F:SER380 4.8 48.4 1.0
SG F:CYS387 4.9 45.2 1.0
CG2 F:VAL207 4.9 51.8 1.0
CA F:GLY382 5.0 46.4 1.0
C F:GLY382 5.0 46.4 1.0

Iron binding site 8 out of 28 in 6yj4

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Iron binding site 8 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:48.2
occ:1.00
 FE2 F:SF4502 0.0 48.2 1.0
SG F:CYS384 2.2 43.9 1.0
S1 F:SF4502 2.3 48.2 1.0
S4 F:SF4502 2.3 48.2 1.0
S3 F:SF4502 2.3 48.2 1.0
FE4 F:SF4502 2.7 48.2 1.0
FE3 F:SF4502 2.7 48.2 1.0
FE1 F:SF4502 2.7 48.2 1.0
CB F:CYS384 3.5 43.9 1.0
N F:CYS384 3.7 43.9 1.0
S2 F:SF4502 3.9 48.2 1.0
CB F:CYS387 4.0 45.2 1.0
CA F:CYS384 4.1 43.9 1.0
O F:CYS384 4.3 43.9 1.0
N F:ILE426 4.6 45.0 1.0
C F:CYS384 4.6 43.9 1.0
SG F:CYS387 4.6 45.2 1.0
CB F:ILE426 4.7 45.0 1.0
SG F:CYS381 4.7 47.7 1.0
CB F:GLN383 4.8 44.9 1.0
SG F:CYS427 4.8 48.3 1.0
C F:GLN383 4.9 44.9 1.0
N F:CYS427 4.9 48.3 1.0
CG1 F:ILE426 4.9 45.0 1.0
CB F:THR425 4.9 45.8 1.0
N F:GLN383 4.9 44.9 1.0
OE1 F:GLN383 5.0 44.9 1.0

Iron binding site 9 out of 28 in 6yj4

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Iron binding site 9 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:48.2
occ:1.00
 FE3 F:SF4502 0.0 48.2 1.0
SG F:CYS427 2.2 48.3 1.0
S1 F:SF4502 2.3 48.2 1.0
S4 F:SF4502 2.3 48.2 1.0
S2 F:SF4502 2.3 48.2 1.0
FE1 F:SF4502 2.7 48.2 1.0
FE2 F:SF4502 2.7 48.2 1.0
FE4 F:SF4502 2.7 48.2 1.0
CB F:CYS427 3.5 48.3 1.0
S3 F:SF4502 3.9 48.2 1.0
N F:CYS427 4.1 48.3 1.0
CB F:LEU429 4.1 50.7 1.0
CA F:CYS427 4.2 48.3 1.0
CG F:PRO225 4.3 48.9 1.0
C F:CYS427 4.5 48.3 1.0
O F:CYS427 4.5 48.3 1.0
N F:LEU429 4.7 50.7 1.0
SG F:CYS381 4.7 47.7 1.0
CG2 F:VAL207 4.7 51.8 1.0
SG F:CYS384 4.7 43.9 1.0
CD F:PRO225 4.8 48.9 1.0
SG F:CYS387 4.9 45.2 1.0
CA F:LEU429 5.0 50.7 1.0

Iron binding site 10 out of 28 in 6yj4

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Iron binding site 10 out of 28 in the Structure of Yarrowia Lipolytica Complex I at 2.7 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Yarrowia Lipolytica Complex I at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:48.2
occ:1.00
 FE4 F:SF4502 0.0 48.2 1.0
S3 F:SF4502 2.3 48.2 1.0
S1 F:SF4502 2.3 48.2 1.0
S2 F:SF4502 2.3 48.2 1.0
SG F:CYS387 2.3 45.2 1.0
FE2 F:SF4502 2.7 48.2 1.0
FE3 F:SF4502 2.7 48.2 1.0
FE1 F:SF4502 2.7 48.2 1.0
CB F:CYS387 2.8 45.2 1.0
OG F:SER380 3.3 48.4 1.0
S4 F:SF4502 3.9 48.2 1.0
CD2 F:LEU429 4.1 50.7 1.0
CA F:CYS387 4.2 45.2 1.0
CB F:SER380 4.2 48.4 1.0
N F:CYS381 4.4 47.7 1.0
CA F:SER380 4.4 48.4 1.0
SG F:CYS384 4.5 43.9 1.0
CB F:LEU429 4.6 50.7 1.0
SG F:CYS427 4.7 48.3 1.0
C F:CYS387 4.7 45.2 1.0
SG F:CYS381 4.8 47.7 1.0
CG F:LEU429 4.8 50.7 1.0
N F:ARG388 4.9 43.9 1.0
C F:SER380 4.9 48.4 1.0
N F:CYS387 5.0 45.2 1.0

Reference:

D.N.Grba, J.Hirst. Mitochondrial Complex I Structure Reveals Ordered Water Molecules For Catalysis and Proton Translocation. Nat.Struct.Mol.Biol. V. 27 892 2020.
ISSN: ESSN 1545-9985
PubMed: 32747785
DOI: 10.1038/S41594-020-0473-X
Page generated: Sun Dec 13 17:37:24 2020

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