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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

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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

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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

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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

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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

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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

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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

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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

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