Iron in PDB 8z1v: Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting State
Enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting State
All present enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting State:
7.4.2.9;
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting State
(pdb code 8z1v). 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 Dppbcdf in the Resting State, PDB code: 8z1v:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 1 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:165.0
occ:1.00
|
FE1
|
C:SF4401
|
0.0
|
165.0
|
1.0
|
S3
|
C:SF4401
|
2.2
|
158.5
|
1.0
|
S4
|
C:SF4401
|
2.3
|
165.5
|
1.0
|
S2
|
C:SF4401
|
2.3
|
163.4
|
1.0
|
SG
|
C:CYS290
|
2.4
|
151.8
|
1.0
|
FE2
|
C:SF4401
|
2.7
|
155.4
|
1.0
|
FE3
|
C:SF4401
|
2.7
|
160.7
|
1.0
|
FE4
|
C:SF4401
|
2.7
|
173.1
|
1.0
|
CB
|
C:CYS290
|
3.1
|
139.3
|
1.0
|
S1
|
C:SF4401
|
3.8
|
173.2
|
1.0
|
CG
|
C:PRO248
|
4.3
|
123.3
|
1.0
|
CA
|
C:CYS290
|
4.6
|
132.7
|
1.0
|
N
|
C:ALA293
|
4.7
|
124.0
|
1.0
|
CA
|
C:ALA293
|
4.7
|
124.1
|
1.0
|
CB
|
C:PRO248
|
4.7
|
117.5
|
1.0
|
SG
|
C:CYS315
|
4.9
|
142.0
|
1.0
|
SG
|
C:CYS297
|
4.9
|
155.9
|
1.0
|
C
|
C:TYR292
|
4.9
|
128.2
|
1.0
|
SG
|
C:CYS284
|
4.9
|
128.9
|
1.0
|
CD2
|
C:LEU286
|
4.9
|
133.1
|
1.0
|
CB
|
C:ALA293
|
5.0
|
123.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 2 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:155.4
occ:1.00
|
FE2
|
C:SF4401
|
0.0
|
155.4
|
1.0
|
S4
|
C:SF4401
|
2.2
|
165.5
|
1.0
|
S1
|
C:SF4401
|
2.3
|
173.2
|
1.0
|
S3
|
C:SF4401
|
2.3
|
158.5
|
1.0
|
SG
|
C:CYS284
|
2.4
|
128.9
|
1.0
|
FE1
|
C:SF4401
|
2.7
|
165.0
|
1.0
|
FE3
|
C:SF4401
|
2.7
|
160.7
|
1.0
|
FE4
|
C:SF4401
|
2.7
|
173.1
|
1.0
|
CB
|
C:CYS284
|
3.2
|
122.5
|
1.0
|
S2
|
C:SF4401
|
3.8
|
163.4
|
1.0
|
CB
|
C:LEU286
|
4.6
|
124.3
|
1.0
|
CA
|
C:CYS284
|
4.6
|
119.3
|
1.0
|
CB
|
C:CYS297
|
4.8
|
141.3
|
1.0
|
SG
|
C:CYS315
|
4.8
|
142.0
|
1.0
|
SG
|
C:CYS297
|
4.8
|
155.9
|
1.0
|
SG
|
C:CYS290
|
4.9
|
151.8
|
1.0
|
CG
|
C:PRO302
|
4.9
|
142.0
|
1.0
|
CB
|
C:CYS290
|
5.0
|
139.3
|
1.0
|
N
|
C:ASN287
|
5.0
|
126.9
|
1.0
|
|
Iron binding site 3 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 3 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:160.7
occ:1.00
|
FE3
|
C:SF4401
|
0.0
|
160.7
|
1.0
|
S2
|
C:SF4401
|
2.2
|
163.4
|
1.0
|
S4
|
C:SF4401
|
2.3
|
165.5
|
1.0
|
S1
|
C:SF4401
|
2.3
|
173.2
|
1.0
|
SG
|
C:CYS315
|
2.3
|
142.0
|
1.0
|
FE4
|
C:SF4401
|
2.7
|
173.1
|
1.0
|
FE1
|
C:SF4401
|
2.7
|
165.0
|
1.0
|
FE2
|
C:SF4401
|
2.7
|
155.4
|
1.0
|
CB
|
C:CYS315
|
3.6
|
135.0
|
1.0
|
S3
|
C:SF4401
|
3.8
|
158.5
|
1.0
|
CA
|
C:CYS315
|
4.0
|
130.1
|
1.0
|
CG
|
C:PRO248
|
4.3
|
123.3
|
1.0
|
N
|
C:HIS316
|
4.3
|
121.9
|
1.0
|
CD
|
C:PRO248
|
4.4
|
122.8
|
1.0
|
C
|
C:CYS315
|
4.6
|
132.0
|
1.0
|
SG
|
C:CYS290
|
4.7
|
151.8
|
1.0
|
SG
|
C:CYS297
|
4.8
|
155.9
|
1.0
|
CE1
|
C:HIS247
|
4.9
|
124.5
|
1.0
|
SG
|
C:CYS284
|
4.9
|
128.9
|
1.0
|
N
|
C:TYR317
|
4.9
|
140.7
|
1.0
|
ND1
|
C:HIS247
|
4.9
|
113.3
|
1.0
|
|
Iron binding site 4 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 4 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:173.1
occ:1.00
|
FE4
|
C:SF4401
|
0.0
|
173.1
|
1.0
|
S1
|
C:SF4401
|
2.2
|
173.2
|
1.0
|
S2
|
C:SF4401
|
2.3
|
163.4
|
1.0
|
S3
|
C:SF4401
|
2.3
|
158.5
|
1.0
|
SG
|
C:CYS297
|
2.4
|
155.9
|
1.0
|
FE3
|
C:SF4401
|
2.7
|
160.7
|
1.0
|
FE2
|
C:SF4401
|
2.7
|
155.4
|
1.0
|
FE1
|
C:SF4401
|
2.7
|
165.0
|
1.0
|
CB
|
C:CYS297
|
3.1
|
141.3
|
1.0
|
S4
|
C:SF4401
|
3.8
|
165.5
|
1.0
|
CA
|
C:CYS297
|
4.3
|
134.6
|
1.0
|
CA
|
C:ALA293
|
4.6
|
124.1
|
1.0
|
SG
|
C:CYS315
|
4.6
|
142.0
|
1.0
|
CB
|
C:CYS284
|
4.7
|
122.5
|
1.0
|
ND1
|
C:HIS316
|
4.8
|
125.0
|
1.0
|
SG
|
C:CYS284
|
4.8
|
128.9
|
1.0
|
SG
|
C:CYS290
|
5.0
|
151.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 5 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:173.4
occ:1.00
|
FE1
|
D:SF4401
|
0.0
|
173.4
|
1.0
|
S3
|
D:SF4401
|
2.2
|
177.7
|
1.0
|
S4
|
D:SF4401
|
2.3
|
172.1
|
1.0
|
S2
|
D:SF4401
|
2.3
|
177.0
|
1.0
|
SG
|
D:CYS293
|
2.5
|
146.9
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
172.0
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
175.5
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
164.5
|
1.0
|
CB
|
D:CYS293
|
3.3
|
135.7
|
1.0
|
S1
|
D:SF4401
|
3.8
|
166.7
|
1.0
|
CB
|
D:PHE295
|
4.7
|
126.8
|
1.0
|
CA
|
D:CYS293
|
4.7
|
127.6
|
1.0
|
N
|
D:ASN296
|
4.7
|
129.9
|
1.0
|
SG
|
D:CYS306
|
4.8
|
167.5
|
1.0
|
C
|
D:PHE295
|
4.9
|
137.3
|
1.0
|
CB
|
D:CYS306
|
4.9
|
147.1
|
1.0
|
CG
|
D:PRO311
|
5.0
|
149.8
|
1.0
|
SG
|
D:CYS299
|
5.0
|
159.3
|
1.0
|
|
Iron binding site 6 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 6 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:172.0
occ:1.00
|
FE2
|
D:SF4401
|
0.0
|
172.0
|
1.0
|
S3
|
D:SF4401
|
2.2
|
177.7
|
1.0
|
S4
|
D:SF4401
|
2.3
|
172.1
|
1.0
|
S1
|
D:SF4401
|
2.3
|
166.7
|
1.0
|
SG
|
D:CYS299
|
2.5
|
159.3
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
173.4
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
175.5
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
164.5
|
1.0
|
CB
|
D:CYS299
|
3.3
|
146.5
|
1.0
|
S2
|
D:SF4401
|
3.8
|
177.0
|
1.0
|
CG
|
D:PRO256
|
4.4
|
130.6
|
1.0
|
CD2
|
D:PHE295
|
4.7
|
131.5
|
1.0
|
CA
|
D:CYS299
|
4.7
|
140.3
|
1.0
|
SG
|
D:CYS323
|
4.7
|
154.3
|
1.0
|
CB
|
D:PRO256
|
4.7
|
123.3
|
1.0
|
N
|
D:ARG302
|
4.8
|
137.2
|
1.0
|
SG
|
D:CYS306
|
4.9
|
167.5
|
1.0
|
CB
|
D:ARG301
|
4.9
|
130.2
|
1.0
|
C
|
D:ARG301
|
4.9
|
131.3
|
1.0
|
CA
|
D:ARG302
|
5.0
|
137.2
|
1.0
|
SG
|
D:CYS293
|
5.0
|
146.9
|
1.0
|
|
Iron binding site 7 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 7 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:164.5
occ:1.00
|
FE3
|
D:SF4401
|
0.0
|
164.5
|
1.0
|
S1
|
D:SF4401
|
2.2
|
166.7
|
1.0
|
S2
|
D:SF4401
|
2.3
|
177.0
|
1.0
|
S4
|
D:SF4401
|
2.3
|
172.1
|
1.0
|
SG
|
D:CYS306
|
2.4
|
167.5
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
175.5
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
172.0
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
173.4
|
1.0
|
CB
|
D:CYS306
|
3.3
|
147.1
|
1.0
|
S3
|
D:SF4401
|
3.8
|
177.7
|
1.0
|
CA
|
D:CYS306
|
4.5
|
142.8
|
1.0
|
CB
|
D:CYS293
|
4.8
|
135.7
|
1.0
|
SG
|
D:CYS323
|
4.8
|
154.3
|
1.0
|
SG
|
D:CYS293
|
4.8
|
146.9
|
1.0
|
CD2
|
D:PHE324
|
4.8
|
135.5
|
1.0
|
N
|
D:PHE324
|
4.9
|
134.5
|
1.0
|
CA
|
D:ARG302
|
4.9
|
137.2
|
1.0
|
SG
|
D:CYS299
|
4.9
|
159.3
|
1.0
|
CB
|
D:PHE324
|
5.0
|
137.0
|
1.0
|
|
Iron binding site 8 out
of 8 in 8z1v
Go back to
Iron Binding Sites List in 8z1v
Iron binding site 8 out
of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf in the Resting 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 Dppbcdf in the Resting State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:175.5
occ:1.00
|
FE4
|
D:SF4401
|
0.0
|
175.5
|
1.0
|
S1
|
D:SF4401
|
2.2
|
166.7
|
1.0
|
S2
|
D:SF4401
|
2.3
|
177.0
|
1.0
|
S3
|
D:SF4401
|
2.3
|
177.7
|
1.0
|
SG
|
D:CYS323
|
2.4
|
154.3
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
164.5
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
172.0
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
173.4
|
1.0
|
CB
|
D:CYS323
|
3.4
|
144.3
|
1.0
|
CA
|
D:CYS323
|
3.6
|
143.4
|
1.0
|
S4
|
D:SF4401
|
3.8
|
172.1
|
1.0
|
N
|
D:PHE324
|
3.9
|
134.5
|
1.0
|
C
|
D:CYS323
|
4.1
|
143.5
|
1.0
|
N
|
D:ALA325
|
4.4
|
145.9
|
1.0
|
CG
|
D:PRO256
|
4.6
|
130.6
|
1.0
|
CD
|
D:PRO256
|
4.6
|
126.7
|
1.0
|
O
|
D:ALA322
|
4.7
|
139.6
|
1.0
|
CB
|
D:ALA325
|
4.8
|
149.3
|
1.0
|
NE2
|
D:HIS255
|
4.9
|
118.7
|
1.0
|
SG
|
D:CYS293
|
4.9
|
146.9
|
1.0
|
N
|
D:CYS323
|
4.9
|
141.3
|
1.0
|
SG
|
D:CYS299
|
4.9
|
159.3
|
1.0
|
SG
|
D:CYS306
|
4.9
|
167.5
|
1.0
|
CA
|
D:PHE324
|
5.0
|
137.6
|
1.0
|
|
Reference:
P.Li,
Y.Huang.
The Structure of Abc Peptide Transporters Reveals the Additional Functional Roles of Novel Domains To Be Published.
Page generated: Sun Feb 9 07:21:11 2025
|