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Iron in PDB 8z1z: Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in Pre- Catalytic State

Enzymatic activity of Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in Pre- Catalytic State

All present enzymatic activity of Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in Pre- Catalytic State:
7.4.2.9;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in Pre- Catalytic State (pdb code 8z1z). 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 DPPAR383D+D436RBCDF in Pre- Catalytic State, PDB code: 8z1z:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8z1z

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Iron binding site 1 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:133.2
occ:1.00
 FE1 C:SF4401 0.0 133.2 1.0
S4 C:SF4401 2.2 139.4 1.0
S2 C:SF4401 2.3 135.1 1.0
S3 C:SF4401 2.3 139.0 1.0
SG C:CYS284 2.4 107.9 1.0
FE2 C:SF4401 2.7 114.2 1.0
FE4 C:SF4401 2.7 128.4 1.0
FE3 C:SF4401 2.7 142.7 1.0
CB C:CYS284 3.2 103.0 1.0
S1 C:SF4401 3.8 128.1 1.0
CB C:CYS297 4.4 125.2 1.0
SG C:CYS297 4.6 127.9 1.0
CA C:CYS284 4.7 107.2 1.0
CB C:LEU286 4.7 107.4 1.0
SG C:CYS315 4.8 114.8 1.0
SG C:CYS290 4.8 100.3 1.0
CB C:CYS290 4.9 98.1 1.0
N C:ASN287 5.0 99.3 1.0

Iron binding site 2 out of 8 in 8z1z

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Iron binding site 2 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:114.2
occ:1.00
 FE2 C:SF4401 0.0 114.2 1.0
S4 C:SF4401 2.2 139.4 1.0
S1 C:SF4401 2.3 128.1 1.0
S3 C:SF4401 2.3 139.0 1.0
SG C:CYS290 2.4 100.3 1.0
FE3 C:SF4401 2.7 142.7 1.0
FE1 C:SF4401 2.7 133.2 1.0
FE4 C:SF4401 2.7 128.4 1.0
CB C:CYS290 3.2 98.1 1.0
CG C:PRO248 3.8 116.0 1.0
S2 C:SF4401 3.8 135.1 1.0
CB C:PRO248 4.2 114.7 1.0
CD C:PRO248 4.5 111.8 1.0
N C:ALA293 4.6 118.6 1.0
SG C:CYS315 4.6 114.8 1.0
CA C:CYS290 4.7 98.5 1.0
C C:TYR292 4.7 115.3 1.0
CA C:ALA293 4.8 117.2 1.0
CD2 C:LEU286 4.8 106.4 1.0
CB C:TYR292 4.9 113.9 1.0
SG C:CYS297 4.9 127.9 1.0
SG C:CYS284 4.9 107.9 1.0
O C:TYR292 5.0 118.7 1.0

Iron binding site 3 out of 8 in 8z1z

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Iron binding site 3 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:142.7
occ:1.00
 FE3 C:SF4401 0.0 142.7 1.0
S1 C:SF4401 2.2 128.1 1.0
S2 C:SF4401 2.3 135.1 1.0
S4 C:SF4401 2.3 139.4 1.0
SG C:CYS297 2.4 127.9 1.0
FE2 C:SF4401 2.7 114.2 1.0
FE4 C:SF4401 2.7 128.4 1.0
FE1 C:SF4401 2.7 133.2 1.0
CB C:CYS297 3.2 125.2 1.0
S3 C:SF4401 3.9 139.0 1.0
CA C:ALA293 4.1 117.2 1.0
CA C:CYS297 4.4 124.0 1.0
O C:TYR292 4.4 118.7 1.0
N C:ALA293 4.6 118.6 1.0
N C:THR294 4.6 124.8 1.0
SG C:CYS315 4.6 114.8 1.0
SG C:CYS290 4.6 100.3 1.0
C C:TYR292 4.7 115.3 1.0
CD2 C:TYR317 4.7 109.4 1.0
CD2 C:HIS316 4.7 107.8 1.0
CB C:ALA293 4.9 118.4 1.0
SG C:CYS284 4.9 107.9 1.0
CB C:CYS284 5.0 103.0 1.0
CE2 C:TYR317 5.0 114.2 1.0
C C:ALA293 5.0 119.0 1.0

Iron binding site 4 out of 8 in 8z1z

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Iron binding site 4 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:128.4
occ:1.00
 FE4 C:SF4401 0.0 128.4 1.0
SG C:CYS315 2.2 114.8 1.0
S2 C:SF4401 2.2 135.1 1.0
S3 C:SF4401 2.3 139.0 1.0
S1 C:SF4401 2.3 128.1 1.0
FE3 C:SF4401 2.7 142.7 1.0
FE1 C:SF4401 2.7 133.2 1.0
FE2 C:SF4401 2.7 114.2 1.0
CB C:CYS315 3.5 108.6 1.0
CA C:CYS315 3.8 105.0 1.0
S4 C:SF4401 3.8 139.4 1.0
N C:HIS316 4.0 113.5 1.0
CD C:PRO248 4.3 111.8 1.0
CG C:PRO248 4.3 116.0 1.0
C C:CYS315 4.4 104.4 1.0
SG C:CYS284 4.8 107.9 1.0
NE2 C:HIS247 4.8 112.0 1.0
O C:LYS314 4.8 104.7 1.0
N C:TYR317 4.8 108.8 1.0
SG C:CYS297 4.9 127.9 1.0
SG C:CYS290 5.0 100.3 1.0

Iron binding site 5 out of 8 in 8z1z

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Iron binding site 5 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:141.2
occ:1.00
 FE1 D:SF4401 0.0 141.2 1.0
S3 D:SF4401 2.2 128.9 1.0
S4 D:SF4401 2.3 135.3 1.0
S2 D:SF4401 2.3 134.2 1.0
FE4 D:SF4401 2.7 120.5 1.0
FE3 D:SF4401 2.7 132.7 1.0
FE2 D:SF4401 2.7 117.7 1.0
SG D:CYS306 2.7 126.8 1.0
CB D:CYS306 3.8 117.7 1.0
S1 D:SF4401 3.9 116.5 1.0
CA D:ARG302 4.4 116.1 1.0
CA D:CYS306 4.5 117.3 1.0
CD2 D:PHE324 4.6 99.3 1.0
SG D:CYS323 4.6 115.1 1.0
N D:PHE303 4.7 119.9 1.0
O D:ARG301 4.7 109.3 1.0
SG D:CYS299 4.7 119.2 1.0
N D:PHE324 4.8 106.5 1.0
CB D:PHE324 4.8 104.6 1.0
N D:ARG302 4.9 112.4 1.0
SG D:CYS293 4.9 108.3 1.0
CB D:ARG302 5.0 114.9 1.0

Iron binding site 6 out of 8 in 8z1z

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Iron binding site 6 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:117.7
occ:1.00
 FE2 D:SF4401 0.0 117.7 1.0
SG D:CYS323 2.2 115.1 1.0
S1 D:SF4401 2.2 116.5 1.0
S3 D:SF4401 2.3 128.9 1.0
S4 D:SF4401 2.3 135.3 1.0
FE3 D:SF4401 2.7 132.7 1.0
FE1 D:SF4401 2.7 141.2 1.0
FE4 D:SF4401 2.7 120.5 1.0
CB D:CYS323 3.3 105.1 1.0
CA D:CYS323 3.7 102.6 1.0
N D:PHE324 3.8 106.5 1.0
S2 D:SF4401 3.8 134.2 1.0
C D:CYS323 4.3 106.5 1.0
CG D:PRO256 4.3 115.0 1.0
CD D:PRO256 4.3 116.8 1.0
N D:ALA325 4.6 98.7 1.0
SG D:CYS299 4.7 119.2 1.0
SG D:CYS293 4.9 108.3 1.0
CA D:PHE324 4.9 103.6 1.0
CB D:ALA325 5.0 111.4 1.0
NE2 D:HIS255 5.0 90.7 1.0

Iron binding site 7 out of 8 in 8z1z

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Iron binding site 7 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:132.7
occ:1.00
 FE3 D:SF4401 0.0 132.7 1.0
S4 D:SF4401 2.2 135.3 1.0
S2 D:SF4401 2.3 134.2 1.0
S1 D:SF4401 2.3 116.5 1.0
SG D:CYS293 2.6 108.3 1.0
FE4 D:SF4401 2.7 120.5 1.0
FE2 D:SF4401 2.7 117.7 1.0
FE1 D:SF4401 2.7 141.2 1.0
CB D:CYS293 3.4 109.9 1.0
S3 D:SF4401 3.8 128.9 1.0
SG D:CYS323 4.7 115.1 1.0
N D:ASN296 4.8 100.4 1.0
CB D:PHE295 4.8 115.3 1.0
CA D:CYS293 4.8 105.9 1.0
SG D:CYS306 4.8 126.8 1.0
SG D:CYS299 4.9 119.2 1.0
C D:PHE295 5.0 113.9 1.0

Iron binding site 8 out of 8 in 8z1z

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Iron binding site 8 out of 8 in the Cryo-Em Structure of Escherichia Coli DPPAR383D+D436RBCDF in 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 DPPAR383D+D436RBCDF in Pre- Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:120.5
occ:1.00
 FE4 D:SF4401 0.0 120.5 1.0
S2 D:SF4401 2.2 134.2 1.0
S3 D:SF4401 2.3 128.9 1.0
S1 D:SF4401 2.3 116.5 1.0
SG D:CYS299 2.3 119.2 1.0
FE1 D:SF4401 2.7 141.2 1.0
FE3 D:SF4401 2.7 132.7 1.0
FE2 D:SF4401 2.7 117.7 1.0
CB D:CYS299 3.2 107.0 1.0
S4 D:SF4401 3.8 135.3 1.0
CG D:PRO256 4.4 115.0 1.0
N D:ARG302 4.6 112.4 1.0
CA D:CYS299 4.6 104.2 1.0
CA D:ARG302 4.7 116.1 1.0
CD2 D:PHE295 4.7 112.4 1.0
SG D:CYS323 4.7 115.1 1.0
C D:ARG301 4.7 106.7 1.0
CB D:PRO256 4.8 107.5 1.0
SG D:CYS306 4.9 126.8 1.0
CB D:ARG302 5.0 114.9 1.0
CB D:ARG301 5.0 106.0 1.0
N D:ARG301 5.0 113.1 1.0

Reference:

P.Li, Y.Huang. Cryo-Em Structure of Escherichia Coli DPPAR383DD436RBCDF in the Catalytic Intermediate State To Be Published.
Page generated: Fri Aug 8 01:50:13 2025

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