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Iron in PDB 8z1x: Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp

Enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp

All present enzymatic activity of Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp:
7.4.2.9;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp (pdb code 8z1x). 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 Complex Bound to Amppnp, PDB code: 8z1x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8z1x

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Iron binding site 1 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1000

b:109.2
occ:1.00
 FE1 C:SF41000 0.0 109.2 1.0
S3 C:SF41000 2.2 109.2 1.0
S4 C:SF41000 2.3 109.2 1.0
SG C:CYS297 2.3 120.0 1.0
S2 C:SF41000 2.3 109.2 1.0
FE2 C:SF41000 2.7 109.2 1.0
FE4 C:SF41000 2.7 109.2 1.0
FE3 C:SF41000 2.7 109.2 1.0
CB C:CYS297 3.1 106.3 1.0
S1 C:SF41000 3.8 109.2 1.0
CA C:CYS297 4.4 92.2 1.0
CA C:ALA293 4.6 83.9 1.0
CB C:CYS284 4.6 87.3 1.0
CD2 C:HIS316 4.6 82.5 1.0
SG C:CYS284 4.7 90.2 1.0
SG C:CYS315 4.8 100.4 1.0
CD2 C:TYR317 4.8 95.2 1.0
N C:THR294 4.9 100.2 1.0

Iron binding site 2 out of 8 in 8z1x

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Iron binding site 2 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1000

b:109.2
occ:1.00
 FE2 C:SF41000 0.0 109.2 1.0
S4 C:SF41000 2.2 109.2 1.0
S1 C:SF41000 2.2 109.2 1.0
S3 C:SF41000 2.3 109.2 1.0
SG C:CYS315 2.6 100.4 1.0
FE3 C:SF41000 2.7 109.2 1.0
FE1 C:SF41000 2.7 109.2 1.0
FE4 C:SF41000 2.7 109.2 1.0
CB C:CYS315 3.6 82.0 1.0
S2 C:SF41000 3.8 109.2 1.0
CA C:CYS315 4.1 71.7 1.0
CG C:PRO248 4.2 77.5 1.0
N C:HIS316 4.4 68.5 1.0
CD C:PRO248 4.5 86.1 1.0
SG C:CYS290 4.6 109.9 1.0
C C:CYS315 4.7 73.0 1.0
SG C:CYS297 4.8 120.0 1.0
SG C:CYS284 4.9 90.2 1.0
N C:TYR317 5.0 89.8 1.0

Iron binding site 3 out of 8 in 8z1x

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Iron binding site 3 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1000

b:109.2
occ:1.00
 FE3 C:SF41000 0.0 109.2 1.0
S2 C:SF41000 2.2 109.2 1.0
S4 C:SF41000 2.3 109.2 1.0
S1 C:SF41000 2.3 109.2 1.0
SG C:CYS290 2.4 109.9 1.0
FE2 C:SF41000 2.7 109.2 1.0
FE4 C:SF41000 2.7 109.2 1.0
FE1 C:SF41000 2.7 109.2 1.0
CB C:CYS290 3.1 99.2 1.0
S3 C:SF41000 3.9 109.2 1.0
N C:ALA293 4.2 88.6 1.0
CA C:ALA293 4.3 83.9 1.0
C C:TYR292 4.5 89.0 1.0
CA C:CYS290 4.6 91.8 1.0
CB C:ALA293 4.7 81.8 1.0
CG C:PRO248 4.7 77.5 1.0
SG C:CYS297 4.8 120.0 1.0
CB C:TYR292 4.8 88.0 1.0
N C:TYR292 4.9 86.9 1.0
O C:TYR292 5.0 94.3 1.0
SG C:CYS284 5.0 90.2 1.0
CB C:PRO248 5.0 66.7 1.0
CA C:TYR292 5.0 86.7 1.0

Iron binding site 4 out of 8 in 8z1x

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Iron binding site 4 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1000

b:109.2
occ:1.00
 FE4 C:SF41000 0.0 109.2 1.0
S1 C:SF41000 2.2 109.2 1.0
S2 C:SF41000 2.3 109.2 1.0
S3 C:SF41000 2.3 109.2 1.0
SG C:CYS284 2.4 90.2 1.0
FE3 C:SF41000 2.7 109.2 1.0
FE1 C:SF41000 2.7 109.2 1.0
FE2 C:SF41000 2.7 109.2 1.0
CB C:CYS284 3.3 87.3 1.0
S4 C:SF41000 3.8 109.2 1.0
CB C:LEU286 4.5 87.2 1.0
SG C:CYS297 4.7 120.0 1.0
CB C:CYS297 4.7 106.3 1.0
CA C:CYS284 4.7 82.7 1.0
SG C:CYS290 4.8 109.9 1.0
N C:ASN287 4.9 95.7 1.0
CB C:CYS290 4.9 99.2 1.0
CG C:PRO302 5.0 99.0 1.0
SG C:CYS315 5.0 100.4 1.0

Iron binding site 5 out of 8 in 8z1x

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Iron binding site 5 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:103.1
occ:1.00
 FE1 D:SF4402 0.0 103.1 1.0
S3 D:SF4402 2.2 103.1 1.0
S4 D:SF4402 2.3 103.1 1.0
S2 D:SF4402 2.3 103.1 1.0
SG D:CYS323 2.4 116.8 1.0
FE2 D:SF4402 2.7 103.1 1.0
FE4 D:SF4402 2.7 103.1 1.0
FE3 D:SF4402 2.7 103.1 1.0
CB D:CYS323 3.4 98.1 1.0
CA D:CYS323 3.6 89.5 1.0
S1 D:SF4402 3.9 103.1 1.0
N D:PHE324 4.0 91.3 1.0
C D:CYS323 4.1 92.6 1.0
N D:ALA325 4.5 102.9 1.0
CD D:PRO256 4.6 94.5 1.0
O D:ALA322 4.7 89.9 1.0
NE2 D:HIS255 4.7 93.6 1.0
CG D:PRO256 4.7 85.8 1.0
SG D:CYS293 4.8 107.9 1.0
SG D:CYS299 4.8 124.8 1.0
CB D:ALA325 4.8 99.9 1.0
N D:CYS323 4.9 93.2 1.0
SG D:CYS306 4.9 119.4 1.0

Iron binding site 6 out of 8 in 8z1x

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Iron binding site 6 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:103.1
occ:1.00
 FE2 D:SF4402 0.0 103.1 1.0
S4 D:SF4402 2.2 103.1 1.0
S3 D:SF4402 2.2 103.1 1.0
S1 D:SF4402 2.3 103.1 1.0
SG D:CYS299 2.4 124.8 1.0
FE1 D:SF4402 2.7 103.1 1.0
FE3 D:SF4402 2.7 103.1 1.0
FE4 D:SF4402 2.7 103.1 1.0
CB D:CYS299 3.2 103.1 1.0
S2 D:SF4402 3.8 103.1 1.0
CG D:PRO256 4.3 85.8 1.0
CD2 D:PHE295 4.5 87.1 1.0
CA D:CYS299 4.6 98.6 1.0
N D:ARG302 4.6 91.6 1.0
CB D:PRO256 4.7 77.1 1.0
SG D:CYS323 4.7 116.8 1.0
C D:ARG301 4.7 100.2 1.0
CB D:ARG301 4.7 101.2 1.0
SG D:CYS306 4.8 119.4 1.0
CA D:ARG302 4.9 90.1 1.0
SG D:CYS293 4.9 107.9 1.0
CD D:PRO256 5.0 94.5 1.0

Iron binding site 7 out of 8 in 8z1x

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Iron binding site 7 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:103.1
occ:1.00
 FE3 D:SF4402 0.0 103.1 1.0
S4 D:SF4402 2.2 103.1 1.0
S2 D:SF4402 2.3 103.1 1.0
S1 D:SF4402 2.3 103.1 1.0
SG D:CYS306 2.4 119.4 1.0
FE4 D:SF4402 2.7 103.1 1.0
FE2 D:SF4402 2.7 103.1 1.0
FE1 D:SF4402 2.7 103.1 1.0
CB D:CYS306 3.4 96.2 1.0
S3 D:SF4402 3.8 103.1 1.0
CA D:CYS306 4.4 94.0 1.0
CB D:CYS293 4.7 96.2 1.0
CA D:ARG302 4.7 90.1 1.0
SG D:CYS293 4.7 107.9 1.0
N D:PHE324 4.8 91.3 1.0
SG D:CYS323 4.8 116.8 1.0
N D:PHE303 4.9 104.1 1.0
SG D:CYS299 4.9 124.8 1.0
CD2 D:PHE324 4.9 89.6 1.0
CB D:PHE324 4.9 95.5 1.0
O D:ARG301 5.0 102.9 1.0
N D:ALA325 5.0 102.9 1.0

Iron binding site 8 out of 8 in 8z1x

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Iron binding site 8 out of 8 in the Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp


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 Complex Bound to Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:103.1
occ:1.00
 FE4 D:SF4402 0.0 103.1 1.0
S2 D:SF4402 2.2 103.1 1.0
S1 D:SF4402 2.3 103.1 1.0
S3 D:SF4402 2.3 103.1 1.0
SG D:CYS293 2.4 107.9 1.0
FE3 D:SF4402 2.7 103.1 1.0
FE1 D:SF4402 2.7 103.1 1.0
FE2 D:SF4402 2.7 103.1 1.0
CB D:CYS293 3.2 96.2 1.0
S4 D:SF4402 3.8 103.1 1.0
CB D:PHE295 4.4 89.1 1.0
CA D:CYS293 4.6 84.0 1.0
SG D:CYS306 4.7 119.4 1.0
N D:ASN296 4.8 93.6 1.0
NE2 D:HIS255 4.9 93.6 1.0
SG D:CYS299 4.9 124.8 1.0
CB D:CYS306 4.9 96.2 1.0
C D:PHE295 4.9 102.3 1.0

Reference:

P.Li, Y.Huang. Cryo-Em Structure of Escherichia Coli Dppbcdf Complex Bound to Amppnp To Be Published.
Page generated: Sun Feb 9 07:21:16 2025

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