Iron in PDB 8h2t: Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
(pdb code 8h2t). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the
Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa, PDB code: 8h2t:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Iron binding site 1 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 1 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:111.4
occ:1.00
|
FE1
|
B:FES501
|
0.0
|
111.4
|
1.0
|
ND1
|
B:HIS87
|
2.1
|
79.6
|
1.0
|
ND1
|
B:HIS109
|
2.1
|
79.0
|
1.0
|
S1
|
B:FES501
|
2.2
|
105.8
|
1.0
|
S2
|
B:FES501
|
2.2
|
104.8
|
1.0
|
FE2
|
B:FES501
|
2.7
|
126.3
|
1.0
|
CG
|
B:HIS87
|
2.9
|
85.1
|
1.0
|
CE1
|
B:HIS109
|
2.9
|
88.7
|
1.0
|
CB
|
B:HIS87
|
3.0
|
85.7
|
1.0
|
CG
|
B:HIS109
|
3.2
|
85.2
|
1.0
|
CE1
|
B:HIS87
|
3.2
|
82.8
|
1.0
|
CB
|
B:HIS109
|
3.6
|
88.8
|
1.0
|
NE2
|
B:HIS109
|
4.1
|
84.9
|
1.0
|
N
|
B:HIS109
|
4.1
|
83.2
|
1.0
|
CD2
|
B:HIS87
|
4.1
|
79.2
|
1.0
|
CD2
|
B:HIS109
|
4.2
|
85.6
|
1.0
|
N
|
B:LYS88
|
4.2
|
71.8
|
1.0
|
NE2
|
B:HIS87
|
4.2
|
86.2
|
1.0
|
CB
|
B:TYR108
|
4.3
|
80.8
|
1.0
|
CA
|
B:HIS87
|
4.3
|
77.6
|
1.0
|
SG
|
B:CYS85
|
4.4
|
77.2
|
1.0
|
CA
|
B:HIS109
|
4.4
|
87.0
|
1.0
|
CD2
|
B:TYR108
|
4.4
|
83.2
|
1.0
|
SG
|
B:CYS106
|
4.5
|
86.2
|
1.0
|
CB
|
B:LYS88
|
4.6
|
79.5
|
1.0
|
C
|
B:HIS87
|
4.6
|
81.0
|
1.0
|
CG
|
B:LYS88
|
4.6
|
80.9
|
1.0
|
CG
|
B:TYR108
|
4.7
|
88.0
|
1.0
|
CD1
|
B:TRP111
|
4.7
|
74.6
|
1.0
|
NE1
|
B:TRP111
|
4.9
|
78.3
|
1.0
|
C
|
B:TYR108
|
4.9
|
79.6
|
1.0
|
CG
|
B:TRP111
|
5.0
|
71.3
|
1.0
|
|
Iron binding site 2 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 2 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:126.3
occ:1.00
|
FE2
|
B:FES501
|
0.0
|
126.3
|
1.0
|
S1
|
B:FES501
|
2.2
|
105.8
|
1.0
|
S2
|
B:FES501
|
2.2
|
104.8
|
1.0
|
SG
|
B:CYS106
|
2.3
|
86.2
|
1.0
|
SG
|
B:CYS85
|
2.3
|
77.2
|
1.0
|
FE1
|
B:FES501
|
2.7
|
111.4
|
1.0
|
CB
|
B:CYS85
|
3.1
|
65.8
|
1.0
|
CB
|
B:CYS106
|
3.2
|
80.1
|
1.0
|
CB
|
B:HIS87
|
3.8
|
85.7
|
1.0
|
CB
|
B:TYR108
|
4.5
|
80.8
|
1.0
|
ND1
|
B:HIS87
|
4.5
|
79.6
|
1.0
|
CA
|
B:CYS85
|
4.5
|
78.3
|
1.0
|
N
|
B:HIS87
|
4.5
|
80.6
|
1.0
|
N
|
B:LYS88
|
4.6
|
71.8
|
1.0
|
CG
|
B:HIS87
|
4.6
|
85.1
|
1.0
|
ND1
|
B:HIS109
|
4.6
|
79.0
|
1.0
|
CB
|
B:SER90
|
4.6
|
84.2
|
1.0
|
CA
|
B:CYS106
|
4.7
|
80.9
|
1.0
|
CB
|
B:TRP111
|
4.7
|
72.3
|
1.0
|
N
|
B:HIS109
|
4.7
|
83.2
|
1.0
|
CA
|
B:HIS87
|
4.7
|
77.6
|
1.0
|
CG
|
B:TRP111
|
4.9
|
71.3
|
1.0
|
N
|
B:SER90
|
4.9
|
80.8
|
1.0
|
C
|
B:CYS85
|
4.9
|
82.0
|
1.0
|
O
|
B:SER90
|
5.0
|
96.6
|
1.0
|
|
Iron binding site 3 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 3 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe503
b:150.2
occ:1.00
|
OD2
|
B:ASP377
|
2.0
|
101.2
|
1.0
|
OD1
|
B:ASP377
|
2.1
|
101.1
|
1.0
|
NE2
|
B:HIS216
|
2.2
|
80.2
|
1.0
|
OD1
|
B:ASN210
|
2.3
|
102.4
|
1.0
|
CG
|
B:ASP377
|
2.3
|
97.5
|
1.0
|
NE2
|
B:HIS221
|
2.7
|
92.8
|
1.0
|
CE1
|
B:HIS216
|
2.9
|
82.8
|
1.0
|
ND2
|
B:ASN210
|
2.9
|
99.2
|
1.0
|
CG
|
B:ASN210
|
2.9
|
98.1
|
1.0
|
CD2
|
B:HIS216
|
3.0
|
77.7
|
1.0
|
CE1
|
B:HIS221
|
3.4
|
95.6
|
1.0
|
CB
|
B:ASP377
|
3.8
|
89.6
|
1.0
|
ND1
|
B:HIS216
|
3.8
|
82.9
|
1.0
|
CD2
|
B:HIS221
|
3.9
|
94.6
|
1.0
|
CG
|
B:HIS216
|
3.9
|
82.0
|
1.0
|
CB
|
B:ASN210
|
4.4
|
94.0
|
1.0
|
ND1
|
B:HIS221
|
4.6
|
90.5
|
1.0
|
O
|
B:ASN210
|
4.6
|
107.1
|
1.0
|
CA
|
B:ASP377
|
4.7
|
88.9
|
1.0
|
OH
|
B:TYR381
|
4.7
|
88.4
|
1.0
|
C8
|
B:IAC502
|
4.8
|
112.4
|
1.0
|
CG
|
B:HIS221
|
4.9
|
90.1
|
1.0
|
N
|
B:IAC502
|
4.9
|
112.0
|
1.0
|
C7
|
B:IAC502
|
5.0
|
116.0
|
1.0
|
|
Iron binding site 4 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 4 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:110.2
occ:1.00
|
FE1
|
D:FES501
|
0.0
|
110.2
|
1.0
|
ND1
|
D:HIS109
|
2.1
|
78.8
|
1.0
|
ND1
|
D:HIS87
|
2.1
|
82.4
|
1.0
|
S1
|
D:FES501
|
2.2
|
106.8
|
1.0
|
S2
|
D:FES501
|
2.2
|
103.1
|
1.0
|
FE2
|
D:FES501
|
2.7
|
123.0
|
1.0
|
CG
|
D:HIS87
|
2.9
|
87.3
|
1.0
|
CE1
|
D:HIS109
|
2.9
|
88.0
|
1.0
|
CB
|
D:HIS87
|
3.0
|
85.6
|
1.0
|
CG
|
D:HIS109
|
3.2
|
86.0
|
1.0
|
CE1
|
D:HIS87
|
3.2
|
85.0
|
1.0
|
CB
|
D:HIS109
|
3.7
|
86.6
|
1.0
|
NE2
|
D:HIS109
|
4.0
|
85.6
|
1.0
|
CD2
|
D:HIS87
|
4.1
|
82.4
|
1.0
|
N
|
D:HIS109
|
4.1
|
81.3
|
1.0
|
CD2
|
D:HIS109
|
4.2
|
87.2
|
1.0
|
N
|
D:LYS88
|
4.2
|
74.0
|
1.0
|
NE2
|
D:HIS87
|
4.2
|
88.2
|
1.0
|
CB
|
D:TYR108
|
4.3
|
82.8
|
1.0
|
CA
|
D:HIS87
|
4.3
|
79.7
|
1.0
|
SG
|
D:CYS85
|
4.4
|
82.7
|
1.0
|
CD2
|
D:TYR108
|
4.4
|
84.3
|
1.0
|
SG
|
D:CYS106
|
4.5
|
84.0
|
1.0
|
CA
|
D:HIS109
|
4.5
|
82.4
|
1.0
|
CB
|
D:LYS88
|
4.6
|
79.5
|
1.0
|
C
|
D:HIS87
|
4.6
|
82.4
|
1.0
|
CG
|
D:LYS88
|
4.6
|
81.4
|
1.0
|
CG
|
D:TYR108
|
4.7
|
89.1
|
1.0
|
CD1
|
D:TRP111
|
4.8
|
75.0
|
1.0
|
NE1
|
D:TRP111
|
4.9
|
78.2
|
1.0
|
C
|
D:TYR108
|
4.9
|
82.1
|
1.0
|
N
|
D:HIS87
|
5.0
|
84.1
|
1.0
|
|
Iron binding site 5 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 5 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:123.0
occ:1.00
|
FE2
|
D:FES501
|
0.0
|
123.0
|
1.0
|
S1
|
D:FES501
|
2.2
|
106.8
|
1.0
|
S2
|
D:FES501
|
2.2
|
103.1
|
1.0
|
SG
|
D:CYS106
|
2.3
|
84.0
|
1.0
|
SG
|
D:CYS85
|
2.3
|
82.7
|
1.0
|
FE1
|
D:FES501
|
2.7
|
110.2
|
1.0
|
CB
|
D:CYS85
|
3.1
|
68.4
|
1.0
|
CB
|
D:CYS106
|
3.2
|
79.3
|
1.0
|
CB
|
D:HIS87
|
3.8
|
85.6
|
1.0
|
CB
|
D:TYR108
|
4.5
|
82.8
|
1.0
|
ND1
|
D:HIS87
|
4.5
|
82.4
|
1.0
|
N
|
D:HIS87
|
4.5
|
84.1
|
1.0
|
CA
|
D:CYS85
|
4.6
|
78.1
|
1.0
|
N
|
D:LYS88
|
4.6
|
74.0
|
1.0
|
ND1
|
D:HIS109
|
4.6
|
78.8
|
1.0
|
CG
|
D:HIS87
|
4.6
|
87.3
|
1.0
|
CA
|
D:CYS106
|
4.6
|
80.0
|
1.0
|
CB
|
D:TRP111
|
4.7
|
74.4
|
1.0
|
CB
|
D:SER90
|
4.7
|
81.0
|
1.0
|
N
|
D:HIS109
|
4.7
|
81.3
|
1.0
|
CA
|
D:HIS87
|
4.7
|
79.7
|
1.0
|
CG
|
D:TRP111
|
4.9
|
73.0
|
1.0
|
N
|
D:SER90
|
4.9
|
73.9
|
1.0
|
C
|
D:CYS85
|
5.0
|
81.9
|
1.0
|
O
|
D:SER90
|
5.0
|
92.2
|
1.0
|
|
Iron binding site 6 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 6 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe503
b:154.4
occ:1.00
|
OD2
|
D:ASP377
|
2.0
|
98.8
|
1.0
|
OD1
|
D:ASP377
|
2.1
|
99.9
|
1.0
|
NE2
|
D:HIS216
|
2.2
|
84.8
|
1.0
|
OD1
|
D:ASN210
|
2.3
|
98.4
|
1.0
|
CG
|
D:ASP377
|
2.3
|
95.8
|
1.0
|
NE2
|
D:HIS221
|
2.7
|
91.2
|
1.0
|
ND2
|
D:ASN210
|
2.9
|
98.2
|
1.0
|
CE1
|
D:HIS216
|
2.9
|
86.1
|
1.0
|
CG
|
D:ASN210
|
2.9
|
94.5
|
1.0
|
CD2
|
D:HIS216
|
3.0
|
82.7
|
1.0
|
CE1
|
D:HIS221
|
3.4
|
93.6
|
1.0
|
CB
|
D:ASP377
|
3.8
|
88.5
|
1.0
|
ND1
|
D:HIS216
|
3.9
|
86.7
|
1.0
|
CD2
|
D:HIS221
|
3.9
|
91.5
|
1.0
|
CG
|
D:HIS216
|
3.9
|
83.7
|
1.0
|
CB
|
D:ASN210
|
4.4
|
91.1
|
1.0
|
ND1
|
D:HIS221
|
4.6
|
86.9
|
1.0
|
O
|
D:ASN210
|
4.7
|
104.3
|
1.0
|
CA
|
D:ASP377
|
4.7
|
89.1
|
1.0
|
OH
|
D:TYR381
|
4.7
|
94.7
|
1.0
|
C8
|
D:IAC502
|
4.7
|
111.5
|
1.0
|
N
|
D:IAC502
|
4.8
|
111.0
|
1.0
|
CG
|
D:HIS221
|
4.9
|
85.3
|
1.0
|
|
Iron binding site 7 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 7 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe501
b:110.5
occ:1.00
|
FE1
|
G:FES501
|
0.0
|
110.5
|
1.0
|
ND1
|
G:HIS87
|
2.1
|
79.1
|
1.0
|
ND1
|
G:HIS109
|
2.1
|
78.6
|
1.0
|
S1
|
G:FES501
|
2.2
|
101.7
|
1.0
|
S2
|
G:FES501
|
2.2
|
106.2
|
1.0
|
FE2
|
G:FES501
|
2.7
|
123.0
|
1.0
|
CE1
|
G:HIS109
|
2.9
|
88.1
|
1.0
|
CG
|
G:HIS87
|
2.9
|
84.9
|
1.0
|
CB
|
G:HIS87
|
3.0
|
84.3
|
1.0
|
CG
|
G:HIS109
|
3.2
|
86.4
|
1.0
|
CE1
|
G:HIS87
|
3.2
|
81.7
|
1.0
|
CB
|
G:HIS109
|
3.7
|
87.6
|
1.0
|
NE2
|
G:HIS109
|
4.0
|
84.2
|
1.0
|
N
|
G:HIS109
|
4.1
|
82.1
|
1.0
|
CD2
|
G:HIS87
|
4.1
|
79.9
|
1.0
|
CD2
|
G:HIS109
|
4.2
|
86.4
|
1.0
|
N
|
G:LYS88
|
4.2
|
75.7
|
1.0
|
CB
|
G:TYR108
|
4.2
|
75.5
|
1.0
|
NE2
|
G:HIS87
|
4.2
|
84.7
|
1.0
|
CD2
|
G:TYR108
|
4.3
|
82.2
|
1.0
|
CA
|
G:HIS87
|
4.4
|
78.2
|
1.0
|
SG
|
G:CYS85
|
4.4
|
79.9
|
1.0
|
SG
|
G:CYS106
|
4.5
|
85.4
|
1.0
|
CA
|
G:HIS109
|
4.5
|
84.2
|
1.0
|
CB
|
G:LYS88
|
4.5
|
79.9
|
1.0
|
C
|
G:HIS87
|
4.6
|
82.2
|
1.0
|
CG
|
G:LYS88
|
4.6
|
83.6
|
1.0
|
CG
|
G:TYR108
|
4.6
|
86.4
|
1.0
|
CD1
|
G:TRP111
|
4.8
|
76.1
|
1.0
|
C
|
G:TYR108
|
4.9
|
77.4
|
1.0
|
NE1
|
G:TRP111
|
4.9
|
78.4
|
1.0
|
CA
|
G:LYS88
|
5.0
|
79.3
|
1.0
|
|
Iron binding site 8 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 8 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe501
b:123.0
occ:1.00
|
FE2
|
G:FES501
|
0.0
|
123.0
|
1.0
|
S1
|
G:FES501
|
2.2
|
101.7
|
1.0
|
S2
|
G:FES501
|
2.2
|
106.2
|
1.0
|
SG
|
G:CYS106
|
2.3
|
85.4
|
1.0
|
SG
|
G:CYS85
|
2.3
|
79.9
|
1.0
|
FE1
|
G:FES501
|
2.7
|
110.5
|
1.0
|
CB
|
G:CYS85
|
3.1
|
69.4
|
1.0
|
CB
|
G:CYS106
|
3.2
|
78.1
|
1.0
|
CB
|
G:HIS87
|
3.7
|
84.3
|
1.0
|
CB
|
G:TYR108
|
4.4
|
75.5
|
1.0
|
ND1
|
G:HIS87
|
4.5
|
79.1
|
1.0
|
CA
|
G:CYS85
|
4.5
|
77.6
|
1.0
|
N
|
G:HIS87
|
4.5
|
83.2
|
1.0
|
N
|
G:LYS88
|
4.6
|
75.7
|
1.0
|
CG
|
G:HIS87
|
4.6
|
84.9
|
1.0
|
ND1
|
G:HIS109
|
4.6
|
78.6
|
1.0
|
CB
|
G:SER90
|
4.6
|
82.8
|
1.0
|
CA
|
G:CYS106
|
4.6
|
79.6
|
1.0
|
CB
|
G:TRP111
|
4.7
|
74.6
|
1.0
|
N
|
G:HIS109
|
4.7
|
82.1
|
1.0
|
CA
|
G:HIS87
|
4.7
|
78.2
|
1.0
|
CG
|
G:TRP111
|
4.9
|
75.2
|
1.0
|
N
|
G:SER90
|
4.9
|
78.2
|
1.0
|
C
|
G:CYS85
|
4.9
|
81.9
|
1.0
|
O
|
G:SER90
|
5.0
|
93.9
|
1.0
|
|
Iron binding site 9 out
of 9 in 8h2t
Go back to
Iron Binding Sites List in 8h2t
Iron binding site 9 out
of 9 in the Cryo-Em Structure of Iadd/E Dioxygenase Bound with Iaa
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 Iadd/E Dioxygenase Bound with Iaa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe503
b:144.6
occ:1.00
|
OD2
|
G:ASP377
|
2.0
|
98.6
|
1.0
|
OD1
|
G:ASP377
|
2.1
|
101.4
|
1.0
|
NE2
|
G:HIS216
|
2.2
|
79.2
|
1.0
|
OD1
|
G:ASN210
|
2.3
|
96.9
|
1.0
|
CG
|
G:ASP377
|
2.3
|
95.3
|
1.0
|
NE2
|
G:HIS221
|
2.7
|
90.0
|
1.0
|
CE1
|
G:HIS216
|
2.9
|
84.4
|
1.0
|
ND2
|
G:ASN210
|
2.9
|
97.1
|
1.0
|
CG
|
G:ASN210
|
2.9
|
94.1
|
1.0
|
CD2
|
G:HIS216
|
3.0
|
77.1
|
1.0
|
CE1
|
G:HIS221
|
3.4
|
95.5
|
1.0
|
CB
|
G:ASP377
|
3.8
|
86.0
|
1.0
|
ND1
|
G:HIS216
|
3.8
|
84.3
|
1.0
|
CD2
|
G:HIS221
|
3.9
|
90.8
|
1.0
|
CG
|
G:HIS216
|
3.9
|
80.8
|
1.0
|
CB
|
G:ASN210
|
4.4
|
90.7
|
1.0
|
ND1
|
G:HIS221
|
4.6
|
90.2
|
1.0
|
O
|
G:ASN210
|
4.7
|
101.3
|
1.0
|
CA
|
G:ASP377
|
4.7
|
87.8
|
1.0
|
OH
|
G:TYR381
|
4.7
|
92.5
|
1.0
|
C8
|
G:IAC502
|
4.8
|
110.8
|
1.0
|
N
|
G:IAC502
|
4.9
|
109.9
|
1.0
|
CG
|
G:HIS221
|
4.9
|
87.2
|
1.0
|
|
Reference:
Y.Ma,
Z.Li,
G.Yu,
H.Zhang.
Cryo-Em Structure of A Bacterial Dioxygenase To Be Published.
Page generated: Sat Aug 10 05:06:44 2024
|