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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

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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

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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

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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

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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

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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

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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

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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

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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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