Iron in PDB 7bok: Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
Enzymatic activity of Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
All present enzymatic activity of Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis:
1.11.1.7;
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
(pdb code 7bok). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis, PDB code: 7bok:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 7bok
Go back to
Iron Binding Sites List in 7bok
Iron binding site 1 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:79.3
occ:1.00
|
FE
|
A:HEM401
|
0.0
|
79.3
|
1.0
|
|
ND
|
A:HEM401
|
1.9
|
79.3
|
1.0
|
|
NA
|
A:HEM401
|
2.0
|
79.3
|
1.0
|
|
NC
|
A:HEM401
|
2.1
|
79.3
|
1.0
|
|
NB
|
A:HEM401
|
2.1
|
79.3
|
1.0
|
|
NE2
|
A:HIS220
|
2.8
|
86.6
|
1.0
|
|
C4D
|
A:HEM401
|
2.8
|
79.3
|
1.0
|
|
C1D
|
A:HEM401
|
2.9
|
79.3
|
1.0
|
|
C1A
|
A:HEM401
|
2.9
|
79.3
|
1.0
|
|
C4C
|
A:HEM401
|
3.0
|
79.3
|
1.0
|
|
C4A
|
A:HEM401
|
3.0
|
79.3
|
1.0
|
|
C1B
|
A:HEM401
|
3.1
|
79.3
|
1.0
|
|
C4B
|
A:HEM401
|
3.1
|
79.3
|
1.0
|
|
C1C
|
A:HEM401
|
3.1
|
79.3
|
1.0
|
|
CD2
|
A:HIS220
|
3.2
|
86.6
|
1.0
|
|
CHA
|
A:HEM401
|
3.3
|
79.3
|
1.0
|
|
CHD
|
A:HEM401
|
3.3
|
79.3
|
1.0
|
|
CHB
|
A:HEM401
|
3.4
|
79.3
|
1.0
|
|
CHC
|
A:HEM401
|
3.5
|
79.3
|
1.0
|
|
ND2
|
A:ASN224
|
3.9
|
85.9
|
1.0
|
|
NE
|
A:ARG238
|
4.0
|
73.4
|
1.0
|
|
CE1
|
A:HIS220
|
4.0
|
86.6
|
1.0
|
|
C2D
|
A:HEM401
|
4.1
|
79.3
|
1.0
|
|
C3D
|
A:HEM401
|
4.1
|
79.3
|
1.0
|
|
C2A
|
A:HEM401
|
4.1
|
79.3
|
1.0
|
|
C3A
|
A:HEM401
|
4.2
|
79.3
|
1.0
|
|
C3C
|
A:HEM401
|
4.2
|
79.3
|
1.0
|
|
C2C
|
A:HEM401
|
4.3
|
79.3
|
1.0
|
|
C2B
|
A:HEM401
|
4.3
|
79.3
|
1.0
|
|
C3B
|
A:HEM401
|
4.3
|
79.3
|
1.0
|
|
ND2
|
A:ASN240
|
4.4
|
71.4
|
1.0
|
|
CG
|
A:HIS220
|
4.5
|
86.6
|
1.0
|
|
CD
|
A:ARG238
|
4.5
|
73.4
|
1.0
|
|
CZ
|
A:ARG238
|
4.8
|
73.4
|
1.0
|
|
ND1
|
A:HIS220
|
4.9
|
86.6
|
1.0
|
|
NH2
|
A:ARG238
|
4.9
|
73.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 7bok
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Iron Binding Sites List in 7bok
Iron binding site 2 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:77.1
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
77.1
|
1.0
|
|
ND
|
B:HEM401
|
1.9
|
77.1
|
1.0
|
|
NA
|
B:HEM401
|
2.0
|
77.1
|
1.0
|
|
NC
|
B:HEM401
|
2.1
|
77.1
|
1.0
|
|
NB
|
B:HEM401
|
2.1
|
77.1
|
1.0
|
|
NE2
|
B:HIS220
|
2.8
|
80.3
|
1.0
|
|
C4D
|
B:HEM401
|
2.9
|
77.1
|
1.0
|
|
C1D
|
B:HEM401
|
2.9
|
77.1
|
1.0
|
|
C1A
|
B:HEM401
|
2.9
|
77.1
|
1.0
|
|
C4C
|
B:HEM401
|
3.0
|
77.1
|
1.0
|
|
C4A
|
B:HEM401
|
3.0
|
77.1
|
1.0
|
|
C1B
|
B:HEM401
|
3.1
|
77.1
|
1.0
|
|
C4B
|
B:HEM401
|
3.1
|
77.1
|
1.0
|
|
C1C
|
B:HEM401
|
3.1
|
77.1
|
1.0
|
|
CD2
|
B:HIS220
|
3.2
|
80.3
|
1.0
|
|
CHA
|
B:HEM401
|
3.3
|
77.1
|
1.0
|
|
CHD
|
B:HEM401
|
3.3
|
77.1
|
1.0
|
|
CHB
|
B:HEM401
|
3.4
|
77.1
|
1.0
|
|
CHC
|
B:HEM401
|
3.5
|
77.1
|
1.0
|
|
ND2
|
B:ASN224
|
3.9
|
80.4
|
1.0
|
|
NE
|
B:ARG238
|
4.0
|
72.5
|
1.0
|
|
CE1
|
B:HIS220
|
4.0
|
80.3
|
1.0
|
|
C2D
|
B:HEM401
|
4.1
|
77.1
|
1.0
|
|
C3D
|
B:HEM401
|
4.1
|
77.1
|
1.0
|
|
C2A
|
B:HEM401
|
4.1
|
77.1
|
1.0
|
|
C3A
|
B:HEM401
|
4.2
|
77.1
|
1.0
|
|
C3C
|
B:HEM401
|
4.2
|
77.1
|
1.0
|
|
C2C
|
B:HEM401
|
4.3
|
77.1
|
1.0
|
|
C2B
|
B:HEM401
|
4.3
|
77.1
|
1.0
|
|
C3B
|
B:HEM401
|
4.3
|
77.1
|
1.0
|
|
ND2
|
B:ASN240
|
4.4
|
73.1
|
1.0
|
|
CG
|
B:HIS220
|
4.5
|
80.3
|
1.0
|
|
CD
|
B:ARG238
|
4.5
|
72.5
|
1.0
|
|
CZ
|
B:ARG238
|
4.8
|
72.5
|
1.0
|
|
ND1
|
B:HIS220
|
4.9
|
80.3
|
1.0
|
|
NH2
|
B:ARG238
|
4.9
|
72.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 7bok
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Iron Binding Sites List in 7bok
Iron binding site 3 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:64.0
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
64.0
|
1.0
|
|
ND
|
C:HEM401
|
1.9
|
64.0
|
1.0
|
|
NA
|
C:HEM401
|
2.0
|
64.0
|
1.0
|
|
NC
|
C:HEM401
|
2.1
|
64.0
|
1.0
|
|
NB
|
C:HEM401
|
2.1
|
64.0
|
1.0
|
|
NE2
|
C:HIS220
|
2.8
|
67.9
|
1.0
|
|
C4D
|
C:HEM401
|
2.9
|
64.0
|
1.0
|
|
C1D
|
C:HEM401
|
2.9
|
64.0
|
1.0
|
|
C1A
|
C:HEM401
|
2.9
|
64.0
|
1.0
|
|
C4C
|
C:HEM401
|
3.0
|
64.0
|
1.0
|
|
C4A
|
C:HEM401
|
3.0
|
64.0
|
1.0
|
|
C1B
|
C:HEM401
|
3.1
|
64.0
|
1.0
|
|
C4B
|
C:HEM401
|
3.1
|
64.0
|
1.0
|
|
C1C
|
C:HEM401
|
3.1
|
64.0
|
1.0
|
|
CD2
|
C:HIS220
|
3.2
|
67.9
|
1.0
|
|
CHA
|
C:HEM401
|
3.3
|
64.0
|
1.0
|
|
CHD
|
C:HEM401
|
3.3
|
64.0
|
1.0
|
|
CHB
|
C:HEM401
|
3.4
|
64.0
|
1.0
|
|
CHC
|
C:HEM401
|
3.5
|
64.0
|
1.0
|
|
ND2
|
C:ASN224
|
3.9
|
68.6
|
1.0
|
|
NE
|
C:ARG238
|
4.0
|
59.5
|
1.0
|
|
CE1
|
C:HIS220
|
4.0
|
67.9
|
1.0
|
|
C2D
|
C:HEM401
|
4.1
|
64.0
|
1.0
|
|
C3D
|
C:HEM401
|
4.1
|
64.0
|
1.0
|
|
C2A
|
C:HEM401
|
4.1
|
64.0
|
1.0
|
|
C3A
|
C:HEM401
|
4.2
|
64.0
|
1.0
|
|
C3C
|
C:HEM401
|
4.2
|
64.0
|
1.0
|
|
C2C
|
C:HEM401
|
4.3
|
64.0
|
1.0
|
|
C2B
|
C:HEM401
|
4.3
|
64.0
|
1.0
|
|
C3B
|
C:HEM401
|
4.3
|
64.0
|
1.0
|
|
ND2
|
C:ASN240
|
4.4
|
61.9
|
1.0
|
|
CG
|
C:HIS220
|
4.5
|
67.9
|
1.0
|
|
CD
|
C:ARG238
|
4.5
|
59.5
|
1.0
|
|
CZ
|
C:ARG238
|
4.8
|
59.5
|
1.0
|
|
ND1
|
C:HIS220
|
4.9
|
67.9
|
1.0
|
|
NH2
|
C:ARG238
|
4.9
|
59.5
|
1.0
|
|
Iron binding site 4 out
of 6 in 7bok
Go back to
Iron Binding Sites List in 7bok
Iron binding site 4 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:78.5
occ:1.00
|
FE
|
D:HEM401
|
0.0
|
78.5
|
1.0
|
|
ND
|
D:HEM401
|
1.9
|
78.5
|
1.0
|
|
NA
|
D:HEM401
|
2.0
|
78.5
|
1.0
|
|
NC
|
D:HEM401
|
2.1
|
78.5
|
1.0
|
|
NB
|
D:HEM401
|
2.1
|
78.5
|
1.0
|
|
NE2
|
D:HIS220
|
2.8
|
81.5
|
1.0
|
|
C4D
|
D:HEM401
|
2.9
|
78.5
|
1.0
|
|
C1D
|
D:HEM401
|
2.9
|
78.5
|
1.0
|
|
C1A
|
D:HEM401
|
2.9
|
78.5
|
1.0
|
|
C4C
|
D:HEM401
|
3.0
|
78.5
|
1.0
|
|
C4A
|
D:HEM401
|
3.0
|
78.5
|
1.0
|
|
C1B
|
D:HEM401
|
3.1
|
78.5
|
1.0
|
|
C4B
|
D:HEM401
|
3.1
|
78.5
|
1.0
|
|
C1C
|
D:HEM401
|
3.1
|
78.5
|
1.0
|
|
CD2
|
D:HIS220
|
3.2
|
81.5
|
1.0
|
|
CHA
|
D:HEM401
|
3.3
|
78.5
|
1.0
|
|
CHD
|
D:HEM401
|
3.3
|
78.5
|
1.0
|
|
CHB
|
D:HEM401
|
3.4
|
78.5
|
1.0
|
|
CHC
|
D:HEM401
|
3.5
|
78.5
|
1.0
|
|
ND2
|
D:ASN224
|
3.9
|
83.5
|
1.0
|
|
NE
|
D:ARG238
|
4.0
|
70.2
|
1.0
|
|
CE1
|
D:HIS220
|
4.0
|
81.5
|
1.0
|
|
C2D
|
D:HEM401
|
4.1
|
78.5
|
1.0
|
|
C3D
|
D:HEM401
|
4.1
|
78.5
|
1.0
|
|
C2A
|
D:HEM401
|
4.1
|
78.5
|
1.0
|
|
C3A
|
D:HEM401
|
4.2
|
78.5
|
1.0
|
|
C3C
|
D:HEM401
|
4.2
|
78.5
|
1.0
|
|
C2C
|
D:HEM401
|
4.3
|
78.5
|
1.0
|
|
C2B
|
D:HEM401
|
4.3
|
78.5
|
1.0
|
|
C3B
|
D:HEM401
|
4.3
|
78.5
|
1.0
|
|
ND2
|
D:ASN240
|
4.4
|
69.1
|
1.0
|
|
CG
|
D:HIS220
|
4.5
|
81.5
|
1.0
|
|
CD
|
D:ARG238
|
4.5
|
70.2
|
1.0
|
|
CZ
|
D:ARG238
|
4.8
|
70.2
|
1.0
|
|
ND1
|
D:HIS220
|
4.9
|
81.5
|
1.0
|
|
NH2
|
D:ARG238
|
4.9
|
70.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 7bok
Go back to
Iron Binding Sites List in 7bok
Iron binding site 5 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:76.8
occ:1.00
|
FE
|
E:HEM401
|
0.0
|
76.8
|
1.0
|
|
ND
|
E:HEM401
|
1.9
|
76.8
|
1.0
|
|
NA
|
E:HEM401
|
2.0
|
76.8
|
1.0
|
|
NC
|
E:HEM401
|
2.1
|
76.8
|
1.0
|
|
NB
|
E:HEM401
|
2.1
|
76.8
|
1.0
|
|
NE2
|
E:HIS220
|
2.8
|
80.2
|
1.0
|
|
C4D
|
E:HEM401
|
2.8
|
76.8
|
1.0
|
|
C1D
|
E:HEM401
|
2.9
|
76.8
|
1.0
|
|
C1A
|
E:HEM401
|
2.9
|
76.8
|
1.0
|
|
C4C
|
E:HEM401
|
3.0
|
76.8
|
1.0
|
|
C4A
|
E:HEM401
|
3.0
|
76.8
|
1.0
|
|
C1B
|
E:HEM401
|
3.1
|
76.8
|
1.0
|
|
C4B
|
E:HEM401
|
3.1
|
76.8
|
1.0
|
|
C1C
|
E:HEM401
|
3.1
|
76.8
|
1.0
|
|
CD2
|
E:HIS220
|
3.2
|
80.2
|
1.0
|
|
CHA
|
E:HEM401
|
3.3
|
76.8
|
1.0
|
|
CHD
|
E:HEM401
|
3.3
|
76.8
|
1.0
|
|
CHB
|
E:HEM401
|
3.4
|
76.8
|
1.0
|
|
CHC
|
E:HEM401
|
3.5
|
76.8
|
1.0
|
|
ND2
|
E:ASN224
|
3.9
|
78.0
|
1.0
|
|
NE
|
E:ARG238
|
4.0
|
71.6
|
1.0
|
|
CE1
|
E:HIS220
|
4.0
|
80.2
|
1.0
|
|
C2D
|
E:HEM401
|
4.1
|
76.8
|
1.0
|
|
C3D
|
E:HEM401
|
4.1
|
76.8
|
1.0
|
|
C2A
|
E:HEM401
|
4.1
|
76.8
|
1.0
|
|
C3A
|
E:HEM401
|
4.2
|
76.8
|
1.0
|
|
C3C
|
E:HEM401
|
4.2
|
76.8
|
1.0
|
|
C2C
|
E:HEM401
|
4.3
|
76.8
|
1.0
|
|
C2B
|
E:HEM401
|
4.3
|
76.8
|
1.0
|
|
C3B
|
E:HEM401
|
4.3
|
76.8
|
1.0
|
|
ND2
|
E:ASN240
|
4.4
|
67.8
|
1.0
|
|
CG
|
E:HIS220
|
4.5
|
80.2
|
1.0
|
|
CD
|
E:ARG238
|
4.5
|
71.6
|
1.0
|
|
CZ
|
E:ARG238
|
4.8
|
71.6
|
1.0
|
|
ND1
|
E:HIS220
|
4.9
|
80.2
|
1.0
|
|
NH2
|
E:ARG238
|
4.9
|
71.6
|
1.0
|
|
Iron binding site 6 out
of 6 in 7bok
Go back to
Iron Binding Sites List in 7bok
Iron binding site 6 out
of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis
 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 Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:68.8
occ:1.00
|
FE
|
F:HEM401
|
0.0
|
68.8
|
1.0
|
|
ND
|
F:HEM401
|
1.9
|
68.8
|
1.0
|
|
NA
|
F:HEM401
|
2.0
|
68.8
|
1.0
|
|
NC
|
F:HEM401
|
2.1
|
68.8
|
1.0
|
|
NB
|
F:HEM401
|
2.1
|
68.8
|
1.0
|
|
NE2
|
F:HIS220
|
2.8
|
77.6
|
1.0
|
|
C4D
|
F:HEM401
|
2.9
|
68.8
|
1.0
|
|
C1D
|
F:HEM401
|
2.9
|
68.8
|
1.0
|
|
C1A
|
F:HEM401
|
2.9
|
68.8
|
1.0
|
|
C4C
|
F:HEM401
|
3.0
|
68.8
|
1.0
|
|
C4A
|
F:HEM401
|
3.0
|
68.8
|
1.0
|
|
C1B
|
F:HEM401
|
3.1
|
68.8
|
1.0
|
|
C4B
|
F:HEM401
|
3.1
|
68.8
|
1.0
|
|
C1C
|
F:HEM401
|
3.1
|
68.8
|
1.0
|
|
CD2
|
F:HIS220
|
3.2
|
77.6
|
1.0
|
|
CHA
|
F:HEM401
|
3.3
|
68.8
|
1.0
|
|
CHD
|
F:HEM401
|
3.3
|
68.8
|
1.0
|
|
CHB
|
F:HEM401
|
3.4
|
68.8
|
1.0
|
|
CHC
|
F:HEM401
|
3.5
|
68.8
|
1.0
|
|
ND2
|
F:ASN224
|
3.9
|
79.8
|
1.0
|
|
NE
|
F:ARG238
|
4.0
|
65.6
|
1.0
|
|
CE1
|
F:HIS220
|
4.0
|
77.6
|
1.0
|
|
C2D
|
F:HEM401
|
4.1
|
68.8
|
1.0
|
|
C3D
|
F:HEM401
|
4.1
|
68.8
|
1.0
|
|
C2A
|
F:HEM401
|
4.1
|
68.8
|
1.0
|
|
C3A
|
F:HEM401
|
4.2
|
68.8
|
1.0
|
|
C3C
|
F:HEM401
|
4.2
|
68.8
|
1.0
|
|
C2C
|
F:HEM401
|
4.3
|
68.8
|
1.0
|
|
C2B
|
F:HEM401
|
4.3
|
68.8
|
1.0
|
|
C3B
|
F:HEM401
|
4.3
|
68.8
|
1.0
|
|
ND2
|
F:ASN240
|
4.4
|
62.3
|
1.0
|
|
CG
|
F:HIS220
|
4.5
|
77.6
|
1.0
|
|
CD
|
F:ARG238
|
4.5
|
65.6
|
1.0
|
|
CZ
|
F:ARG238
|
4.8
|
65.6
|
1.0
|
|
ND1
|
F:HIS220
|
4.9
|
77.6
|
1.0
|
|
NH2
|
F:ARG238
|
4.9
|
65.6
|
1.0
|
|
Reference:
Y.T.Tang,
A.Mu,
W.W.Wang,
S.Zhou,
Y.Y.Zhang,
X.T.Zhou,
F.J.Liu,
X.N.Yang,
H.R.Gong,
Q.Wang,
Z.H.Rao.
Cryo-Em Structure of A Native Cargo-Loaded Encapsulin From Mycobacterium Smegmatis To Be Published.
Page generated: Thu Aug 8 00:04:13 2024
|
