Iron in PDB 8a6t: Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
Enzymatic activity of Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
All present enzymatic activity of Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State:
1.12.1.3;
Other elements in 8a6t:
The structure of Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State also contains other interesting chemical elements:
Iron Binding Sites:
Iron binding site 1 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 1 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:1.4
occ:1.00
|
FE1
|
A:SF4601
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS354
|
2.3
|
1.4
|
1.0
|
S3
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S2
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S4
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
FE4
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE2
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE3
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS354
|
3.1
|
1.4
|
1.0
|
S1
|
A:SF4601
|
3.9
|
1.4
|
1.0
|
CA
|
A:CYS354
|
4.2
|
1.4
|
1.0
|
SG
|
A:CYS496
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS299
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS500
|
4.8
|
1.4
|
1.0
|
O5
|
A:HC1602
|
4.9
|
39.2
|
1.0
|
N
|
A:ILE355
|
4.9
|
1.4
|
1.0
|
CD
|
A:PRO300
|
4.9
|
1.4
|
1.0
|
OG
|
A:SER301
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 2 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 2 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:1.4
occ:1.00
|
FE2
|
A:SF4601
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS299
|
2.3
|
1.4
|
1.0
|
S3
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S4
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S1
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
FE1
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE4
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE3
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS299
|
3.6
|
1.4
|
1.0
|
S2
|
A:SF4601
|
3.9
|
1.4
|
1.0
|
CA
|
A:CYS299
|
4.1
|
1.4
|
1.0
|
N
|
A:ALA495
|
4.3
|
1.4
|
1.0
|
CB
|
A:ALA495
|
4.4
|
1.4
|
1.0
|
CD
|
A:PRO300
|
4.6
|
1.4
|
1.0
|
OG
|
A:SER301
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS496
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS500
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS354
|
4.8
|
1.4
|
1.0
|
C
|
A:CYS299
|
4.8
|
1.4
|
1.0
|
N
|
A:CYS496
|
4.9
|
1.4
|
1.0
|
N
|
A:PRO300
|
4.9
|
1.4
|
1.0
|
CA
|
A:ALA495
|
4.9
|
1.4
|
1.0
|
CB
|
A:SER301
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 3 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 3 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:1.4
occ:1.00
|
FE3
|
A:SF4601
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS500
|
2.3
|
1.4
|
1.0
|
S1
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S4
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S2
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
FE2
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE4
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE1
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS500
|
3.4
|
1.4
|
1.0
|
CA
|
A:CYS500
|
3.7
|
1.4
|
1.0
|
S3
|
A:SF4601
|
3.9
|
1.4
|
1.0
|
N
|
A:CYS500
|
4.3
|
1.4
|
1.0
|
O5
|
A:HC1602
|
4.3
|
39.2
|
1.0
|
O3
|
A:HC1602
|
4.5
|
39.2
|
1.0
|
O6
|
A:HC1602
|
4.5
|
39.2
|
1.0
|
SG
|
A:CYS299
|
4.8
|
1.4
|
1.0
|
SG
|
A:CYS354
|
4.8
|
1.4
|
1.0
|
SG
|
A:CYS496
|
4.8
|
1.4
|
1.0
|
C
|
A:GLY499
|
4.9
|
1.4
|
1.0
|
C
|
A:CYS500
|
4.9
|
1.4
|
1.0
|
CB
|
A:CYS354
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 4 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 4 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:1.4
occ:1.00
|
FE4
|
A:SF4601
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS496
|
2.3
|
1.4
|
1.0
|
S2
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S3
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
S1
|
A:SF4601
|
2.3
|
1.4
|
1.0
|
FE1
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE2
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
FE3
|
A:SF4601
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS496
|
3.3
|
1.4
|
1.0
|
N
|
A:CYS496
|
3.8
|
1.4
|
1.0
|
S4
|
A:SF4601
|
3.9
|
1.4
|
1.0
|
CA
|
A:CYS496
|
4.2
|
1.4
|
1.0
|
SG
|
A:CYS354
|
4.7
|
1.4
|
1.0
|
C
|
A:ALA495
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS299
|
4.7
|
1.4
|
1.0
|
SG
|
A:CYS500
|
4.8
|
1.4
|
1.0
|
CA
|
A:CYS500
|
4.8
|
1.4
|
1.0
|
CB
|
A:ALA495
|
4.8
|
1.4
|
1.0
|
CA
|
A:GLY503
|
4.8
|
1.4
|
1.0
|
N
|
A:ALA495
|
4.9
|
1.4
|
1.0
|
O
|
A:GLY499
|
4.9
|
1.4
|
1.0
|
O
|
A:CYS192
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 5 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 5 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:39.2
occ:1.00
|
FE1
|
A:HC1602
|
0.0
|
39.2
|
1.0
|
C4
|
A:HC1602
|
1.8
|
39.2
|
1.0
|
C3
|
A:HC1602
|
1.8
|
39.2
|
1.0
|
C5
|
A:HC1602
|
2.1
|
39.2
|
1.0
|
S2
|
A:HC1602
|
2.3
|
39.2
|
1.0
|
S1
|
A:HC1602
|
2.3
|
39.2
|
1.0
|
FE2
|
A:HC1602
|
2.5
|
39.2
|
1.0
|
O4
|
A:HC1602
|
2.9
|
39.2
|
1.0
|
O3
|
A:HC1602
|
3.0
|
39.2
|
1.0
|
O5
|
A:HC1602
|
3.0
|
39.2
|
1.0
|
O1
|
A:HC1602
|
3.4
|
39.2
|
1.0
|
C7
|
A:HC1602
|
3.7
|
39.2
|
1.0
|
CD
|
A:PRO230
|
3.8
|
0.3
|
1.0
|
C6
|
A:HC1602
|
3.8
|
39.2
|
1.0
|
CB
|
A:ALA229
|
4.0
|
1.4
|
1.0
|
SD
|
A:MET352
|
4.1
|
1.4
|
1.0
|
O7
|
A:HC1602
|
4.6
|
39.2
|
1.0
|
CG
|
A:PRO230
|
4.7
|
0.3
|
1.0
|
CA
|
A:ALA229
|
4.7
|
1.4
|
1.0
|
O6
|
A:HC1602
|
4.7
|
39.2
|
1.0
|
CE
|
A:MET352
|
4.7
|
1.4
|
1.0
|
N
|
A:PRO230
|
4.8
|
0.3
|
1.0
|
|
Iron binding site 6 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 6 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:39.2
occ:1.00
|
FE2
|
A:HC1602
|
0.0
|
39.2
|
1.0
|
C7
|
A:HC1602
|
1.8
|
39.2
|
1.0
|
C6
|
A:HC1602
|
1.9
|
39.2
|
1.0
|
C5
|
A:HC1602
|
2.0
|
39.2
|
1.0
|
S1
|
A:HC1602
|
2.3
|
39.2
|
1.0
|
S2
|
A:HC1602
|
2.3
|
39.2
|
1.0
|
FE1
|
A:HC1602
|
2.5
|
39.2
|
1.0
|
O5
|
A:HC1602
|
2.9
|
39.2
|
1.0
|
O7
|
A:HC1602
|
3.0
|
39.2
|
1.0
|
O6
|
A:HC1602
|
3.0
|
39.2
|
1.0
|
C4
|
A:HC1602
|
3.6
|
39.2
|
1.0
|
C3
|
A:HC1602
|
3.7
|
39.2
|
1.0
|
O2
|
A:HC1602
|
4.3
|
39.2
|
1.0
|
CG
|
A:PRO323
|
4.3
|
12.9
|
1.0
|
CD
|
A:PRO323
|
4.4
|
12.9
|
1.0
|
O4
|
A:HC1602
|
4.5
|
39.2
|
1.0
|
O3
|
A:HC1602
|
4.6
|
39.2
|
1.0
|
NZ
|
A:LYS357
|
4.7
|
1.4
|
1.0
|
CB
|
A:PRO323
|
4.8
|
12.9
|
1.0
|
CE
|
A:LYS357
|
4.9
|
1.4
|
1.0
|
O
|
A:CYS298
|
4.9
|
1.4
|
1.0
|
|
Iron binding site 7 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 7 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe603
b:1.4
occ:1.00
|
FE1
|
A:FES603
|
0.0
|
1.4
|
1.0
|
S1
|
A:FES603
|
2.2
|
1.4
|
1.0
|
S2
|
A:FES603
|
2.2
|
1.4
|
1.0
|
SG
|
A:CYS50
|
2.3
|
1.4
|
1.0
|
SG
|
A:CYS63
|
2.3
|
1.4
|
1.0
|
FE2
|
A:FES603
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS63
|
3.1
|
1.4
|
1.0
|
CB
|
A:CYS50
|
3.7
|
1.4
|
1.0
|
N
|
A:CYS63
|
4.3
|
1.4
|
1.0
|
CA
|
A:CYS63
|
4.3
|
1.4
|
1.0
|
SG
|
A:CYS47
|
4.4
|
1.4
|
1.0
|
SG
|
A:CYS36
|
4.5
|
1.4
|
1.0
|
N
|
A:CYS50
|
4.6
|
1.4
|
1.0
|
CB
|
A:ALA61
|
4.7
|
1.4
|
1.0
|
CA
|
A:CYS50
|
4.8
|
1.4
|
1.0
|
|
Iron binding site 8 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 8 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe603
b:1.4
occ:1.00
|
FE2
|
A:FES603
|
0.0
|
1.4
|
1.0
|
S2
|
A:FES603
|
2.2
|
1.4
|
1.0
|
S1
|
A:FES603
|
2.2
|
1.4
|
1.0
|
SG
|
A:CYS47
|
2.3
|
1.4
|
1.0
|
SG
|
A:CYS36
|
2.3
|
1.4
|
1.0
|
FE1
|
A:FES603
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS36
|
3.7
|
1.4
|
1.0
|
CB
|
A:CYS47
|
3.7
|
1.4
|
1.0
|
N
|
A:CYS47
|
3.8
|
1.4
|
1.0
|
N
|
A:CYS36
|
4.0
|
1.4
|
1.0
|
N
|
A:ARG48
|
4.1
|
1.4
|
1.0
|
CA
|
A:CYS47
|
4.2
|
1.4
|
1.0
|
CA
|
A:CYS36
|
4.3
|
1.4
|
1.0
|
N
|
A:ALA46
|
4.4
|
1.4
|
1.0
|
SG
|
A:CYS63
|
4.4
|
1.4
|
1.0
|
SG
|
A:CYS50
|
4.5
|
1.4
|
1.0
|
C
|
A:CYS36
|
4.6
|
1.4
|
1.0
|
C
|
A:CYS47
|
4.6
|
1.4
|
1.0
|
N
|
A:LEU35
|
4.6
|
1.4
|
1.0
|
CA
|
A:GLY45
|
4.7
|
1.4
|
1.0
|
N
|
A:ASP37
|
4.7
|
1.4
|
1.0
|
N
|
A:GLY45
|
4.7
|
1.4
|
1.0
|
N
|
A:LEU49
|
4.8
|
1.4
|
1.0
|
C
|
A:ALA46
|
4.9
|
1.4
|
1.0
|
OD1
|
A:ASP37
|
4.9
|
1.4
|
1.0
|
C
|
A:GLY45
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 9 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 9 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe604
b:1.4
occ:1.00
|
FE1
|
A:SF4604
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS99
|
2.3
|
1.4
|
1.0
|
S2
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
S3
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
S4
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
FE4
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
FE3
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
FE2
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS99
|
3.8
|
1.4
|
1.0
|
CE1
|
D:PHE100
|
3.9
|
1.4
|
1.0
|
S1
|
A:SF4604
|
3.9
|
1.4
|
1.0
|
CA
|
A:CYS99
|
4.2
|
1.4
|
1.0
|
CZ
|
D:PHE100
|
4.3
|
1.4
|
1.0
|
NE2
|
A:HIS95
|
4.5
|
1.4
|
1.0
|
SG
|
A:CYS102
|
4.7
|
1.4
|
1.0
|
N
|
A:CYS99
|
4.7
|
1.4
|
1.0
|
CB
|
A:CYS102
|
4.8
|
1.4
|
1.0
|
SG
|
A:CYS108
|
4.9
|
1.4
|
1.0
|
CD2
|
A:HIS95
|
4.9
|
1.4
|
1.0
|
CB
|
A:GLN111
|
4.9
|
1.4
|
1.0
|
CD1
|
D:PHE100
|
5.0
|
1.4
|
1.0
|
|
Iron binding site 10 out
of 72 in 8a6t
Go back to
Iron Binding Sites List in 8a6t
Iron binding site 10 out
of 72 in the Cryo-Em Structure of the Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State
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 Electron Bifurcating Fe-Fe Hydrogenase Hydabc Complex From Thermoanaerobacter Kivui in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe604
b:1.4
occ:1.00
|
FE2
|
A:SF4604
|
0.0
|
1.4
|
1.0
|
SG
|
A:CYS108
|
2.3
|
1.4
|
1.0
|
S3
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
S1
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
S4
|
A:SF4604
|
2.3
|
1.4
|
1.0
|
FE4
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
FE3
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
FE1
|
A:SF4604
|
2.7
|
1.4
|
1.0
|
CB
|
A:CYS108
|
3.1
|
1.4
|
1.0
|
S2
|
A:SF4604
|
3.9
|
1.4
|
1.0
|
CB
|
A:GLN111
|
4.5
|
1.4
|
1.0
|
N
|
A:GLN111
|
4.6
|
1.4
|
1.0
|
CA
|
A:CYS108
|
4.6
|
1.4
|
1.0
|
NE2
|
A:HIS95
|
4.6
|
1.4
|
1.0
|
SG
|
A:CYS102
|
4.7
|
1.4
|
1.0
|
CB
|
A:LEU110
|
4.7
|
1.4
|
1.0
|
N
|
A:GLY202
|
4.8
|
1.4
|
1.0
|
SG
|
A:CYS99
|
4.9
|
1.4
|
1.0
|
|
Reference:
A.Katsyv,
A.Kumar,
P.Saura,
M.C.Poeverlein,
S.A.Freibert,
S.Stripp,
S.Jain,
A.P.Gamiz-Hernandez,
V.R.I.Kaila,
V.Mueller,
J.M.Schuller.
Molecular Basis of the Electron Bifurcation Mechanism in the [Fefe]-Hydrogenase Complex Hydabc J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.2C11683
Page generated: Fri Aug 9 16:11:29 2024
|