Iron in PDB 7deg: Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
Other elements in 7deg:
The structure of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
(pdb code 7deg). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism, PDB code: 7deg:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7deg
Go back to
Iron Binding Sites List in 7deg
Iron binding site 1 out
of 4 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
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 Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:24.4
occ:1.00
|
FE
|
A:HAS601
|
0.0
|
24.4
|
1.0
|
NE2
|
A:HIS383
|
1.9
|
19.1
|
1.0
|
ND
|
A:HAS601
|
2.1
|
24.4
|
1.0
|
NC
|
A:HAS601
|
2.1
|
24.4
|
1.0
|
NA
|
A:HAS601
|
2.1
|
24.4
|
1.0
|
NB
|
A:HAS601
|
2.1
|
24.4
|
1.0
|
CD2
|
A:HIS383
|
2.8
|
19.1
|
1.0
|
CE1
|
A:HIS383
|
2.9
|
19.1
|
1.0
|
C1A
|
A:HAS601
|
3.0
|
24.4
|
1.0
|
C1C
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C4D
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C1D
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C4C
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C1B
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C4A
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
C4B
|
A:HAS601
|
3.1
|
24.4
|
1.0
|
CHC
|
A:HAS601
|
3.6
|
24.4
|
1.0
|
CHA
|
A:HAS601
|
3.6
|
24.4
|
1.0
|
CHB
|
A:HAS601
|
3.6
|
24.4
|
1.0
|
CHD
|
A:HAS601
|
3.6
|
24.4
|
1.0
|
CE1
|
A:HIS222
|
3.9
|
30.1
|
1.0
|
CG
|
A:HIS383
|
4.0
|
19.1
|
1.0
|
ND1
|
A:HIS383
|
4.0
|
19.1
|
1.0
|
C3C
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C2D
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C2C
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C2A
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C2B
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C3D
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C3A
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
C3B
|
A:HAS601
|
4.3
|
24.4
|
1.0
|
CG1
|
A:VAL225
|
4.5
|
23.9
|
1.0
|
NE2
|
A:HIS222
|
4.6
|
30.1
|
1.0
|
ND1
|
A:HIS222
|
4.8
|
30.1
|
1.0
|
CG2
|
A:VAL225
|
4.9
|
23.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 7deg
Go back to
Iron Binding Sites List in 7deg
Iron binding site 2 out
of 4 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
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 Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:17.6
occ:1.00
|
FE
|
A:HEM602
|
0.0
|
17.6
|
1.0
|
NE2
|
A:HIS60
|
1.7
|
16.8
|
1.0
|
NC
|
A:HEM602
|
1.9
|
17.6
|
1.0
|
NA
|
A:HEM602
|
2.0
|
17.6
|
1.0
|
CE1
|
A:HIS60
|
2.0
|
16.8
|
1.0
|
NB
|
A:HEM602
|
2.0
|
17.6
|
1.0
|
ND
|
A:HEM602
|
2.0
|
17.6
|
1.0
|
NE2
|
A:HIS385
|
2.5
|
17.2
|
1.0
|
C1C
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C4C
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C4A
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C1A
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C1B
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
CD2
|
A:HIS60
|
3.0
|
16.8
|
1.0
|
C4D
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C1D
|
A:HEM602
|
3.0
|
17.6
|
1.0
|
C4B
|
A:HEM602
|
3.1
|
17.6
|
1.0
|
CE1
|
A:HIS385
|
3.2
|
17.2
|
1.0
|
ND1
|
A:HIS60
|
3.3
|
16.8
|
1.0
|
CHB
|
A:HEM602
|
3.4
|
17.6
|
1.0
|
CHA
|
A:HEM602
|
3.4
|
17.6
|
1.0
|
CHC
|
A:HEM602
|
3.4
|
17.6
|
1.0
|
CHD
|
A:HEM602
|
3.4
|
17.6
|
1.0
|
CD2
|
A:HIS385
|
3.5
|
17.2
|
1.0
|
CG
|
A:HIS60
|
3.8
|
16.8
|
1.0
|
C2C
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C3C
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C2A
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C3A
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C3D
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C2B
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C2D
|
A:HEM602
|
4.2
|
17.6
|
1.0
|
C3B
|
A:HEM602
|
4.3
|
17.6
|
1.0
|
ND1
|
A:HIS385
|
4.4
|
17.2
|
1.0
|
CG
|
A:HIS385
|
4.5
|
17.2
|
1.0
|
CA
|
A:GLY32
|
4.8
|
17.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 7deg
Go back to
Iron Binding Sites List in 7deg
Iron binding site 3 out
of 4 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
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 Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe602
b:24.4
occ:1.00
|
FE
|
D:HAS602
|
0.0
|
24.4
|
1.0
|
NE2
|
D:HIS383
|
1.9
|
19.1
|
1.0
|
ND
|
D:HAS602
|
2.1
|
24.4
|
1.0
|
NC
|
D:HAS602
|
2.1
|
24.4
|
1.0
|
NA
|
D:HAS602
|
2.1
|
24.4
|
1.0
|
NB
|
D:HAS602
|
2.1
|
24.4
|
1.0
|
CD2
|
D:HIS383
|
2.8
|
19.1
|
1.0
|
CE1
|
D:HIS383
|
2.9
|
19.1
|
1.0
|
C1A
|
D:HAS602
|
3.0
|
24.4
|
1.0
|
C1C
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C4D
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C1D
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C4C
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C1B
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C4A
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
C4B
|
D:HAS602
|
3.1
|
24.4
|
1.0
|
CHC
|
D:HAS602
|
3.6
|
24.4
|
1.0
|
CHA
|
D:HAS602
|
3.6
|
24.4
|
1.0
|
CHB
|
D:HAS602
|
3.6
|
24.4
|
1.0
|
CHD
|
D:HAS602
|
3.6
|
24.4
|
1.0
|
CE1
|
D:HIS222
|
3.9
|
30.1
|
1.0
|
CG
|
D:HIS383
|
4.0
|
19.1
|
1.0
|
ND1
|
D:HIS383
|
4.0
|
19.1
|
1.0
|
C3C
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C2D
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C2C
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C2A
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C2B
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C3D
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C3A
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
C3B
|
D:HAS602
|
4.3
|
24.4
|
1.0
|
CG1
|
D:VAL225
|
4.5
|
23.9
|
1.0
|
NE2
|
D:HIS222
|
4.6
|
30.1
|
1.0
|
ND1
|
D:HIS222
|
4.8
|
30.1
|
1.0
|
CG2
|
D:VAL225
|
4.9
|
23.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 7deg
Go back to
Iron Binding Sites List in 7deg
Iron binding site 4 out
of 4 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism
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 Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe603
b:17.6
occ:1.00
|
FE
|
D:HEM603
|
0.0
|
17.6
|
1.0
|
NE2
|
D:HIS60
|
1.7
|
16.8
|
1.0
|
NC
|
D:HEM603
|
1.9
|
17.6
|
1.0
|
NA
|
D:HEM603
|
2.0
|
17.6
|
1.0
|
CE1
|
D:HIS60
|
2.0
|
16.8
|
1.0
|
NB
|
D:HEM603
|
2.0
|
17.6
|
1.0
|
ND
|
D:HEM603
|
2.0
|
17.6
|
1.0
|
NE2
|
D:HIS385
|
2.4
|
17.2
|
1.0
|
C1C
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C4C
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C4A
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C1A
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C1B
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
CD2
|
D:HIS60
|
3.0
|
16.8
|
1.0
|
C4D
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C1D
|
D:HEM603
|
3.0
|
17.6
|
1.0
|
C4B
|
D:HEM603
|
3.1
|
17.6
|
1.0
|
CE1
|
D:HIS385
|
3.2
|
17.2
|
1.0
|
ND1
|
D:HIS60
|
3.3
|
16.8
|
1.0
|
CHB
|
D:HEM603
|
3.4
|
17.6
|
1.0
|
CHA
|
D:HEM603
|
3.4
|
17.6
|
1.0
|
CHC
|
D:HEM603
|
3.4
|
17.6
|
1.0
|
CHD
|
D:HEM603
|
3.4
|
17.6
|
1.0
|
CD2
|
D:HIS385
|
3.5
|
17.2
|
1.0
|
CG
|
D:HIS60
|
3.8
|
16.8
|
1.0
|
C2C
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C3C
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C2A
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C3A
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C3D
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C2B
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C2D
|
D:HEM603
|
4.2
|
17.6
|
1.0
|
C3B
|
D:HEM603
|
4.3
|
17.6
|
1.0
|
ND1
|
D:HIS385
|
4.4
|
17.2
|
1.0
|
CG
|
D:HIS385
|
4.5
|
17.2
|
1.0
|
CA
|
D:GLY32
|
4.8
|
17.9
|
1.0
|
|
Reference:
G.Zhu,
H.Zeng,
S.Zhang,
J.Juli,
L.Tai,
D.Zhang,
X.Pang,
Y.Zhang,
S.M.Lam,
Y.Zhu,
G.Peng,
H.Michel,
F.Sun.
The Unusual Homodimer of A Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew.Chem.Int.Ed.Engl. V. 60 13323 2021.
ISSN: ESSN 1521-3773
PubMed: 33665933
DOI: 10.1002/ANIE.202016785
Page generated: Thu Aug 8 03:49:24 2024
|