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Iron in PDB 6rfs: Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4

Enzymatic activity of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4

All present enzymatic activity of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4:
1.6.5.3; 1.6.99.3; 7.1.1.2;

Other elements in 6rfs:

The structure of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 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 Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 (pdb code 6rfs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4, PDB code: 6rfs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6rfs

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Iron binding site 1 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:0.3
occ:1.00
 FE1 A:SF4801 0.0 0.3 1.0
S2 A:SF4801 2.2 0.3 1.0
S3 A:SF4801 2.3 0.3 1.0
S4 A:SF4801 2.3 0.3 1.0
SG A:CYS142 2.3 0.8 1.0
CB A:CYS142 2.6 0.8 1.0
FE4 A:SF4801 2.6 0.3 1.0
FE3 A:SF4801 2.6 0.3 1.0
FE2 A:SF4801 2.7 0.3 1.0
O A:GLN138 3.7 0.4 1.0
S1 A:SF4801 3.9 0.3 1.0
OE1 A:GLN145 4.0 0.8 1.0
CA A:CYS142 4.1 0.8 1.0
CB A:GLN145 4.3 0.8 1.0
SG A:CYS136 4.3 0.6 1.0
CD A:GLN145 4.7 0.8 1.0
NE2 A:HIS129 4.8 95.9 1.0
SG A:CYS133 4.8 0.3 1.0
C A:GLN138 4.8 0.4 1.0
CB A:CYS136 4.9 0.6 1.0
N A:CYS142 4.9 0.8 1.0
C A:CYS142 5.0 0.8 1.0

Iron binding site 2 out of 28 in 6rfs

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Iron binding site 2 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:0.3
occ:1.00
 FE2 A:SF4801 0.0 0.3 1.0
S1 A:SF4801 2.2 0.3 1.0
S4 A:SF4801 2.3 0.3 1.0
S3 A:SF4801 2.3 0.3 1.0
SG A:CYS133 2.3 0.3 1.0
FE3 A:SF4801 2.6 0.3 1.0
FE4 A:SF4801 2.6 0.3 1.0
FE1 A:SF4801 2.7 0.3 1.0
CA A:CYS133 3.0 0.3 1.0
CB A:CYS133 3.0 0.3 1.0
N A:CYS133 3.4 0.3 1.0
S2 A:SF4801 3.8 0.3 1.0
C A:ASP132 4.2 0.1 1.0
C A:CYS133 4.3 0.3 1.0
NE2 A:HIS129 4.3 95.9 1.0
CB A:CYS136 4.4 0.6 1.0
OE1 A:GLN145 4.5 0.8 1.0
O A:CYS133 4.5 0.3 1.0
O A:ASP132 4.6 0.1 1.0
CE C:MET378 4.8 1.0 1.0
SG A:CYS136 4.8 0.6 1.0
CG2 C:ILE382 4.8 0.3 1.0
SG A:CYS142 4.8 0.8 1.0
CD A:GLN145 4.9 0.8 1.0

Iron binding site 3 out of 28 in 6rfs

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Iron binding site 3 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:0.3
occ:1.00
 FE3 A:SF4801 0.0 0.3 1.0
NE2 A:HIS129 2.1 95.9 1.0
S4 A:SF4801 2.2 0.3 1.0
S2 A:SF4801 2.3 0.3 1.0
S1 A:SF4801 2.3 0.3 1.0
FE4 A:SF4801 2.6 0.3 1.0
FE2 A:SF4801 2.6 0.3 1.0
FE1 A:SF4801 2.6 0.3 1.0
CE1 A:HIS129 3.0 95.9 1.0
CD2 A:HIS129 3.1 95.9 1.0
S3 A:SF4801 3.8 0.3 1.0
SG A:CYS142 3.9 0.8 1.0
ND1 A:HIS129 4.1 95.9 1.0
CG A:HIS129 4.2 95.9 1.0
SG A:CYS133 4.3 0.3 1.0
CD2 A:LEU144 4.7 0.3 1.0
SG A:CYS136 4.7 0.6 1.0
CE C:MET378 4.8 1.0 1.0

Iron binding site 4 out of 28 in 6rfs

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Iron binding site 4 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:0.3
occ:1.00
 FE4 A:SF4801 0.0 0.3 1.0
S3 A:SF4801 2.2 0.3 1.0
S1 A:SF4801 2.3 0.3 1.0
S2 A:SF4801 2.3 0.3 1.0
SG A:CYS136 2.3 0.6 1.0
CB A:CYS136 2.6 0.6 1.0
FE3 A:SF4801 2.6 0.3 1.0
FE1 A:SF4801 2.6 0.3 1.0
FE2 A:SF4801 2.6 0.3 1.0
S4 A:SF4801 3.8 0.3 1.0
CD A:ARG182 4.0 0.7 1.0
CA A:CYS136 4.1 0.6 1.0
NE2 A:HIS129 4.1 95.9 1.0
CA A:CYS133 4.4 0.3 1.0
O A:ASP132 4.5 0.1 1.0
O A:GLN138 4.5 0.4 1.0
N A:CYS133 4.5 0.3 1.0
NE A:ARG182 4.6 0.7 1.0
C A:ASP132 4.6 0.1 1.0
SG A:CYS142 4.6 0.8 1.0
CE1 A:HIS129 4.6 95.9 1.0
N A:GLY236 4.7 0.8 1.0
C A:CYS136 4.7 0.6 1.0
N A:CYS136 4.8 0.6 1.0
SG A:CYS133 4.8 0.3 1.0
CB A:CYS142 4.9 0.8 1.0

Iron binding site 5 out of 28 in 6rfs

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Iron binding site 5 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:0.1
occ:1.00
 FE1 A:SF4802 0.0 0.1 1.0
S2 A:SF4802 2.2 0.1 1.0
S3 A:SF4802 2.3 0.1 1.0
S4 A:SF4802 2.3 0.1 1.0
SG A:CYS186 2.3 0.4 1.0
FE4 A:SF4802 2.6 0.1 1.0
FE3 A:SF4802 2.7 0.1 1.0
FE2 A:SF4802 2.7 0.1 1.0
CB A:CYS186 3.5 0.4 1.0
N A:CYS186 3.5 0.4 1.0
SG A:CYS233 3.7 0.8 1.0
S1 A:SF4802 3.8 0.1 1.0
CA A:CYS186 3.9 0.4 1.0
CD A:PRO234 4.1 0.7 1.0
N A:THR187 4.3 0.2 1.0
SG A:CYS183 4.3 0.7 1.0
C A:CYS186 4.3 0.4 1.0
CB A:CYS233 4.4 0.8 1.0
CA A:CYS233 4.5 0.8 1.0
C A:HIS185 4.6 0.4 1.0
N A:ARG188 4.7 0.7 1.0
N A:HIS185 4.7 0.4 1.0
CG1 A:ILE184 4.8 0.4 1.0
N A:CYS189 4.9 0.3 1.0
CA A:HIS185 4.9 0.4 1.0
SG A:CYS189 4.9 0.3 1.0
N A:ILE184 4.9 0.4 1.0
O A:CYS186 5.0 0.4 1.0

Iron binding site 6 out of 28 in 6rfs

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Iron binding site 6 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:0.1
occ:1.00
 FE2 A:SF4802 0.0 0.1 1.0
S1 A:SF4802 2.3 0.1 1.0
S3 A:SF4802 2.3 0.1 1.0
S4 A:SF4802 2.3 0.1 1.0
SG A:CYS183 2.3 0.7 1.0
FE3 A:SF4802 2.7 0.1 1.0
FE1 A:SF4802 2.7 0.1 1.0
FE4 A:SF4802 2.7 0.1 1.0
CB A:CYS183 3.6 0.7 1.0
S2 A:SF4802 3.8 0.1 1.0
N A:HIS185 4.0 0.4 1.0
CA A:HIS185 4.1 0.4 1.0
CG1 A:ILE213 4.1 0.9 1.0
N A:CYS186 4.2 0.4 1.0
SG A:CYS189 4.2 0.3 1.0
CA A:CYS183 4.4 0.7 1.0
N A:ILE184 4.5 0.4 1.0
SG A:CYS233 4.7 0.8 1.0
C A:HIS185 4.7 0.4 1.0
CB A:ILE213 4.7 0.9 1.0
SG A:CYS186 4.7 0.4 1.0
CE A:MET180 4.8 0.5 1.0
CG2 A:ILE213 4.9 0.9 1.0
C A:CYS183 4.9 0.7 1.0

Iron binding site 7 out of 28 in 6rfs

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Iron binding site 7 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:0.1
occ:1.00
 FE3 A:SF4802 0.0 0.1 1.0
S4 A:SF4802 2.2 0.1 1.0
S2 A:SF4802 2.3 0.1 1.0
SG A:CYS189 2.3 0.3 1.0
S1 A:SF4802 2.3 0.1 1.0
FE1 A:SF4802 2.7 0.1 1.0
FE2 A:SF4802 2.7 0.1 1.0
CB A:CYS189 2.7 0.3 1.0
FE4 A:SF4802 2.7 0.1 1.0
N A:CYS189 3.2 0.3 1.0
CA A:CYS189 3.5 0.3 1.0
S3 A:SF4802 3.8 0.1 1.0
SG A:CYS186 4.1 0.4 1.0
N A:ARG188 4.2 0.7 1.0
N A:THR187 4.3 0.2 1.0
C A:ARG188 4.4 0.7 1.0
N A:VAL190 4.5 0.8 1.0
C A:CYS189 4.6 0.3 1.0
C A:THR187 4.6 0.2 1.0
SG A:CYS233 4.7 0.8 1.0
CB A:CYS233 4.7 0.8 1.0
CA A:ARG188 4.8 0.7 1.0
CA A:THR187 4.8 0.2 1.0
N A:CYS186 4.9 0.4 1.0
CG2 A:ILE213 4.9 0.9 1.0
SG A:CYS183 5.0 0.7 1.0

Iron binding site 8 out of 28 in 6rfs

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Iron binding site 8 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:0.1
occ:1.00
 FE4 A:SF4802 0.0 0.1 1.0
S3 A:SF4802 2.2 0.1 1.0
S1 A:SF4802 2.3 0.1 1.0
S2 A:SF4802 2.3 0.1 1.0
SG A:CYS233 2.3 0.8 1.0
FE1 A:SF4802 2.6 0.1 1.0
FE2 A:SF4802 2.7 0.1 1.0
FE3 A:SF4802 2.7 0.1 1.0
CB A:CYS233 3.0 0.8 1.0
S4 A:SF4802 3.8 0.1 1.0
CA A:CYS233 4.0 0.8 1.0
CB A:ALA237 4.0 0.4 1.0
CD1 A:LEU238 4.2 0.7 1.0
CG A:LEU238 4.4 0.7 1.0
SG A:CYS183 4.4 0.7 1.0
CB A:CYS189 4.5 0.3 1.0
SG A:CYS189 4.6 0.3 1.0
SG A:CYS186 4.7 0.4 1.0
N A:LEU238 4.8 0.7 1.0
CB A:CYS183 4.9 0.7 1.0
CB A:LEU238 4.9 0.7 1.0
C A:CYS233 4.9 0.8 1.0

Iron binding site 9 out of 28 in 6rfs

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Iron binding site 9 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:0.9
occ:1.00
 FE1 A:FES803 0.0 0.9 1.0
S2 A:FES803 2.2 0.9 1.0
S1 A:FES803 2.2 0.9 1.0
SG A:CYS69 2.3 0.8 1.0
SG A:CYS80 2.3 0.4 1.0
N A:CYS80 2.8 0.4 1.0
CB A:CYS80 2.9 0.4 1.0
FE2 A:FES803 3.0 0.9 1.0
CA A:CYS80 3.3 0.4 1.0
C A:GLY78 3.5 0.5 1.0
N A:ASN79 3.5 0.3 1.0
O A:ALA77 3.6 0.9 1.0
N A:ARG81 3.6 0.8 1.0
CA A:GLY78 3.7 0.5 1.0
CB A:CYS69 3.8 0.8 1.0
C A:ASN79 3.9 0.3 1.0
C A:CYS80 3.9 0.4 1.0
O A:GLY78 4.0 0.5 1.0
SG A:CYS97 4.1 0.1 1.0
N A:CYS69 4.2 0.8 1.0
CA A:CYS69 4.3 0.8 1.0
CA A:ASN79 4.3 0.3 1.0
C A:CYS69 4.3 0.8 1.0
N A:TYR70 4.5 0.8 1.0
C A:ALA77 4.5 0.9 1.0
N A:GLY78 4.6 0.5 1.0
N A:MET82 4.8 0.1 1.0
O A:CYS69 4.8 0.8 1.0
CA A:ARG81 4.8 0.8 1.0
CB A:CYS97 4.9 0.1 1.0
SG A:CYS83 4.9 0.0 1.0
O A:ASN79 4.9 0.3 1.0
O A:CYS80 5.0 0.4 1.0

Iron binding site 10 out of 28 in 6rfs

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Iron binding site 10 out of 28 in the Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of A Respiratory Complex I Mutant Lacking NDUFS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:0.9
occ:1.00
 FE2 A:FES803 0.0 0.9 1.0
SG A:CYS83 2.2 0.0 1.0
S2 A:FES803 2.2 0.9 1.0
S1 A:FES803 2.2 0.9 1.0
SG A:CYS97 2.3 0.1 1.0
CB A:CYS97 2.7 0.1 1.0
FE1 A:FES803 3.0 0.9 1.0
CB A:CYS83 3.5 0.0 1.0
N A:CYS97 3.7 0.1 1.0
SG A:CYS80 3.7 0.4 1.0
CA A:CYS97 3.8 0.1 1.0
N A:CYS83 4.1 0.0 1.0
CB A:ALA95 4.1 0.2 1.0
CA A:CYS83 4.4 0.0 1.0
N A:SER96 4.7 0.6 1.0
CA A:GLY78 4.8 0.5 1.0
C A:CYS97 4.8 0.1 1.0
C A:SER96 4.9 0.6 1.0
CB A:TYR70 4.9 0.8 1.0
CA A:ALA95 4.9 0.2 1.0
SG A:CYS69 5.0 0.8 1.0

Reference:

K.Parey, O.Haapanen, V.Sharma, H.Kofeler, T.Zullig, S.Prinz, K.Siegmund, I.Wittig, D.J.Mills, J.Vonck, W.Kuhlbrandt, V.Zickermann. High-Resolution Cryo-Em Structures of Respiratory Complex I: Mechanism, Assembly, and Disease. Sci Adv V. 5 X9484 2019.
ISSN: ESSN 2375-2548
PubMed: 31844670
DOI: 10.1126/SCIADV.AAX9484
Page generated: Wed Aug 7 08:43:22 2024

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