Iron in PDB 8z1y: Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State
Enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State
All present enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State:
7.4.2.9;
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State
(pdb code 8z1y). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State, PDB code: 8z1y:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 1 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:148.4
occ:1.00
|
FE1
|
C:SF4402
|
0.0
|
148.4
|
1.0
|
S3
|
C:SF4402
|
2.2
|
144.0
|
1.0
|
S2
|
C:SF4402
|
2.3
|
132.7
|
1.0
|
S4
|
C:SF4402
|
2.3
|
138.9
|
1.0
|
SG
|
C:CYS284
|
2.4
|
119.2
|
1.0
|
FE2
|
C:SF4402
|
2.7
|
130.5
|
1.0
|
FE4
|
C:SF4402
|
2.7
|
130.2
|
1.0
|
FE3
|
C:SF4402
|
2.7
|
146.7
|
1.0
|
CB
|
C:CYS284
|
3.3
|
107.7
|
1.0
|
S1
|
C:SF4402
|
3.8
|
130.3
|
1.0
|
CB
|
C:LEU286
|
4.5
|
98.0
|
1.0
|
CG
|
C:PRO302
|
4.6
|
110.7
|
1.0
|
SG
|
C:CYS315
|
4.7
|
101.8
|
1.0
|
CB
|
C:CYS297
|
4.7
|
123.4
|
1.0
|
SG
|
C:CYS297
|
4.7
|
135.7
|
1.0
|
CA
|
C:CYS284
|
4.7
|
110.7
|
1.0
|
O
|
C:LYS314
|
4.9
|
102.0
|
1.0
|
SG
|
C:CYS290
|
4.9
|
99.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 2 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:130.5
occ:1.00
|
FE2
|
C:SF4402
|
0.0
|
130.5
|
1.0
|
S4
|
C:SF4402
|
2.2
|
138.9
|
1.0
|
S1
|
C:SF4402
|
2.3
|
130.3
|
1.0
|
S3
|
C:SF4402
|
2.3
|
144.0
|
1.0
|
SG
|
C:CYS290
|
2.3
|
99.8
|
1.0
|
FE3
|
C:SF4402
|
2.7
|
146.7
|
1.0
|
FE1
|
C:SF4402
|
2.7
|
148.4
|
1.0
|
FE4
|
C:SF4402
|
2.7
|
130.2
|
1.0
|
CB
|
C:CYS290
|
3.2
|
103.7
|
1.0
|
S2
|
C:SF4402
|
3.8
|
132.7
|
1.0
|
CG
|
C:PRO248
|
4.2
|
99.2
|
1.0
|
CB
|
C:PRO248
|
4.5
|
96.8
|
1.0
|
CA
|
C:CYS290
|
4.6
|
106.3
|
1.0
|
CD2
|
C:LEU286
|
4.6
|
100.8
|
1.0
|
CA
|
C:ALA293
|
4.7
|
113.0
|
1.0
|
N
|
C:ALA293
|
4.7
|
113.5
|
1.0
|
SG
|
C:CYS315
|
4.8
|
101.8
|
1.0
|
CB
|
C:LEU286
|
4.8
|
98.0
|
1.0
|
C
|
C:TYR292
|
4.8
|
113.0
|
1.0
|
SG
|
C:CYS284
|
4.9
|
119.2
|
1.0
|
SG
|
C:CYS297
|
4.9
|
135.7
|
1.0
|
CD
|
C:PRO248
|
5.0
|
93.0
|
1.0
|
CB
|
C:ALA293
|
5.0
|
116.7
|
1.0
|
|
Iron binding site 3 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 3 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:146.7
occ:1.00
|
FE3
|
C:SF4402
|
0.0
|
146.7
|
1.0
|
S1
|
C:SF4402
|
2.2
|
130.3
|
1.0
|
S2
|
C:SF4402
|
2.3
|
132.7
|
1.0
|
S4
|
C:SF4402
|
2.3
|
138.9
|
1.0
|
SG
|
C:CYS297
|
2.4
|
135.7
|
1.0
|
FE2
|
C:SF4402
|
2.7
|
130.5
|
1.0
|
FE4
|
C:SF4402
|
2.7
|
130.2
|
1.0
|
FE1
|
C:SF4402
|
2.7
|
148.4
|
1.0
|
CB
|
C:CYS297
|
3.2
|
123.4
|
1.0
|
S3
|
C:SF4402
|
3.8
|
144.0
|
1.0
|
CA
|
C:ALA293
|
4.3
|
113.0
|
1.0
|
CA
|
C:CYS297
|
4.4
|
119.5
|
1.0
|
SG
|
C:CYS290
|
4.6
|
99.8
|
1.0
|
O
|
C:TYR292
|
4.6
|
117.0
|
1.0
|
CD2
|
C:TYR317
|
4.7
|
106.6
|
1.0
|
N
|
C:THR294
|
4.7
|
124.8
|
1.0
|
SG
|
C:CYS315
|
4.7
|
101.8
|
1.0
|
CD2
|
C:HIS316
|
4.8
|
105.9
|
1.0
|
CB
|
C:CYS284
|
4.8
|
107.7
|
1.0
|
SG
|
C:CYS284
|
4.8
|
119.2
|
1.0
|
N
|
C:ALA293
|
4.9
|
113.5
|
1.0
|
CB
|
C:ALA293
|
4.9
|
116.7
|
1.0
|
CE2
|
C:TYR317
|
4.9
|
111.4
|
1.0
|
C
|
C:TYR292
|
5.0
|
113.0
|
1.0
|
|
Iron binding site 4 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 4 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:130.2
occ:1.00
|
FE4
|
C:SF4402
|
0.0
|
130.2
|
1.0
|
SG
|
C:CYS315
|
2.2
|
101.8
|
1.0
|
S1
|
C:SF4402
|
2.3
|
130.3
|
1.0
|
S2
|
C:SF4402
|
2.3
|
132.7
|
1.0
|
S3
|
C:SF4402
|
2.3
|
144.0
|
1.0
|
FE3
|
C:SF4402
|
2.7
|
146.7
|
1.0
|
FE1
|
C:SF4402
|
2.7
|
148.4
|
1.0
|
FE2
|
C:SF4402
|
2.7
|
130.5
|
1.0
|
CB
|
C:CYS315
|
3.5
|
96.9
|
1.0
|
S4
|
C:SF4402
|
3.9
|
138.9
|
1.0
|
CA
|
C:CYS315
|
3.9
|
93.4
|
1.0
|
CG
|
C:PRO248
|
4.1
|
99.2
|
1.0
|
N
|
C:HIS316
|
4.2
|
115.1
|
1.0
|
CD
|
C:PRO248
|
4.3
|
93.0
|
1.0
|
C
|
C:CYS315
|
4.5
|
98.9
|
1.0
|
N
|
C:TYR317
|
4.7
|
108.1
|
1.0
|
SG
|
C:CYS290
|
4.8
|
99.8
|
1.0
|
SG
|
C:CYS297
|
4.9
|
135.7
|
1.0
|
SG
|
C:CYS284
|
4.9
|
119.2
|
1.0
|
CD2
|
C:TYR317
|
4.9
|
106.6
|
1.0
|
NE2
|
C:HIS247
|
5.0
|
94.3
|
1.0
|
|
Iron binding site 5 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 5 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:145.7
occ:1.00
|
FE1
|
D:SF4401
|
0.0
|
145.7
|
1.0
|
S3
|
D:SF4401
|
2.2
|
113.4
|
1.0
|
S2
|
D:SF4401
|
2.3
|
120.8
|
1.0
|
S4
|
D:SF4401
|
2.3
|
120.9
|
1.0
|
SG
|
D:CYS306
|
2.4
|
123.8
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
125.3
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
128.9
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
141.3
|
1.0
|
CB
|
D:CYS306
|
3.4
|
121.0
|
1.0
|
S1
|
D:SF4401
|
3.8
|
131.6
|
1.0
|
O
|
D:ARG301
|
4.4
|
111.4
|
1.0
|
CA
|
D:CYS306
|
4.5
|
122.9
|
1.0
|
SG
|
D:CYS299
|
4.6
|
120.7
|
1.0
|
SG
|
D:CYS323
|
4.7
|
119.2
|
1.0
|
SG
|
D:CYS293
|
4.8
|
113.1
|
1.0
|
CB
|
D:CYS293
|
4.9
|
108.5
|
1.0
|
CD2
|
D:PHE324
|
4.9
|
104.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 6 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:125.3
occ:1.00
|
FE2
|
D:SF4401
|
0.0
|
125.3
|
1.0
|
S4
|
D:SF4401
|
2.2
|
120.9
|
1.0
|
S3
|
D:SF4401
|
2.3
|
113.4
|
1.0
|
SG
|
D:CYS323
|
2.3
|
119.2
|
1.0
|
S1
|
D:SF4401
|
2.3
|
131.6
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
145.7
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
141.3
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
128.9
|
1.0
|
CB
|
D:CYS323
|
3.5
|
109.9
|
1.0
|
S2
|
D:SF4401
|
3.8
|
120.8
|
1.0
|
CA
|
D:CYS323
|
3.9
|
103.3
|
1.0
|
N
|
D:PHE324
|
4.1
|
107.0
|
1.0
|
CG
|
D:PRO256
|
4.3
|
105.4
|
1.0
|
C
|
D:CYS323
|
4.4
|
109.2
|
1.0
|
CD
|
D:PRO256
|
4.4
|
104.7
|
1.0
|
N
|
D:ALA325
|
4.5
|
100.1
|
1.0
|
NE2
|
D:HIS255
|
4.6
|
94.8
|
1.0
|
CB
|
D:ALA325
|
4.7
|
108.5
|
1.0
|
SG
|
D:CYS293
|
4.7
|
113.1
|
1.0
|
SG
|
D:CYS306
|
4.9
|
123.8
|
1.0
|
CE1
|
D:HIS255
|
4.9
|
91.3
|
1.0
|
SG
|
D:CYS299
|
4.9
|
120.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 7 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:141.3
occ:1.00
|
FE3
|
D:SF4401
|
0.0
|
141.3
|
1.0
|
S1
|
D:SF4401
|
2.3
|
131.6
|
1.0
|
S2
|
D:SF4401
|
2.3
|
120.8
|
1.0
|
S4
|
D:SF4401
|
2.3
|
120.9
|
1.0
|
SG
|
D:CYS293
|
2.3
|
113.1
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
125.3
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
128.9
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
145.7
|
1.0
|
CB
|
D:CYS293
|
3.2
|
108.5
|
1.0
|
S3
|
D:SF4401
|
3.8
|
113.4
|
1.0
|
SG
|
D:CYS306
|
4.6
|
123.8
|
1.0
|
CA
|
D:CYS293
|
4.6
|
107.8
|
1.0
|
CB
|
D:PHE295
|
4.6
|
98.8
|
1.0
|
CB
|
D:CYS306
|
4.7
|
121.0
|
1.0
|
SG
|
D:CYS323
|
4.8
|
119.2
|
1.0
|
SG
|
D:CYS299
|
4.8
|
120.7
|
1.0
|
N
|
D:ASN296
|
4.9
|
114.0
|
1.0
|
NE2
|
D:HIS255
|
4.9
|
94.8
|
1.0
|
CE1
|
D:HIS255
|
4.9
|
91.3
|
1.0
|
|
Iron binding site 8 out
of 8 in 8z1y
Go back to
Iron Binding Sites List in 8z1y
Iron binding site 8 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic 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 Escherichia Coli Dppabcdf in the Pre-Catalytic State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:128.9
occ:1.00
|
FE4
|
D:SF4401
|
0.0
|
128.9
|
1.0
|
S2
|
D:SF4401
|
2.3
|
120.8
|
1.0
|
S3
|
D:SF4401
|
2.3
|
113.4
|
1.0
|
S1
|
D:SF4401
|
2.3
|
131.6
|
1.0
|
SG
|
D:CYS299
|
2.3
|
120.7
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
145.7
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
141.3
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
125.3
|
1.0
|
CB
|
D:CYS299
|
3.3
|
112.3
|
1.0
|
CG
|
D:PRO256
|
3.7
|
105.4
|
1.0
|
S4
|
D:SF4401
|
3.8
|
120.9
|
1.0
|
CD2
|
D:PHE295
|
4.4
|
106.4
|
1.0
|
CD
|
D:PRO256
|
4.7
|
104.7
|
1.0
|
SG
|
D:CYS323
|
4.7
|
119.2
|
1.0
|
CA
|
D:CYS299
|
4.7
|
105.2
|
1.0
|
O
|
D:ARG301
|
4.8
|
111.4
|
1.0
|
CB
|
D:ARG301
|
4.8
|
110.9
|
1.0
|
SG
|
D:CYS293
|
4.9
|
113.1
|
1.0
|
C
|
D:ARG301
|
4.9
|
110.5
|
1.0
|
CB
|
D:PRO256
|
4.9
|
104.2
|
1.0
|
SG
|
D:CYS306
|
5.0
|
123.8
|
1.0
|
|
Reference:
P.Li,
Y.Huang.
Cryo-Em Structure of Escherichia Coli Dppabcdf in the Pre-Catalytic State To Be Published.
Page generated: Sun Feb 9 07:21:20 2025
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