Iron in PDB 8rwy: Dtpb Hexamer From Streptomyces Lividans
Iron Binding Sites:
The binding sites of Iron atom in the Dtpb Hexamer From Streptomyces Lividans
(pdb code 8rwy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Dtpb Hexamer From Streptomyces Lividans, PDB code: 8rwy:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 1 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:98.7
occ:1.00
|
FE
|
A:HEM401
|
0.0
|
98.7
|
1.0
|
|
NC
|
A:HEM401
|
2.0
|
98.7
|
1.0
|
|
ND
|
A:HEM401
|
2.0
|
98.7
|
1.0
|
|
NB
|
A:HEM401
|
2.0
|
98.7
|
1.0
|
|
NA
|
A:HEM401
|
2.0
|
98.7
|
1.0
|
|
NE2
|
A:HIS225
|
2.1
|
91.9
|
1.0
|
|
CE1
|
A:HIS225
|
2.7
|
91.9
|
1.0
|
|
C1B
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C1D
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C4D
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C4C
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C4A
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C1C
|
A:HEM401
|
3.0
|
98.7
|
1.0
|
|
C4B
|
A:HEM401
|
3.1
|
98.7
|
1.0
|
|
C1A
|
A:HEM401
|
3.1
|
98.7
|
1.0
|
|
CD2
|
A:HIS225
|
3.3
|
91.9
|
1.0
|
|
CHB
|
A:HEM401
|
3.4
|
98.7
|
1.0
|
|
CHD
|
A:HEM401
|
3.4
|
98.7
|
1.0
|
|
CHA
|
A:HEM401
|
3.4
|
98.7
|
1.0
|
|
CHC
|
A:HEM401
|
3.4
|
98.7
|
1.0
|
|
ND1
|
A:HIS225
|
4.0
|
91.9
|
1.0
|
|
C3D
|
A:HEM401
|
4.2
|
98.7
|
1.0
|
|
C2D
|
A:HEM401
|
4.2
|
98.7
|
1.0
|
|
CG
|
A:HIS225
|
4.3
|
91.9
|
1.0
|
|
C2B
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
C3A
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
C2C
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
C3C
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
C3B
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
C2A
|
A:HEM401
|
4.3
|
98.7
|
1.0
|
|
NH1
|
A:ARG243
|
4.4
|
94.1
|
1.0
|
|
CD
|
A:ARG243
|
4.6
|
94.1
|
1.0
|
|
ND2
|
A:ASN245
|
4.7
|
99.0
|
1.0
|
|
CZ
|
A:ARG243
|
4.9
|
94.1
|
1.0
|
|
NE
|
A:ARG243
|
4.9
|
94.1
|
1.0
|
|
CG2
|
A:THR229
|
5.0
|
96.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 2 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:97.2
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
97.2
|
1.0
|
|
NC
|
B:HEM401
|
2.0
|
97.2
|
1.0
|
|
NA
|
B:HEM401
|
2.0
|
97.2
|
1.0
|
|
ND
|
B:HEM401
|
2.0
|
97.2
|
1.0
|
|
NB
|
B:HEM401
|
2.0
|
97.2
|
1.0
|
|
NE2
|
B:HIS225
|
2.1
|
91.9
|
1.0
|
|
CE1
|
B:HIS225
|
2.9
|
91.9
|
1.0
|
|
C1D
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C1B
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C4D
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C4C
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C4A
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C1C
|
B:HEM401
|
3.0
|
97.2
|
1.0
|
|
C1A
|
B:HEM401
|
3.1
|
97.2
|
1.0
|
|
C4B
|
B:HEM401
|
3.1
|
97.2
|
1.0
|
|
CD2
|
B:HIS225
|
3.2
|
91.9
|
1.0
|
|
CHB
|
B:HEM401
|
3.4
|
97.2
|
1.0
|
|
CHD
|
B:HEM401
|
3.4
|
97.2
|
1.0
|
|
CHA
|
B:HEM401
|
3.4
|
97.2
|
1.0
|
|
CHC
|
B:HEM401
|
3.4
|
97.2
|
1.0
|
|
ND1
|
B:HIS225
|
4.1
|
91.9
|
1.0
|
|
C2D
|
B:HEM401
|
4.2
|
97.2
|
1.0
|
|
NE
|
B:ARG243
|
4.2
|
95.0
|
1.0
|
|
C3D
|
B:HEM401
|
4.2
|
97.2
|
1.0
|
|
CG
|
B:HIS225
|
4.2
|
91.9
|
1.0
|
|
C2B
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
C3A
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
C2C
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
C3C
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
C3B
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
C2A
|
B:HEM401
|
4.3
|
97.2
|
1.0
|
|
ND2
|
B:ASN245
|
4.7
|
98.8
|
1.0
|
|
CD
|
B:ARG243
|
4.7
|
95.0
|
1.0
|
|
CZ
|
B:ARG243
|
4.8
|
95.0
|
1.0
|
|
NH2
|
B:ARG243
|
4.9
|
95.0
|
1.0
|
|
CG2
|
B:THR229
|
5.0
|
97.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 3 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:96.2
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
96.2
|
1.0
|
|
NC
|
C:HEM401
|
2.0
|
96.2
|
1.0
|
|
NB
|
C:HEM401
|
2.0
|
96.2
|
1.0
|
|
ND
|
C:HEM401
|
2.0
|
96.2
|
1.0
|
|
NA
|
C:HEM401
|
2.0
|
96.2
|
1.0
|
|
NE2
|
C:HIS225
|
2.1
|
89.3
|
1.0
|
|
CE1
|
C:HIS225
|
2.7
|
89.3
|
1.0
|
|
C4D
|
C:HEM401
|
3.0
|
96.2
|
1.0
|
|
C1D
|
C:HEM401
|
3.0
|
96.2
|
1.0
|
|
C4B
|
C:HEM401
|
3.0
|
96.2
|
1.0
|
|
C1C
|
C:HEM401
|
3.0
|
96.2
|
1.0
|
|
C1A
|
C:HEM401
|
3.1
|
96.2
|
1.0
|
|
C4C
|
C:HEM401
|
3.1
|
96.2
|
1.0
|
|
C1B
|
C:HEM401
|
3.1
|
96.2
|
1.0
|
|
C4A
|
C:HEM401
|
3.1
|
96.2
|
1.0
|
|
CD2
|
C:HIS225
|
3.3
|
89.3
|
1.0
|
|
CHC
|
C:HEM401
|
3.4
|
96.2
|
1.0
|
|
CHA
|
C:HEM401
|
3.4
|
96.2
|
1.0
|
|
CHD
|
C:HEM401
|
3.4
|
96.2
|
1.0
|
|
CHB
|
C:HEM401
|
3.4
|
96.2
|
1.0
|
|
ND1
|
C:HIS225
|
3.9
|
89.3
|
1.0
|
|
NE
|
C:ARG243
|
4.1
|
95.7
|
1.0
|
|
C2D
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C3D
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
CG
|
C:HIS225
|
4.3
|
89.3
|
1.0
|
|
C2C
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C2A
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C3A
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C3B
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C2B
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
C3C
|
C:HEM401
|
4.3
|
96.2
|
1.0
|
|
CD
|
C:ARG243
|
4.3
|
95.7
|
1.0
|
|
ND2
|
C:ASN245
|
4.5
|
99.5
|
1.0
|
|
Iron binding site 4 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 4 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:97.4
occ:1.00
|
FE
|
D:HEM401
|
0.0
|
97.4
|
1.0
|
|
NC
|
D:HEM401
|
2.0
|
97.4
|
1.0
|
|
NA
|
D:HEM401
|
2.0
|
97.4
|
1.0
|
|
ND
|
D:HEM401
|
2.0
|
97.4
|
1.0
|
|
NB
|
D:HEM401
|
2.0
|
97.4
|
1.0
|
|
NE2
|
D:HIS225
|
2.1
|
90.9
|
1.0
|
|
CE1
|
D:HIS225
|
2.7
|
90.9
|
1.0
|
|
C1D
|
D:HEM401
|
3.0
|
97.4
|
1.0
|
|
C1B
|
D:HEM401
|
3.0
|
97.4
|
1.0
|
|
C4A
|
D:HEM401
|
3.0
|
97.4
|
1.0
|
|
C4C
|
D:HEM401
|
3.0
|
97.4
|
1.0
|
|
C1C
|
D:HEM401
|
3.0
|
97.4
|
1.0
|
|
C4D
|
D:HEM401
|
3.1
|
97.4
|
1.0
|
|
C1A
|
D:HEM401
|
3.1
|
97.4
|
1.0
|
|
C4B
|
D:HEM401
|
3.1
|
97.4
|
1.0
|
|
CD2
|
D:HIS225
|
3.3
|
90.9
|
1.0
|
|
CHB
|
D:HEM401
|
3.4
|
97.4
|
1.0
|
|
CHD
|
D:HEM401
|
3.4
|
97.4
|
1.0
|
|
CHC
|
D:HEM401
|
3.4
|
97.4
|
1.0
|
|
CHA
|
D:HEM401
|
3.4
|
97.4
|
1.0
|
|
ND1
|
D:HIS225
|
3.9
|
90.9
|
1.0
|
|
NE
|
D:ARG243
|
4.1
|
96.5
|
1.0
|
|
C2D
|
D:HEM401
|
4.2
|
97.4
|
1.0
|
|
C3D
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
CG
|
D:HIS225
|
4.3
|
90.9
|
1.0
|
|
C2B
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
C3A
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
C2A
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
C2C
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
C3C
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
C3B
|
D:HEM401
|
4.3
|
97.4
|
1.0
|
|
ND2
|
D:ASN245
|
4.4
|
97.5
|
1.0
|
|
CD
|
D:ARG243
|
4.5
|
96.5
|
1.0
|
|
CZ
|
D:ARG243
|
4.9
|
96.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 5 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:95.2
occ:1.00
|
FE
|
E:HEM401
|
0.0
|
95.2
|
1.0
|
|
NC
|
E:HEM401
|
2.0
|
95.2
|
1.0
|
|
NA
|
E:HEM401
|
2.0
|
95.2
|
1.0
|
|
NB
|
E:HEM401
|
2.0
|
95.2
|
1.0
|
|
ND
|
E:HEM401
|
2.0
|
95.2
|
1.0
|
|
NE2
|
E:HIS225
|
2.1
|
89.5
|
1.0
|
|
CE1
|
E:HIS225
|
2.8
|
89.5
|
1.0
|
|
C1D
|
E:HEM401
|
3.0
|
95.2
|
1.0
|
|
C4A
|
E:HEM401
|
3.0
|
95.2
|
1.0
|
|
C4C
|
E:HEM401
|
3.0
|
95.2
|
1.0
|
|
C1B
|
E:HEM401
|
3.0
|
95.2
|
1.0
|
|
C1C
|
E:HEM401
|
3.1
|
95.2
|
1.0
|
|
C1A
|
E:HEM401
|
3.1
|
95.2
|
1.0
|
|
C4D
|
E:HEM401
|
3.1
|
95.2
|
1.0
|
|
C4B
|
E:HEM401
|
3.1
|
95.2
|
1.0
|
|
CD2
|
E:HIS225
|
3.2
|
89.5
|
1.0
|
|
CHB
|
E:HEM401
|
3.4
|
95.2
|
1.0
|
|
CHD
|
E:HEM401
|
3.4
|
95.2
|
1.0
|
|
CHC
|
E:HEM401
|
3.4
|
95.2
|
1.0
|
|
CHA
|
E:HEM401
|
3.4
|
95.2
|
1.0
|
|
ND1
|
E:HIS225
|
4.0
|
89.5
|
1.0
|
|
NE
|
E:ARG243
|
4.1
|
95.8
|
1.0
|
|
CG
|
E:HIS225
|
4.2
|
89.5
|
1.0
|
|
C2D
|
E:HEM401
|
4.2
|
95.2
|
1.0
|
|
C3D
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C3A
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C2B
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C2A
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C3C
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C2C
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
C3B
|
E:HEM401
|
4.3
|
95.2
|
1.0
|
|
CD
|
E:ARG243
|
4.5
|
95.8
|
1.0
|
|
ND2
|
E:ASN245
|
4.5
|
98.4
|
1.0
|
|
Iron binding site 6 out
of 6 in 8rwy
Go back to
Iron Binding Sites List in 8rwy
Iron binding site 6 out
of 6 in the Dtpb Hexamer From Streptomyces Lividans
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Dtpb Hexamer From Streptomyces Lividans within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:94.8
occ:1.00
|
FE
|
F:HEM401
|
0.0
|
94.8
|
1.0
|
|
NC
|
F:HEM401
|
2.0
|
94.8
|
1.0
|
|
NA
|
F:HEM401
|
2.0
|
94.8
|
1.0
|
|
ND
|
F:HEM401
|
2.0
|
94.8
|
1.0
|
|
NB
|
F:HEM401
|
2.0
|
94.8
|
1.0
|
|
NE2
|
F:HIS225
|
2.1
|
88.0
|
1.0
|
|
CE1
|
F:HIS225
|
2.7
|
88.0
|
1.0
|
|
C1B
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C1D
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C4C
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C4A
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C1C
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C4D
|
F:HEM401
|
3.0
|
94.8
|
1.0
|
|
C1A
|
F:HEM401
|
3.1
|
94.8
|
1.0
|
|
C4B
|
F:HEM401
|
3.1
|
94.8
|
1.0
|
|
CD2
|
F:HIS225
|
3.3
|
88.0
|
1.0
|
|
CHB
|
F:HEM401
|
3.4
|
94.8
|
1.0
|
|
CHD
|
F:HEM401
|
3.4
|
94.8
|
1.0
|
|
CHC
|
F:HEM401
|
3.4
|
94.8
|
1.0
|
|
CHA
|
F:HEM401
|
3.4
|
94.8
|
1.0
|
|
NH1
|
F:ARG243
|
3.7
|
91.7
|
1.0
|
|
ND1
|
F:HIS225
|
4.0
|
88.0
|
1.0
|
|
C2D
|
F:HEM401
|
4.2
|
94.8
|
1.0
|
|
C2B
|
F:HEM401
|
4.2
|
94.8
|
1.0
|
|
C3D
|
F:HEM401
|
4.2
|
94.8
|
1.0
|
|
C3A
|
F:HEM401
|
4.3
|
94.8
|
1.0
|
|
C2C
|
F:HEM401
|
4.3
|
94.8
|
1.0
|
|
C3B
|
F:HEM401
|
4.3
|
94.8
|
1.0
|
|
C3C
|
F:HEM401
|
4.3
|
94.8
|
1.0
|
|
CG
|
F:HIS225
|
4.3
|
88.0
|
1.0
|
|
C2A
|
F:HEM401
|
4.3
|
94.8
|
1.0
|
|
ND2
|
F:ASN245
|
4.6
|
95.0
|
1.0
|
|
CD
|
F:ARG243
|
4.7
|
91.7
|
1.0
|
|
CZ
|
F:ARG243
|
4.8
|
91.7
|
1.0
|
|
Reference:
M.Lucic,
T.Allport,
T.A.Clarke,
L.J.Williams,
M.T.Wilson,
A.K.Chaplin,
J.A.R.Worrall.
The Oligomeric States of Dye-Decolorizing Peroxidases From Streptomyces Lividans and Their Implications For Mechanism of Substrate Oxidation. Protein Sci. V. 33 E5073 2024.
ISSN: ESSN 1469-896X
PubMed: 38864770
DOI: 10.1002/PRO.5073
Page generated: Sat Aug 10 17:13:07 2024
|
