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Iron in PDB 5ldw: Structure of Mammalian Respiratory Complex I, CLASS1

Enzymatic activity of Structure of Mammalian Respiratory Complex I, CLASS1

All present enzymatic activity of Structure of Mammalian Respiratory Complex I, CLASS1:
1.6.5.3; 1.6.99.3;

Other elements in 5ldw:

The structure of Structure of Mammalian Respiratory Complex I, CLASS1 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 Mammalian Respiratory Complex I, CLASS1 (pdb code 5ldw). 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 Mammalian Respiratory Complex I, CLASS1, PDB code: 5ldw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 5ldw

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Iron binding site 1 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:30.1
occ:1.00
 FE1 B:SF4201 0.0 30.1 1.0
S3 B:SF4201 2.3 30.6 1.0
S2 B:SF4201 2.3 30.3 1.0
S4 B:SF4201 2.3 30.6 1.0
SG B:CYS119 2.3 29.6 1.0
FE4 B:SF4201 2.7 30.5 1.0
FE3 B:SF4201 2.7 30.8 1.0
FE2 B:SF4201 2.7 31.0 1.0
CB B:CYS119 3.2 29.1 1.0
S1 B:SF4201 3.9 30.7 1.0
N B:CYS119 4.0 28.6 1.0
OG1 B:THR91 4.1 32.6 1.0
CA B:CYS119 4.2 28.7 1.0
OG B:SER118 4.5 28.5 1.0
CA B:GLY90 4.7 34.0 1.0
SG B:CYS149 4.7 30.4 1.0
SG B:CYS55 4.8 32.1 1.0
N B:THR91 4.8 33.2 1.0
SG B:CYS54 4.8 32.3 1.0
CE2 B:TYR126 5.0 26.9 1.0

Iron binding site 2 out of 28 in 5ldw

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Iron binding site 2 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:31.0
occ:1.00
 FE2 B:SF4201 0.0 31.0 1.0
S1 B:SF4201 2.3 30.7 1.0
S4 B:SF4201 2.3 30.6 1.0
S3 B:SF4201 2.3 30.6 1.0
SG B:CYS55 2.3 32.1 1.0
FE3 B:SF4201 2.7 30.8 1.0
FE1 B:SF4201 2.7 30.1 1.0
FE4 B:SF4201 2.7 30.5 1.0
CB B:CYS55 3.4 32.5 1.0
N B:CYS55 3.7 33.1 1.0
S2 B:SF4201 3.9 30.3 1.0
CA B:CYS55 3.9 33.0 1.0
CA B:GLY90 4.5 34.0 1.0
CA B:GLY117 4.5 28.5 1.0
C B:CYS54 4.7 33.4 1.0
SG B:CYS54 4.7 32.3 1.0
CD B:PRO151 4.7 33.4 1.0
SG B:CYS119 4.8 29.6 1.0
CB B:ALA53 4.8 37.0 1.0
SG B:CYS149 4.8 30.4 1.0
CA B:CYS149 4.8 30.7 1.0
CB B:CYS54 4.9 32.9 1.0
N B:SER118 4.9 28.4 1.0
N B:CYS54 4.9 34.6 1.0
CB B:CYS119 5.0 29.1 1.0

Iron binding site 3 out of 28 in 5ldw

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Iron binding site 3 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:30.8
occ:1.00
 FE3 B:SF4201 0.0 30.8 1.0
S4 B:SF4201 2.3 30.6 1.0
S1 B:SF4201 2.3 30.7 1.0
S2 B:SF4201 2.3 30.3 1.0
SG B:CYS54 2.3 32.3 1.0
FE2 B:SF4201 2.7 31.0 1.0
FE1 B:SF4201 2.7 30.1 1.0
FE4 B:SF4201 2.7 30.5 1.0
CB B:CYS54 3.2 32.9 1.0
N B:CYS54 3.9 34.6 1.0
S3 B:SF4201 3.9 30.6 1.0
CA B:CYS54 4.0 33.6 1.0
N B:CYS55 4.1 33.1 1.0
CE1 D:HIS190 4.1 39.0 1.0
C B:CYS54 4.4 33.4 1.0
CG D:ARG105 4.7 35.4 1.0
SG B:CYS55 4.8 32.1 1.0
SG B:CYS149 4.8 30.4 1.0
SG B:CYS119 4.8 29.6 1.0
ND1 D:HIS190 4.9 38.9 1.0
CB D:ARG105 5.0 35.4 1.0

Iron binding site 4 out of 28 in 5ldw

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Iron binding site 4 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:30.5
occ:1.00
 FE4 B:SF4201 0.0 30.5 1.0
S3 B:SF4201 2.3 30.6 1.0
S2 B:SF4201 2.3 30.3 1.0
S1 B:SF4201 2.3 30.7 1.0
SG B:CYS149 2.3 30.4 1.0
FE1 B:SF4201 2.7 30.1 1.0
FE3 B:SF4201 2.7 30.8 1.0
FE2 B:SF4201 2.7 31.0 1.0
CB B:CYS149 3.3 30.5 1.0
CA B:CYS149 3.7 30.7 1.0
S4 B:SF4201 3.9 30.6 1.0
CD B:PRO150 3.9 32.0 1.0
N B:PRO150 4.2 31.8 1.0
OG B:SER118 4.2 28.5 1.0
NE D:ARG105 4.4 35.5 1.0
C B:CYS149 4.4 31.3 1.0
CD D:ARG105 4.6 35.4 1.0
CG D:ARG105 4.6 35.4 1.0
ND1 D:HIS190 4.7 38.9 1.0
CE1 D:HIS190 4.7 39.0 1.0
SG B:CYS119 4.8 29.6 1.0
SG B:CYS55 4.8 32.1 1.0
SG B:CYS54 4.8 32.3 1.0
CG2 I:ILE117 4.9 23.1 1.0
N B:CYS149 5.0 30.4 1.0

Iron binding site 5 out of 28 in 5ldw

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Iron binding site 5 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:0.7
occ:1.00
 FE1 E:FES301 0.0 0.7 1.0
SG E:CYS108 2.2 0.2 1.0
S2 E:FES301 2.2 1.0 1.0
SG E:CYS103 2.2 99.4 1.0
S1 E:FES301 2.2 0.6 1.0
FE2 E:FES301 2.9 0.2 1.0
CB E:CYS103 3.5 98.8 1.0
CB E:CYS108 3.5 0.1 1.0
SG E:CYS144 4.4 0.5 1.0
N E:CYS108 4.5 99.3 1.0
SG E:CYS148 4.6 100.0 1.0
CA E:CYS108 4.6 99.9 1.0
CB E:THR105 4.6 96.4 1.0
N E:LEU145 4.7 0.8 1.0
CA E:CYS144 4.7 0.3 1.0
CB E:MET153 4.7 97.5 1.0
CA E:CYS103 4.8 98.4 1.0
CB E:CYS144 4.9 0.3 1.0

Iron binding site 6 out of 28 in 5ldw

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Iron binding site 6 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:0.2
occ:1.00
 FE2 E:FES301 0.0 0.2 1.0
S1 E:FES301 2.2 0.6 1.0
S2 E:FES301 2.2 1.0 1.0
SG E:CYS148 2.2 100.0 1.0
SG E:CYS144 2.2 0.5 1.0
FE1 E:FES301 2.9 0.7 1.0
CB E:CYS148 3.6 99.7 1.0
CB E:CYS144 3.6 0.3 1.0
CA E:CYS144 4.2 0.3 1.0
N E:LEU145 4.2 0.8 1.0
CA E:CYS148 4.2 99.1 1.0
N E:GLY146 4.3 0.9 1.0
N F:GLY103 4.4 0.2 1.0
O E:GLY146 4.4 0.8 1.0
SG E:CYS103 4.4 99.4 1.0
N E:CYS148 4.5 99.6 1.0
CA F:PRO102 4.5 0.1 1.0
CB F:PRO102 4.5 0.9 1.0
O E:ALA147 4.5 0.2 1.0
C E:CYS144 4.6 1.0 1.0
SG E:CYS108 4.6 0.2 1.0
C E:GLY146 4.6 0.8 1.0
C E:ALA147 4.6 0.2 1.0
CA E:GLY146 4.9 0.9 1.0
C F:PRO102 5.0 0.2 1.0

Iron binding site 7 out of 28 in 5ldw

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Iron binding site 7 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:65.4
occ:1.00
 FE1 F:SF4502 0.0 65.4 1.0
S2 F:SF4502 2.3 65.5 1.0
S4 F:SF4502 2.3 64.9 1.0
SG F:CYS362 2.3 66.0 1.0
S3 F:SF4502 2.3 65.0 1.0
FE2 F:SF4502 2.7 64.2 1.0
FE3 F:SF4502 2.7 65.4 1.0
FE4 F:SF4502 2.7 65.3 1.0
CB F:CYS362 3.2 65.1 1.0
N F:CYS362 3.6 63.9 1.0
S1 F:SF4502 3.9 64.9 1.0
CA F:CYS362 4.0 64.3 1.0
CB F:GLN361 4.4 63.4 1.0
N F:ILE404 4.6 67.1 1.0
CB F:CYS365 4.6 63.5 1.0
N F:CYS405 4.6 67.3 1.0
SG F:CYS365 4.7 63.6 1.0
C F:GLN361 4.7 63.5 1.0
SG F:CYS359 4.8 65.8 1.0
O F:CYS362 4.8 64.2 1.0
SG F:CYS405 4.8 67.0 1.0
CB F:ILE404 4.8 66.9 1.0
C F:CYS362 4.9 64.0 1.0
CA F:GLN361 4.9 63.5 1.0
N F:GLN361 5.0 63.7 1.0

Iron binding site 8 out of 28 in 5ldw

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Iron binding site 8 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:64.2
occ:1.00
 FE2 F:SF4502 0.0 64.2 1.0
S3 F:SF4502 2.3 65.0 1.0
SG F:CYS365 2.3 63.6 1.0
S1 F:SF4502 2.3 64.9 1.0
S4 F:SF4502 2.3 64.9 1.0
FE1 F:SF4502 2.7 65.4 1.0
FE4 F:SF4502 2.7 65.3 1.0
FE3 F:SF4502 2.7 65.4 1.0
CB F:CYS365 3.1 63.5 1.0
S2 F:SF4502 3.9 65.5 1.0
CA F:CYS365 4.6 63.3 1.0
N F:CYS359 4.7 65.4 1.0
SG F:CYS362 4.8 66.0 1.0
CD2 F:LEU407 4.8 72.8 1.0
SG F:CYS405 4.8 67.0 1.0
SG F:CYS359 4.8 65.8 1.0
CB F:CYS362 4.9 65.1 1.0
O F:CYS362 4.9 64.2 1.0
C F:CYS365 5.0 63.5 1.0

Iron binding site 9 out of 28 in 5ldw

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Iron binding site 9 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:65.4
occ:1.00
 FE3 F:SF4502 0.0 65.4 1.0
S4 F:SF4502 2.3 64.9 1.0
S2 F:SF4502 2.3 65.5 1.0
SG F:CYS405 2.3 67.0 1.0
S1 F:SF4502 2.3 64.9 1.0
FE1 F:SF4502 2.7 65.4 1.0
FE2 F:SF4502 2.7 64.2 1.0
FE4 F:SF4502 2.7 65.3 1.0
CB F:CYS405 3.3 67.3 1.0
S3 F:SF4502 3.9 65.0 1.0
N F:CYS405 4.1 67.3 1.0
CA F:CYS405 4.1 67.7 1.0
CB F:LEU407 4.5 73.0 1.0
C F:CYS405 4.5 68.2 1.0
N F:GLY408 4.6 74.9 1.0
O F:CYS405 4.7 67.9 1.0
CG F:PRO203 4.8 67.3 1.0
SG F:CYS359 4.8 65.8 1.0
SG F:CYS362 4.8 66.0 1.0
SG F:CYS365 4.8 63.6 1.0
N F:LEU407 4.9 72.1 1.0
CD2 F:LEU407 5.0 72.8 1.0

Iron binding site 10 out of 28 in 5ldw

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Iron binding site 10 out of 28 in the Structure of Mammalian Respiratory Complex I, CLASS1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Mammalian Respiratory Complex I, CLASS1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:65.3
occ:1.00
 FE4 F:SF4502 0.0 65.3 1.0
S3 F:SF4502 2.3 65.0 1.0
S1 F:SF4502 2.3 64.9 1.0
SG F:CYS359 2.3 65.8 1.0
S2 F:SF4502 2.3 65.5 1.0
FE2 F:SF4502 2.7 64.2 1.0
FE3 F:SF4502 2.7 65.4 1.0
FE1 F:SF4502 2.7 65.4 1.0
CB F:CYS359 3.3 65.4 1.0
S4 F:SF4502 3.9 64.9 1.0
N F:CYS359 3.9 65.4 1.0
N F:GLY360 4.0 64.8 1.0
CA F:CYS359 4.1 65.3 1.0
N F:GLN361 4.2 63.7 1.0
CB F:GLN361 4.2 63.4 1.0
CD F:PRO203 4.4 67.3 1.0
OE1 F:GLN361 4.5 63.9 1.0
C F:CYS359 4.5 65.2 1.0
CA F:GLN361 4.7 63.5 1.0
N F:CYS362 4.7 63.9 1.0
SG F:CYS405 4.8 67.0 1.0
SG F:CYS362 4.8 66.0 1.0
SG F:CYS365 4.8 63.6 1.0
CG F:PRO203 4.8 67.3 1.0
CG F:GLN361 4.8 63.6 1.0
C F:GLY360 4.9 64.0 1.0

Reference:

J.Zhu, K.R.Vinothkumar, J.Hirst. Structure of Mammalian Respiratory Complex I. Nature V. 536 354 2016.
ISSN: ESSN 1476-4687
PubMed: 27509854
DOI: 10.1038/NATURE19095
Page generated: Tue Aug 6 04:10:00 2024

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