Iron in PDB 7de4: Hybrid Cluster Protein (Hcp) From Escherichia Coli

Enzymatic activity of Hybrid Cluster Protein (Hcp) From Escherichia Coli

All present enzymatic activity of Hybrid Cluster Protein (Hcp) From Escherichia Coli:
1.7.99.1;

Protein crystallography data

The structure of Hybrid Cluster Protein (Hcp) From Escherichia Coli, PDB code: 7de4 was solved by T.Fujishiro, M.Ooi, K.Takaoka, Y.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 3.61
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 142.54, 142.54, 117.1, 90, 90, 90
R / Rfree (%) 20.3 / 27.8

Iron Binding Sites:

The binding sites of Iron atom in the Hybrid Cluster Protein (Hcp) From Escherichia Coli (pdb code 7de4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Hybrid Cluster Protein (Hcp) From Escherichia Coli, PDB code: 7de4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7de4

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Iron binding site 1 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:110.1
occ:1.00
 FE1 A:SF4601 0.0 110.1 1.0
S3 A:SF4601 2.2 104.0 1.0
S2 A:SF4601 2.3 121.5 1.0
S4 A:SF4601 2.3 148.9 1.0
SG A:CYS6 2.3 133.9 1.0
FE3 A:SF4601 2.7 136.7 1.0
FE4 A:SF4601 2.7 114.4 1.0
FE2 A:SF4601 2.8 100.0 1.0
CB A:CYS6 3.0 139.1 1.0
N A:CYS6 3.7 126.6 1.0
S1 A:SF4601 3.8 115.7 1.0
CA A:CYS6 3.9 125.1 1.0
OG1 A:THR75 4.3 117.5 1.0
CG2 A:THR75 4.4 106.0 1.0
SG A:CYS25 4.6 157.5 1.0
NE2 A:GLN5 4.7 139.9 1.0
C A:CYS6 4.7 118.6 1.0
CB A:CYS25 4.8 147.9 1.0
C A:GLN5 4.8 130.2 1.0
OG1 A:THR9 4.8 132.0 1.0
SG A:CYS3 4.8 123.1 1.0
O A:CYS6 4.9 123.8 1.0
N A:THR9 4.9 117.6 1.0
CA A:THR9 4.9 121.4 1.0
SG A:CYS18 5.0 166.9 1.0
N A:GLN5 5.0 137.1 1.0

Iron binding site 2 out of 8 in 7de4

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Iron binding site 2 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:100.0
occ:1.00
 FE2 A:SF4601 0.0 100.0 1.0
S4 A:SF4601 2.2 148.9 1.0
S3 A:SF4601 2.3 104.0 1.0
S1 A:SF4601 2.3 115.7 1.0
SG A:CYS3 2.3 123.1 1.0
FE3 A:SF4601 2.8 136.7 1.0
FE1 A:SF4601 2.8 110.1 1.0
FE4 A:SF4601 2.9 114.4 1.0
NE2 A:GLN5 3.4 139.9 1.0
S2 A:SF4601 4.0 121.5 1.0
CB A:CYS3 4.0 129.4 1.0
C A:CYS3 4.4 142.6 1.0
CD A:GLN5 4.5 144.1 1.0
O A:CYS3 4.5 130.4 1.0
CD A:LYS27 4.6 129.0 1.0
NZ A:LYS27 4.6 143.8 1.0
N A:VAL4 4.7 148.2 1.0
SG A:CYS25 4.7 157.5 1.0
OG A:SER32 4.8 172.0 1.0
CG A:GLN5 4.8 144.3 1.0
CA A:CYS3 4.8 143.4 1.0
OG1 A:THR75 4.9 117.5 1.0
N A:GLN5 4.9 137.1 1.0

Iron binding site 3 out of 8 in 7de4

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Iron binding site 3 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:136.7
occ:1.00
 FE3 A:SF4601 0.0 136.7 1.0
S1 A:SF4601 2.2 115.7 1.0
S2 A:SF4601 2.3 121.5 1.0
S4 A:SF4601 2.3 148.9 1.0
SG A:CYS25 2.3 157.5 1.0
FE4 A:SF4601 2.7 114.4 1.0
FE1 A:SF4601 2.7 110.1 1.0
FE2 A:SF4601 2.8 100.0 1.0
CB A:CYS25 3.2 147.9 1.0
S3 A:SF4601 3.8 104.0 1.0
N A:CYS25 3.8 140.3 1.0
CA A:GLY23 4.1 134.4 1.0
N A:MET24 4.1 136.1 1.0
CA A:CYS25 4.1 135.3 1.0
NZ A:LYS27 4.5 143.8 1.0
SG A:CYS6 4.6 133.9 1.0
C A:GLY23 4.6 131.7 1.0
SG A:CYS18 4.6 166.9 1.0
C A:CYS25 4.7 121.4 1.0
CG A:LYS27 4.8 126.5 1.0
SG A:CYS3 4.9 123.1 1.0
C A:MET24 4.9 140.0 1.0
CD A:LYS27 4.9 129.0 1.0
CA A:MET24 5.0 141.8 1.0

Iron binding site 4 out of 8 in 7de4

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Iron binding site 4 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:114.4
occ:1.00
 FE4 A:SF4601 0.0 114.4 1.0
S2 A:SF4601 2.2 121.5 1.0
S1 A:SF4601 2.3 115.7 1.0
S3 A:SF4601 2.3 104.0 1.0
SG A:CYS18 2.4 166.9 1.0
FE3 A:SF4601 2.7 136.7 1.0
FE1 A:SF4601 2.7 110.1 1.0
FE2 A:SF4601 2.9 100.0 1.0
CB A:CYS18 3.4 178.1 1.0
S4 A:SF4601 3.9 148.9 1.0
CG2 A:THR9 3.9 106.5 1.0
N A:MET24 4.1 136.1 1.0
CA A:THR9 4.2 121.4 1.0
SG A:CYS3 4.2 123.1 1.0
O A:CYS3 4.4 130.4 1.0
CA A:GLY23 4.4 134.4 1.0
SG A:CYS6 4.4 133.9 1.0
CB A:THR9 4.6 115.9 1.0
CA A:CYS18 4.6 171.5 1.0
N A:CYS18 4.7 178.5 1.0
C A:GLY23 4.8 131.7 1.0
OG1 A:THR9 4.8 132.0 1.0
CB A:MET24 4.9 154.1 1.0
SG A:CYS25 4.9 157.5 1.0
N A:THR9 4.9 117.6 1.0
C A:CYS3 5.0 142.6 1.0
O A:GLN8 5.0 130.9 1.0

Iron binding site 5 out of 8 in 7de4

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Iron binding site 5 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:126.6
occ:1.00
 FE5 A:FS2602 0.0 126.6 1.0
O1 A:FS2602 1.9 136.8 1.0
S6 A:FS2602 2.0 155.8 1.0
SG A:CYS433 2.1 97.4 1.0
S5 A:FS2602 2.2 144.3 1.0
FE6 A:FS2602 2.4 136.6 1.0
OE2 A:GLU273 3.0 129.5 1.0
FE8 A:FS2602 3.1 164.7 1.0
O8 A:FS2602 3.4 136.2 1.0
CB A:CYS433 3.5 105.5 1.0
FE7 A:FS2602 3.7 123.7 1.0
N A:CYS433 3.8 103.0 1.0
O9 A:FS2602 4.0 151.4 1.0
CA A:CYS433 4.1 112.0 1.0
CD A:GLU273 4.1 119.1 1.0
CD1 A:TRP297 4.4 120.0 1.0
SG A:CYS317 4.4 104.8 1.0
CA A:CSS405 4.5 117.8 1.0
CG A:GLU273 4.5 108.6 1.0
CB A:CSS405 4.5 125.4 1.0
SD A:CSS405 4.6 182.8 1.0
CE1 A:HIS249 4.7 176.5 1.0
SG A:CSS405 4.8 153.4 1.0
CB A:GLU273 4.8 101.2 1.0
NE2 A:HIS249 4.9 158.4 1.0
N A:ASP406 5.0 108.5 1.0

Iron binding site 6 out of 8 in 7de4

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Iron binding site 6 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:136.6
occ:1.00
 FE6 A:FS2602 0.0 136.6 1.0
O8 A:FS2602 1.9 136.2 1.0
S6 A:FS2602 2.1 155.8 1.0
S5 A:FS2602 2.2 144.3 1.0
SG A:CYS317 2.3 104.8 1.0
FE5 A:FS2602 2.4 126.6 1.0
FE8 A:FS2602 2.6 164.7 1.0
O1 A:FS2602 3.1 136.8 1.0
CD1 A:TRP297 3.3 120.0 1.0
SG A:CYS433 3.6 97.4 1.0
CB A:CYS317 3.7 110.4 1.0
NE1 A:TRP297 3.8 126.2 1.0
SD A:CSS405 3.9 182.8 1.0
O9 A:FS2602 4.1 151.4 1.0
OE2 A:GLU492 4.2 181.0 1.0
CG A:TRP297 4.2 117.9 1.0
CG A:GLU492 4.4 125.0 1.0
CB A:CSS405 4.6 125.4 1.0
CD1 A:PHE491 4.7 90.7 1.0
CB A:TRP297 4.8 117.5 1.0
OD1 A:ASN316 4.8 121.0 1.0
FE7 A:FS2602 4.8 123.7 1.0
CD A:GLU492 4.8 136.1 1.0
CE2 A:TRP297 4.8 120.5 1.0
CA A:CYS317 4.9 113.0 1.0
SG A:CSS405 5.0 153.4 1.0

Iron binding site 7 out of 8 in 7de4

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Iron binding site 7 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:123.7
occ:1.00
 FE7 A:FS2602 0.0 123.7 1.0
O9 A:FS2602 1.9 151.4 1.0
O1 A:FS2602 1.9 136.8 1.0
NE2 A:HIS249 1.9 158.4 1.0
OE2 A:GLU273 2.1 129.5 1.0
SG A:CYS458 2.3 135.0 1.0
CE1 A:HIS249 2.7 176.5 1.0
CD A:GLU273 2.9 119.1 1.0
CD2 A:HIS249 3.1 151.1 1.0
FE8 A:FS2602 3.2 164.7 1.0
CB A:CYS458 3.2 130.3 1.0
OE1 A:GLU273 3.3 131.5 1.0
FE5 A:FS2602 3.7 126.6 1.0
ND1 A:HIS249 3.9 164.4 1.0
O8 A:FS2602 4.0 136.2 1.0
S5 A:FS2602 4.0 144.3 1.0
CG A:GLU273 4.0 108.6 1.0
CG A:HIS249 4.1 146.7 1.0
CD A:LYS494 4.2 117.1 1.0
OE2 A:GLU492 4.3 181.0 1.0
CB A:GLU273 4.3 101.2 1.0
S6 A:FS2602 4.3 155.8 1.0
N A:CYS458 4.3 109.7 1.0
CA A:CYS458 4.4 113.3 1.0
CE A:LYS494 4.4 130.5 1.0
FE6 A:FS2602 4.8 136.6 1.0
OH A:TYR165 5.0 89.7 1.0

Iron binding site 8 out of 8 in 7de4

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Iron binding site 8 out of 8 in the Hybrid Cluster Protein (Hcp) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hybrid Cluster Protein (Hcp) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:164.7
occ:1.00
 FE8 A:FS2602 0.0 164.7 1.0
O8 A:FS2602 1.9 136.2 1.0
O9 A:FS2602 2.0 151.4 1.0
OE2 A:GLU492 2.0 181.0 1.0
S6 A:FS2602 2.1 155.8 1.0
O1 A:FS2602 2.1 136.8 1.0
SD A:CSS405 2.4 182.8 1.0
FE6 A:FS2602 2.6 136.6 1.0
FE5 A:FS2602 3.1 126.6 1.0
CD A:GLU492 3.1 136.1 1.0
FE7 A:FS2602 3.2 123.7 1.0
CG A:GLU492 3.5 125.0 1.0
S5 A:FS2602 3.5 144.3 1.0
SG A:CSS405 3.8 153.4 1.0
OE1 A:GLU492 4.1 124.6 1.0
OE2 A:GLU273 4.2 129.5 1.0
OD1 A:ASN316 4.2 121.0 1.0
SG A:CYS317 4.5 104.8 1.0
CD A:LYS494 4.5 117.1 1.0
CB A:CSS405 4.5 125.4 1.0
SG A:CYS458 4.6 135.0 1.0
CE1 A:HIS249 4.6 176.5 1.0
NE2 A:HIS249 4.7 158.4 1.0
CB A:CYS458 4.9 130.3 1.0
SG A:CYS433 4.9 97.4 1.0
CB A:GLU492 5.0 101.6 1.0

Reference:

T.Fujishiro, M.Ooi, K.Takaoka. Crystal Structure of Escherichia Coli Class II Hybrid Cluster Protein, Hcp, Reveals A [4FE-4S] Cluster at the N-Terminal Protrusion. Febs J. 2021.
ISSN: ISSN 1742-464X
PubMed: 34101368
DOI: 10.1111/FEBS.16062
Page generated: Sat Jul 10 15:19:30 2021

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