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Iron in PDB 8oz5: Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa

Other elements in 8oz5:

The structure of Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Potassium (K) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa (pdb code 8oz5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa, PDB code: 8oz5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 8oz5

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Iron binding site 1 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:75.3
occ:1.00
 O9 A:BYN601 1.9 70.5 1.0
OE1 A:GLU235 1.9 66.7 1.0
ND1 A:HIS189 2.1 64.0 1.0
ND1 A:HIS166 2.1 65.2 1.0
CD A:GLU235 2.9 66.7 1.0
CE1 A:HIS166 2.9 65.2 1.0
CG A:HIS189 3.0 64.0 1.0
P1 A:BYN601 3.1 70.5 1.0
CE1 A:HIS189 3.1 64.0 1.0
CG A:HIS166 3.2 65.2 1.0
O8 A:BYN601 3.2 70.5 1.0
OE2 A:GLU235 3.2 66.7 1.0
CB A:HIS189 3.2 64.0 1.0
CB A:HIS166 3.6 65.2 1.0
O10 A:BYN601 3.6 70.5 1.0
K A:K605 4.0 64.2 1.0
O A:ILE167 4.1 64.5 1.0
CA A:HIS166 4.1 65.2 1.0
NE2 A:HIS166 4.1 65.2 1.0
CD2 A:HIS189 4.2 64.0 1.0
CG A:GLU235 4.2 66.7 1.0
NE2 A:HIS189 4.2 64.0 1.0
CD2 A:HIS166 4.2 65.2 1.0
N A:ILE167 4.2 64.5 1.0
O A:HOH718 4.2 66.6 1.0
O7 A:BYN601 4.4 70.5 1.0
CZ A:PHE161 4.5 68.2 1.0
C A:HIS166 4.6 65.2 1.0
CA A:HIS189 4.7 64.0 1.0
C A:ILE167 4.7 64.5 1.0
O A:HOH711 4.9 68.9 1.0

Iron binding site 2 out of 12 in 8oz5

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Iron binding site 2 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:74.5
occ:1.00
 O A:ARG430 2.7 57.3 1.0
O A:ASP476 2.8 56.5 1.0
O A:THR478 2.8 55.9 1.0
OD2 A:ASP436 2.8 60.6 1.0
O A:HOH736 3.4 66.7 1.0
O A:HOH734 3.4 62.8 1.0
CG A:ASP436 3.5 60.6 1.0
N A:THR478 3.8 55.9 1.0
OD1 A:ASP436 3.8 60.6 1.0
C A:ASP476 3.8 56.5 1.0
C A:THR478 3.9 55.9 1.0
C A:ARG430 3.9 57.3 1.0
C A:ALA477 4.1 53.9 1.0
CA A:ALA477 4.1 53.9 1.0
CG A:ASP476 4.3 56.5 1.0
OD2 A:ASP476 4.4 56.5 1.0
N A:ALA477 4.4 53.9 1.0
OD1 A:ASP476 4.4 56.5 1.0
CA A:THR478 4.4 55.9 1.0
CB A:ASP436 4.4 60.6 1.0
OG1 A:THR478 4.6 55.9 1.0
CA A:VAL431 4.6 57.8 1.0
N A:VAL431 4.7 57.8 1.0
CB A:ASP476 4.8 56.5 1.0
N A:ASN432 4.9 61.6 1.0
CB A:ARG430 4.9 57.3 1.0
O A:ALA477 4.9 53.9 1.0
CA A:ARG430 4.9 57.3 1.0
CA A:ASP476 5.0 56.5 1.0

Iron binding site 3 out of 12 in 8oz5

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Iron binding site 3 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe603

b:75.5
occ:1.00
 O9 B:BYN601 1.9 70.2 1.0
OE1 B:GLU235 1.9 66.6 1.0
ND1 B:HIS189 2.1 63.3 1.0
ND1 B:HIS166 2.1 64.6 1.0
CD B:GLU235 2.9 66.6 1.0
CE1 B:HIS166 2.9 64.6 1.0
CG B:HIS189 3.0 63.3 1.0
P1 B:BYN601 3.1 70.2 1.0
CE1 B:HIS189 3.1 63.3 1.0
CG B:HIS166 3.2 64.6 1.0
O8 B:BYN601 3.2 70.2 1.0
OE2 B:GLU235 3.2 66.6 1.0
CB B:HIS189 3.2 63.3 1.0
CB B:HIS166 3.6 64.6 1.0
O10 B:BYN601 3.6 70.2 1.0
K B:K605 4.0 64.1 1.0
O B:ILE167 4.1 65.0 1.0
CA B:HIS166 4.1 64.6 1.0
NE2 B:HIS166 4.1 64.6 1.0
CD2 B:HIS189 4.2 63.3 1.0
CG B:GLU235 4.2 66.6 1.0
NE2 B:HIS189 4.2 63.3 1.0
CD2 B:HIS166 4.2 64.6 1.0
N B:ILE167 4.2 65.0 1.0
O7 B:BYN601 4.4 70.2 1.0
CZ B:PHE161 4.5 67.7 1.0
C B:HIS166 4.6 64.6 1.0
CA B:HIS189 4.7 63.3 1.0
C B:ILE167 4.7 65.0 1.0
O B:HOH706 4.9 69.0 1.0

Iron binding site 4 out of 12 in 8oz5

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Iron binding site 4 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:73.4
occ:1.00
 O B:ARG430 2.7 56.9 1.0
O B:ASP476 2.8 56.8 1.0
O B:THR478 2.8 56.3 1.0
OD2 B:ASP436 2.8 61.1 1.0
CG B:ASP436 3.5 61.1 1.0
O B:HOH712 3.5 64.0 1.0
N B:THR478 3.8 56.3 1.0
OD1 B:ASP436 3.8 61.1 1.0
C B:ASP476 3.8 56.8 1.0
C B:THR478 3.9 56.3 1.0
C B:ARG430 3.9 56.9 1.0
C B:ALA477 4.1 54.0 1.0
CA B:ALA477 4.1 54.0 1.0
CG B:ASP476 4.3 56.8 1.0
OD2 B:ASP476 4.4 56.8 1.0
N B:ALA477 4.4 54.0 1.0
OD1 B:ASP476 4.4 56.8 1.0
CA B:THR478 4.4 56.3 1.0
CB B:ASP436 4.4 61.1 1.0
OG1 B:THR478 4.6 56.3 1.0
CA B:VAL431 4.6 57.2 1.0
N B:VAL431 4.7 57.2 1.0
CB B:ASP476 4.8 56.8 1.0
N B:ASN432 4.9 61.6 1.0
CB B:ARG430 4.9 56.9 1.0
O B:ALA477 4.9 54.0 1.0
CA B:ARG430 4.9 56.9 1.0
CA B:ASP476 5.0 56.8 1.0

Iron binding site 5 out of 12 in 8oz5

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Iron binding site 5 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe603

b:75.1
occ:1.00
 O9 C:BYN601 1.9 70.4 1.0
OE1 C:GLU235 1.9 66.6 1.0
ND1 C:HIS189 2.1 63.0 1.0
ND1 C:HIS166 2.1 64.7 1.0
CD C:GLU235 2.9 66.6 1.0
CE1 C:HIS166 2.9 64.7 1.0
CG C:HIS189 3.0 63.0 1.0
P1 C:BYN601 3.1 70.4 1.0
CE1 C:HIS189 3.1 63.0 1.0
CG C:HIS166 3.2 64.7 1.0
O8 C:BYN601 3.2 70.4 1.0
OE2 C:GLU235 3.2 66.6 1.0
CB C:HIS189 3.2 63.0 1.0
CB C:HIS166 3.6 64.7 1.0
O10 C:BYN601 3.6 70.4 1.0
K C:K605 4.0 64.6 1.0
O C:ILE167 4.1 65.0 1.0
CA C:HIS166 4.1 64.7 1.0
NE2 C:HIS166 4.1 64.7 1.0
CD2 C:HIS189 4.2 63.0 1.0
CG C:GLU235 4.2 66.6 1.0
NE2 C:HIS189 4.2 63.0 1.0
CD2 C:HIS166 4.2 64.7 1.0
N C:ILE167 4.2 65.0 1.0
O7 C:BYN601 4.4 70.4 1.0
CZ C:PHE161 4.5 67.8 1.0
C C:HIS166 4.6 64.7 1.0
CA C:HIS189 4.7 63.0 1.0
C C:ILE167 4.7 65.0 1.0
O C:HOH707 4.9 69.2 1.0

Iron binding site 6 out of 12 in 8oz5

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Iron binding site 6 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe604

b:73.3
occ:1.00
 O C:ARG430 2.7 57.3 1.0
O C:ASP476 2.8 57.0 1.0
O C:THR478 2.8 56.3 1.0
OD2 C:ASP436 2.8 61.3 1.0
O C:HOH716 3.4 67.0 1.0
CG C:ASP436 3.5 61.3 1.0
O C:HOH713 3.5 63.5 1.0
N C:THR478 3.8 56.3 1.0
OD1 C:ASP436 3.8 61.3 1.0
C C:ASP476 3.8 57.0 1.0
C C:THR478 3.9 56.3 1.0
C C:ARG430 3.9 57.3 1.0
C C:ALA477 4.1 54.4 1.0
CA C:ALA477 4.1 54.4 1.0
CG C:ASP476 4.3 57.0 1.0
OD2 C:ASP476 4.4 57.0 1.0
N C:ALA477 4.4 54.4 1.0
OD1 C:ASP476 4.4 57.0 1.0
CA C:THR478 4.4 56.3 1.0
CB C:ASP436 4.4 61.3 1.0
OG1 C:THR478 4.6 56.3 1.0
CA C:VAL431 4.6 57.7 1.0
N C:VAL431 4.7 57.7 1.0
CB C:ASP476 4.8 57.0 1.0
N C:ASN432 4.9 62.0 1.0
CB C:ARG430 4.9 57.3 1.0
O C:ALA477 4.9 54.4 1.0
CA C:ARG430 4.9 57.3 1.0
CA C:ASP476 5.0 57.0 1.0

Iron binding site 7 out of 12 in 8oz5

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Iron binding site 7 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe603

b:75.2
occ:1.00
 O9 D:BYN601 1.9 70.4 1.0
OE1 D:GLU235 1.9 66.3 1.0
ND1 D:HIS189 2.1 63.3 1.0
ND1 D:HIS166 2.1 64.9 1.0
CD D:GLU235 2.9 66.3 1.0
CE1 D:HIS166 2.9 64.9 1.0
CG D:HIS189 3.0 63.3 1.0
P1 D:BYN601 3.1 70.4 1.0
CE1 D:HIS189 3.1 63.3 1.0
CG D:HIS166 3.2 64.9 1.0
O8 D:BYN601 3.2 70.4 1.0
OE2 D:GLU235 3.2 66.3 1.0
CB D:HIS189 3.2 63.3 1.0
CB D:HIS166 3.6 64.9 1.0
O10 D:BYN601 3.6 70.4 1.0
K D:K605 4.0 64.3 1.0
O D:ILE167 4.1 64.2 1.0
CA D:HIS166 4.1 64.9 1.0
NE2 D:HIS166 4.1 64.9 1.0
CD2 D:HIS189 4.2 63.3 1.0
CG D:GLU235 4.2 66.3 1.0
NE2 D:HIS189 4.2 63.3 1.0
N D:ILE167 4.2 64.2 1.0
CD2 D:HIS166 4.2 64.9 1.0
O7 D:BYN601 4.4 70.4 1.0
CZ D:PHE161 4.5 67.8 1.0
C D:HIS166 4.6 64.9 1.0
CA D:HIS189 4.7 63.3 1.0
C D:ILE167 4.7 64.2 1.0
O D:HOH705 4.9 68.5 1.0

Iron binding site 8 out of 12 in 8oz5

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Iron binding site 8 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


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 Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe604

b:74.7
occ:1.00
 O D:ARG430 2.7 56.8 1.0
O D:ASP476 2.8 56.8 1.0
O D:THR478 2.8 56.1 1.0
OD2 D:ASP436 2.8 60.5 1.0
O D:HOH712 3.4 62.9 1.0
CG D:ASP436 3.5 60.5 1.0
N D:THR478 3.8 56.1 1.0
OD1 D:ASP436 3.8 60.5 1.0
C D:ASP476 3.8 56.8 1.0
C D:THR478 3.9 56.1 1.0
C D:ARG430 3.9 56.8 1.0
C D:ALA477 4.1 53.9 1.0
CA D:ALA477 4.1 53.9 1.0
CG D:ASP476 4.3 56.8 1.0
OD2 D:ASP476 4.4 56.8 1.0
N D:ALA477 4.4 53.9 1.0
OD1 D:ASP476 4.4 56.8 1.0
CA D:THR478 4.4 56.1 1.0
CB D:ASP436 4.4 60.5 1.0
OG1 D:THR478 4.6 56.1 1.0
CA D:VAL431 4.6 57.6 1.0
N D:VAL431 4.7 57.6 1.0
CB D:ASP476 4.8 56.8 1.0
N D:ASN432 4.9 61.3 1.0
CB D:ARG430 4.9 56.8 1.0
O D:ALA477 4.9 53.9 1.0
CA D:ARG430 4.9 56.8 1.0
CA D:ASP476 5.0 56.8 1.0

Iron binding site 9 out of 12 in 8oz5

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Iron binding site 9 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe603

b:75.5
occ:1.00
 O9 E:BYN601 1.9 69.8 1.0
OE1 E:GLU235 1.9 66.4 1.0
ND1 E:HIS189 2.1 63.6 1.0
ND1 E:HIS166 2.1 64.3 1.0
CD E:GLU235 2.9 66.4 1.0
CE1 E:HIS166 2.9 64.3 1.0
CG E:HIS189 3.0 63.6 1.0
P1 E:BYN601 3.1 69.8 1.0
CE1 E:HIS189 3.1 63.6 1.0
CG E:HIS166 3.2 64.3 1.0
O8 E:BYN601 3.2 69.8 1.0
OE2 E:GLU235 3.2 66.4 1.0
CB E:HIS189 3.2 63.6 1.0
CB E:HIS166 3.6 64.3 1.0
O10 E:BYN601 3.6 69.8 1.0
K E:K605 4.0 63.0 1.0
O E:ILE167 4.1 63.8 1.0
CA E:HIS166 4.1 64.3 1.0
NE2 E:HIS166 4.1 64.3 1.0
CD2 E:HIS189 4.2 63.6 1.0
CG E:GLU235 4.2 66.4 1.0
NE2 E:HIS189 4.2 63.6 1.0
CD2 E:HIS166 4.2 64.3 1.0
N E:ILE167 4.2 63.8 1.0
O7 E:BYN601 4.4 69.8 1.0
CZ E:PHE161 4.5 67.5 1.0
C E:HIS166 4.6 64.3 1.0
CA E:HIS189 4.7 63.6 1.0
C E:ILE167 4.7 63.8 1.0
O E:HOH705 4.9 68.1 1.0

Iron binding site 10 out of 12 in 8oz5

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Iron binding site 10 out of 12 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe604

b:73.8
occ:1.00
 O E:ARG430 2.7 57.5 1.0
O E:ASP476 2.8 57.2 1.0
O E:THR478 2.8 56.5 1.0
OD2 E:ASP436 2.8 61.1 1.0
O E:HOH712 3.4 66.5 1.0
CG E:ASP436 3.5 61.1 1.0
O E:HOH710 3.6 62.7 1.0
N E:THR478 3.8 56.5 1.0
OD1 E:ASP436 3.8 61.1 1.0
C E:ASP476 3.8 57.2 1.0
C E:THR478 3.9 56.5 1.0
C E:ARG430 3.9 57.5 1.0
C E:ALA477 4.1 54.5 1.0
CA E:ALA477 4.1 54.5 1.0
CG E:ASP476 4.3 57.2 1.0
OD2 E:ASP476 4.4 57.2 1.0
N E:ALA477 4.4 54.5 1.0
OD1 E:ASP476 4.4 57.2 1.0
CA E:THR478 4.4 56.5 1.0
CB E:ASP436 4.4 61.1 1.0
OG1 E:THR478 4.6 56.5 1.0
CA E:VAL431 4.6 57.8 1.0
N E:VAL431 4.7 57.8 1.0
CB E:ASP476 4.8 57.2 1.0
N E:ASN432 4.9 61.4 1.0
CB E:ARG430 4.9 57.5 1.0
O E:ALA477 4.9 54.5 1.0
CA E:ARG430 4.9 57.5 1.0
CA E:ASP476 5.0 57.2 1.0

Reference:

K.Kayastha, U.Ermler. Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Substrate Analog/Inhibitor, 2-Cn-Benzoyl-Coa To Be Published.
Page generated: Sat Aug 10 08:39:54 2024

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