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Iron in PDB 8gs8: Cryo-Em Structure of the Human Respiratory Complex II

Enzymatic activity of Cryo-Em Structure of the Human Respiratory Complex II

All present enzymatic activity of Cryo-Em Structure of the Human Respiratory Complex II:
1.3.5.1;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Human Respiratory Complex II (pdb code 8gs8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cryo-Em Structure of the Human Respiratory Complex II, PDB code: 8gs8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8gs8

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Iron binding site 1 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.7
occ:1.00
 FE1 B:FES301 0.0 25.7 1.0
SG B:CYS93 2.2 41.5 1.0
S2 B:FES301 2.2 25.7 1.0
S1 B:FES301 2.2 25.7 1.0
SG B:CYS98 2.3 30.2 1.0
FE2 B:FES301 3.1 25.7 1.0
N B:CYS93 3.2 41.5 1.0
CB B:CYS93 3.2 41.5 1.0
CB B:CYS98 3.7 30.2 1.0
CA B:CYS93 3.7 41.5 1.0
N B:GLY99 3.9 30.0 1.0
N B:ARG94 3.9 50.7 1.0
N B:SER100 4.0 29.8 1.0
N B:CYS98 4.0 30.2 1.0
CA B:CYS98 4.2 30.2 1.0
N B:SER92 4.2 40.5 1.0
C B:CYS98 4.2 30.2 1.0
C B:SER92 4.3 40.5 1.0
C B:CYS93 4.3 41.5 1.0
OG B:SER100 4.4 29.8 1.0
CB B:SER100 4.5 29.8 1.0
CB B:SER92 4.5 40.5 1.0
CA B:SER92 4.5 40.5 1.0
CA B:GLY99 4.6 30.0 1.0
N B:ILE97 4.7 35.3 1.0
SG B:CYS113 4.7 41.2 1.0
N B:GLY96 4.8 36.7 1.0
CA B:SER100 4.8 29.8 1.0
C B:GLY99 4.8 30.0 1.0
N B:CYS101 4.9 33.5 1.0
SG B:CYS101 4.9 33.5 1.0
CA B:GLY96 5.0 36.7 1.0

Iron binding site 2 out of 10 in 8gs8

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Iron binding site 2 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.7
occ:1.00
 FE2 B:FES301 0.0 25.7 1.0
SG B:CYS101 2.1 33.5 1.0
SG B:CYS113 2.2 41.2 1.0
S2 B:FES301 2.2 25.7 1.0
S1 B:FES301 2.2 25.7 1.0
CB B:CYS113 3.0 41.2 1.0
FE1 B:FES301 3.1 25.7 1.0
CB B:CYS101 3.3 33.5 1.0
N B:CYS113 4.0 41.2 1.0
N B:CYS101 4.0 33.5 1.0
SG B:CYS93 4.0 41.5 1.0
CA B:CYS113 4.1 41.2 1.0
CA B:CYS101 4.3 33.5 1.0
N B:GLY96 4.3 36.7 1.0
CA B:GLY96 4.4 36.7 1.0
N B:ARG94 4.4 50.7 1.0
CB B:LEU111 4.6 32.8 1.0
CD2 B:LEU73 4.7 43.1 1.0
N B:SER100 4.7 29.8 1.0
CA B:ARG94 4.8 50.7 1.0
C B:CYS101 4.9 33.5 1.0
N B:GLU95 4.9 47.0 1.0
N B:ALA112 4.9 35.8 1.0
CD2 B:LEU111 5.0 32.8 1.0
N B:GLY99 5.0 30.0 1.0

Iron binding site 3 out of 10 in 8gs8

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Iron binding site 3 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:21.9
occ:1.00
 FE1 B:SF4302 0.0 21.9 1.0
SG B:CYS192 2.1 26.1 1.0
S2 B:SF4302 2.1 21.9 1.0
S4 B:SF4302 2.1 21.9 1.0
S3 B:SF4302 2.1 21.9 1.0
FE2 B:SF4302 2.7 21.9 1.0
CB B:CYS192 2.8 26.1 1.0
FE3 B:SF4302 2.9 21.9 1.0
FE4 B:SF4302 3.0 21.9 1.0
S1 B:SF4302 3.6 21.9 1.0
N B:CYS192 3.7 26.1 1.0
CA B:CYS192 3.9 26.1 1.0
CB B:ALA210 4.0 21.4 1.0
CG B:PRO259 4.4 23.4 1.0
CA B:ALA210 4.5 21.4 1.0
SG B:CYS253 4.7 30.4 1.0
SG B:CYS186 4.7 31.5 1.0
N B:SER193 4.8 26.0 1.0
C B:CYS192 4.8 26.1 1.0
SG B:CYS189 4.8 27.3 1.0
N B:CYS191 4.9 27.3 1.0
C B:CYS191 4.9 27.3 1.0
N B:ALA210 4.9 21.4 1.0

Iron binding site 4 out of 10 in 8gs8

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Iron binding site 4 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:21.9
occ:1.00
 FE2 B:SF4302 0.0 21.9 1.0
S1 B:SF4302 2.1 21.9 1.0
S4 B:SF4302 2.1 21.9 1.0
S3 B:SF4302 2.2 21.9 1.0
SG B:CYS253 2.2 30.4 1.0
FE1 B:SF4302 2.7 21.9 1.0
FE3 B:SF4302 3.0 21.9 1.0
FE4 B:SF4302 3.0 21.9 1.0
CB B:CYS253 3.3 30.4 1.0
S2 B:SF4302 3.7 21.9 1.0
CA B:CYS253 3.9 30.4 1.0
CD B:PRO254 4.5 29.8 1.0
CB B:LEU257 4.5 26.8 1.0
SG B:CYS192 4.6 26.1 1.0
CB B:CYS192 4.6 26.1 1.0
C B:CYS253 4.6 30.4 1.0
CG B:PRO259 4.6 23.4 1.0
CD1 B:LEU257 4.7 26.8 1.0
CG B:LEU257 4.7 26.8 1.0
N B:PRO254 4.8 29.8 1.0
SG B:CYS189 4.8 27.3 1.0
CB B:LYS255 4.9 31.8 1.0
SG B:CYS186 4.9 31.5 1.0

Iron binding site 5 out of 10 in 8gs8

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Iron binding site 5 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:21.9
occ:1.00
 FE3 B:SF4302 0.0 21.9 1.0
S1 B:SF4302 2.1 21.9 1.0
S2 B:SF4302 2.1 21.9 1.0
S4 B:SF4302 2.1 21.9 1.0
SG B:CYS186 2.2 31.5 1.0
FE4 B:SF4302 2.6 21.9 1.0
FE1 B:SF4302 2.9 21.9 1.0
FE2 B:SF4302 3.0 21.9 1.0
CB B:CYS186 3.5 31.5 1.0
S3 B:SF4302 3.6 21.9 1.0
CA B:CYS186 3.9 31.5 1.0
N B:LEU188 3.9 26.8 1.0
N B:ILE187 4.0 28.5 1.0
C B:CYS186 4.3 31.5 1.0
CA B:LEU188 4.3 26.8 1.0
N B:CYS189 4.5 27.3 1.0
CB B:ALA210 4.6 21.4 1.0
SG B:CYS189 4.7 27.3 1.0
SG B:CYS192 4.7 26.1 1.0
C B:ILE187 4.8 28.5 1.0
CA B:ILE187 4.9 28.5 1.0
CD1 B:LEU257 4.9 26.8 1.0

Iron binding site 6 out of 10 in 8gs8

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Iron binding site 6 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:21.9
occ:1.00
 FE4 B:SF4302 0.0 21.9 1.0
S3 B:SF4302 2.1 21.9 1.0
S1 B:SF4302 2.1 21.9 1.0
S2 B:SF4302 2.2 21.9 1.0
SG B:CYS189 2.2 27.3 1.0
FE3 B:SF4302 2.6 21.9 1.0
FE1 B:SF4302 3.0 21.9 1.0
FE2 B:SF4302 3.0 21.9 1.0
N B:CYS189 3.4 27.3 1.0
CB B:CYS189 3.6 27.3 1.0
S4 B:SF4302 3.7 21.9 1.0
CA B:CYS189 3.9 27.3 1.0
N B:ALA190 4.1 24.9 1.0
C B:CYS189 4.2 27.3 1.0
N B:CYS191 4.3 27.3 1.0
CG1 B:ILE187 4.4 28.5 1.0
N B:LEU188 4.4 26.8 1.0
CD B:PRO254 4.5 29.8 1.0
C B:LEU188 4.5 26.8 1.0
CB B:CYS191 4.6 27.3 1.0
SG B:CYS186 4.7 31.5 1.0
CA B:LEU188 4.7 26.8 1.0
CG B:PRO254 4.7 29.8 1.0
SG B:CYS192 4.8 26.1 1.0
N B:CYS192 4.8 26.1 1.0
SG B:CYS253 4.9 30.4 1.0
N B:ILE187 4.9 28.5 1.0
CA B:ALA190 5.0 24.9 1.0

Iron binding site 7 out of 10 in 8gs8

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Iron binding site 7 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:21.2
occ:1.00
 FE1 B:F3S303 0.0 21.2 1.0
SG B:CYS243 2.2 31.0 1.0
S3 B:F3S303 2.2 21.2 1.0
S1 B:F3S303 2.3 21.2 1.0
S2 B:F3S303 2.3 21.2 1.0
FE3 B:F3S303 2.6 21.2 1.0
FE4 B:F3S303 2.7 21.2 1.0
CB B:CYS243 3.5 31.0 1.0
CA B:CYS243 3.8 31.0 1.0
S4 B:F3S303 3.8 21.2 1.0
OH B:TYR206 3.8 21.9 1.0
N B:HIS244 4.0 36.7 1.0
N B:THR245 4.1 37.9 1.0
SG B:CYS196 4.3 31.6 1.0
N B:ILE246 4.3 38.1 1.0
C B:CYS243 4.4 31.0 1.0
CA B:THR245 4.4 37.9 1.0
CD1 B:ILE263 4.6 24.2 1.0
SG B:CYS249 4.8 32.6 1.0
N B:MET247 4.8 37.3 1.0
C B:THR245 4.8 37.9 1.0
CZ B:TYR206 4.9 21.9 1.0
C B:HIS244 4.9 36.7 1.0

Iron binding site 8 out of 10 in 8gs8

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Iron binding site 8 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:21.2
occ:1.00
 FE3 B:F3S303 0.0 21.2 1.0
SG B:CYS196 2.1 31.6 1.0
S1 B:F3S303 2.3 21.2 1.0
S4 B:F3S303 2.3 21.2 1.0
S3 B:F3S303 2.3 21.2 1.0
FE1 B:F3S303 2.6 21.2 1.0
FE4 B:F3S303 2.7 21.2 1.0
CB B:CYS196 3.0 31.6 1.0
CA B:CYS196 3.5 31.6 1.0
S2 B:F3S303 3.8 21.2 1.0
C B:CYS196 4.3 31.6 1.0
CD1 B:ILE246 4.4 38.1 1.0
OH B:TYR206 4.5 21.9 1.0
SG B:CYS249 4.6 32.6 1.0
CD B:PRO197 4.6 33.0 1.0
N B:PRO197 4.6 33.0 1.0
CB B:ILE246 4.7 38.1 1.0
CD B:PRO209 4.7 22.5 1.0
SG B:CYS243 4.7 31.0 1.0
N B:CYS196 4.8 31.6 1.0
CG1 B:ILE246 4.8 38.1 1.0
OG B:SER198 4.8 30.8 1.0
CG B:PRO209 4.8 22.5 1.0
N B:SER198 4.9 30.8 1.0
CB B:SER198 4.9 30.8 1.0
CE1 B:TYR206 4.9 21.9 1.0

Iron binding site 9 out of 10 in 8gs8

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Iron binding site 9 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:21.2
occ:1.00
 FE4 B:F3S303 0.0 21.2 1.0
SG B:CYS249 2.1 32.6 1.0
S2 B:F3S303 2.3 21.2 1.0
S4 B:F3S303 2.3 21.2 1.0
S3 B:F3S303 2.3 21.2 1.0
FE1 B:F3S303 2.7 21.2 1.0
FE3 B:F3S303 2.7 21.2 1.0
CB B:CYS249 3.3 32.6 1.0
N B:CYS249 4.0 32.6 1.0
S1 B:F3S303 4.0 21.2 1.0
N B:MET247 4.1 37.3 1.0
N B:ASN248 4.2 38.6 1.0
CB B:PRO209 4.3 22.5 1.0
CA B:MET247 4.3 37.3 1.0
CA B:CYS249 4.3 32.6 1.0
CG B:PRO209 4.4 22.5 1.0
SG B:CYS243 4.4 31.0 1.0
CD1 B:ILE263 4.5 24.2 1.0
SG B:CYS196 4.6 31.6 1.0
C B:MET247 4.6 37.3 1.0
CA B:GLY260 4.7 24.8 1.0
C B:ASN248 4.9 38.6 1.0
CB B:CYS196 4.9 31.6 1.0
CD B:PRO209 4.9 22.5 1.0

Iron binding site 10 out of 10 in 8gs8

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Iron binding site 10 out of 10 in the Cryo-Em Structure of the Human Respiratory Complex II


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 the Human Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:55.0
occ:1.00
 FE D:HEM201 0.0 55.0 1.0
NA D:HEM201 2.0 62.3 1.0
NC D:HEM201 2.0 58.6 1.0
ND D:HEM201 2.0 54.8 1.0
NB D:HEM201 2.0 59.7 1.0
NE2 D:HIS102 2.2 45.8 1.0
NE2 C:HIS127 2.2 51.9 1.0
C1D D:HEM201 3.0 59.5 1.0
CD2 C:HIS127 3.0 51.9 1.0
CD2 D:HIS102 3.0 45.8 1.0
C4C D:HEM201 3.0 58.9 1.0
C1A D:HEM201 3.0 60.1 1.0
C4D D:HEM201 3.1 60.4 1.0
C4A D:HEM201 3.1 63.3 1.0
C4B D:HEM201 3.1 61.3 1.0
C1C D:HEM201 3.1 59.2 1.0
C1B D:HEM201 3.1 65.3 1.0
CE1 D:HIS102 3.2 45.8 1.0
CE1 C:HIS127 3.3 51.9 1.0
CHD D:HEM201 3.3 57.5 1.0
CHC D:HEM201 3.4 58.0 1.0
CHA D:HEM201 3.4 57.1 1.0
CHB D:HEM201 3.4 65.8 1.0
CG D:HIS102 4.2 45.8 1.0
CG C:HIS127 4.2 51.9 1.0
C3C D:HEM201 4.2 64.5 1.0
C2D D:HEM201 4.2 58.1 1.0
C3D D:HEM201 4.2 62.4 1.0
C2A D:HEM201 4.2 64.4 1.0
C2C D:HEM201 4.2 65.1 1.0
ND1 D:HIS102 4.2 45.8 1.0
C2B D:HEM201 4.3 64.1 1.0
C3A D:HEM201 4.3 62.9 1.0
C3B D:HEM201 4.3 61.2 1.0
ND1 C:HIS127 4.3 51.9 1.0

Reference:

Z.Du, X.Zhou, Y.Lai, J.Xu, Y.Zhang, S.Zhou, Z.Feng, L.Yu, Y.Tang, W.Wang, L.Yu, C.Tian, T.Ran, H.Chen, L.W.Guddat, F.Liu, Y.Gao, Z.Rao, H.Gong. Structure of the Human Respiratory Complex II. Proc.Natl.Acad.Sci.Usa V. 120 13120 2023.
ISSN: ESSN 1091-6490
PubMed: 37098072
DOI: 10.1073/PNAS.2216713120
Page generated: Sat Aug 10 04:59:05 2024

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