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Calcium 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:

Iron (Fe) 12 atoms
Potassium (K) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8oz5

Go back to Calcium Binding Sites List in 8oz5
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca606

b:71.0
occ:1.00
 OG1 A:THR342 2.4 67.3 1.0
O A:ILE366 2.5 56.6 1.0
OE2 A:GLU346 2.7 60.9 1.0
CB A:THR342 3.4 67.3 1.0
C A:ILE366 3.6 56.6 1.0
CD A:GLU346 3.7 60.9 1.0
CE1 A:HIS365 4.2 54.1 1.0
OE1 A:GLU346 4.3 60.9 1.0
CG2 A:THR342 4.3 67.3 1.0
N A:ILE366 4.3 56.6 1.0
CA A:ILE366 4.3 56.6 1.0
CB A:ILE366 4.4 56.6 1.0
OD1 A:ASN339 4.4 70.5 1.0
C A:THR342 4.4 67.3 1.0
ND1 A:HIS365 4.4 54.1 1.0
CA A:THR342 4.5 67.3 1.0
O A:THR342 4.6 67.3 1.0
N A:PRO367 4.6 57.0 1.0
O A:ALA338 4.6 70.8 1.0
CA A:PRO367 4.7 57.0 1.0
CG A:GLU346 4.7 60.9 1.0
N A:SER343 4.8 65.0 1.0
C A:PRO367 4.8 57.0 1.0
CA A:ASN339 5.0 70.5 1.0
CG2 A:ILE366 5.0 56.6 1.0

Calcium binding site 2 out of 6 in 8oz5

Go back to Calcium Binding Sites List in 8oz5
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
B:Ca606

b:72.3
occ:1.00
 OG1 B:THR342 2.4 66.4 1.0
O B:ILE366 2.5 56.9 1.0
OE2 B:GLU346 2.7 60.2 1.0
CB B:THR342 3.4 66.4 1.0
C B:ILE366 3.6 56.9 1.0
CD B:GLU346 3.7 60.2 1.0
CE1 B:HIS365 4.2 54.1 1.0
OE1 B:GLU346 4.3 60.2 1.0
CG2 B:THR342 4.3 66.4 1.0
CA B:ILE366 4.3 56.9 1.0
N B:ILE366 4.3 56.9 1.0
CB B:ILE366 4.4 56.9 1.0
OD1 B:ASN339 4.4 70.3 1.0
C B:THR342 4.4 66.4 1.0
ND1 B:HIS365 4.4 54.1 1.0
CA B:THR342 4.5 66.4 1.0
O B:THR342 4.6 66.4 1.0
N B:PRO367 4.6 57.4 1.0
O B:ALA338 4.6 70.4 1.0
CA B:PRO367 4.7 57.4 1.0
CG B:GLU346 4.7 60.2 1.0
N B:SER343 4.8 64.8 1.0
C B:PRO367 4.8 57.4 1.0
CA B:ASN339 5.0 70.3 1.0
CG2 B:ILE366 5.0 56.9 1.0

Calcium binding site 3 out of 6 in 8oz5

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Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
C:Ca606

b:72.1
occ:1.00
 OG1 C:THR342 2.4 66.5 1.0
O C:ILE366 2.5 56.9 1.0
OE2 C:GLU346 2.7 60.2 1.0
CB C:THR342 3.4 66.5 1.0
C C:ILE366 3.6 56.9 1.0
CD C:GLU346 3.7 60.2 1.0
CE1 C:HIS365 4.2 54.0 1.0
OE1 C:GLU346 4.3 60.2 1.0
CG2 C:THR342 4.3 66.5 1.0
N C:ILE366 4.3 56.9 1.0
CA C:ILE366 4.3 56.9 1.0
CB C:ILE366 4.4 56.9 1.0
OD1 C:ASN339 4.4 70.6 1.0
C C:THR342 4.4 66.5 1.0
ND1 C:HIS365 4.4 54.0 1.0
CA C:THR342 4.5 66.5 1.0
O C:THR342 4.6 66.5 1.0
N C:PRO367 4.6 57.5 1.0
O C:ALA338 4.6 70.7 1.0
CA C:PRO367 4.7 57.5 1.0
CG C:GLU346 4.7 60.2 1.0
N C:SER343 4.8 64.9 1.0
C C:PRO367 4.8 57.5 1.0
CA C:ASN339 5.0 70.6 1.0
CG2 C:ILE366 5.0 56.9 1.0

Calcium binding site 4 out of 6 in 8oz5

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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
D:Ca606

b:71.3
occ:1.00
 OG1 D:THR342 2.4 67.1 1.0
O D:ILE366 2.5 56.3 1.0
OE2 D:GLU346 2.7 60.9 1.0
CB D:THR342 3.4 67.1 1.0
C D:ILE366 3.6 56.3 1.0
CD D:GLU346 3.7 60.9 1.0
CE1 D:HIS365 4.2 53.7 1.0
OE1 D:GLU346 4.3 60.9 1.0
CG2 D:THR342 4.3 67.1 1.0
CA D:ILE366 4.3 56.3 1.0
N D:ILE366 4.3 56.3 1.0
CB D:ILE366 4.4 56.3 1.0
OD1 D:ASN339 4.4 70.5 1.0
C D:THR342 4.4 67.1 1.0
ND1 D:HIS365 4.4 53.7 1.0
CA D:THR342 4.5 67.1 1.0
O D:THR342 4.6 67.1 1.0
N D:PRO367 4.6 56.6 1.0
O D:ALA338 4.6 70.7 1.0
CA D:PRO367 4.7 56.6 1.0
CG D:GLU346 4.7 60.9 1.0
N D:SER343 4.8 64.8 1.0
C D:PRO367 4.8 56.6 1.0
CA D:ASN339 5.0 70.5 1.0
CG2 D:ILE366 5.0 56.3 1.0

Calcium binding site 5 out of 6 in 8oz5

Go back to Calcium Binding Sites List in 8oz5
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca 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
E:Ca606

b:72.0
occ:1.00
 OG1 E:THR342 2.4 66.9 1.0
O E:ILE366 2.5 56.8 1.0
OE2 E:GLU346 2.7 60.5 1.0
CB E:THR342 3.4 66.9 1.0
C E:ILE366 3.6 56.8 1.0
CD E:GLU346 3.7 60.5 1.0
CE1 E:HIS365 4.2 54.1 1.0
OE1 E:GLU346 4.3 60.5 1.0
CG2 E:THR342 4.3 66.9 1.0
CA E:ILE366 4.3 56.8 1.0
N E:ILE366 4.3 56.8 1.0
CB E:ILE366 4.4 56.8 1.0
OD1 E:ASN339 4.4 69.8 1.0
C E:THR342 4.4 66.9 1.0
ND1 E:HIS365 4.4 54.1 1.0
CA E:THR342 4.5 66.9 1.0
O E:THR342 4.6 66.9 1.0
N E:PRO367 4.6 57.3 1.0
O E:ALA338 4.6 70.0 1.0
CA E:PRO367 4.7 57.3 1.0
CG E:GLU346 4.7 60.5 1.0
N E:SER343 4.8 64.4 1.0
C E:PRO367 4.8 57.3 1.0
CA E:ASN339 5.0 69.8 1.0
CG2 E:ILE366 5.0 56.8 1.0

Calcium binding site 6 out of 6 in 8oz5

Go back to Calcium Binding Sites List in 8oz5
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca 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
F:Ca606

b:72.7
occ:1.00
 OG1 F:THR342 2.4 66.8 1.0
O F:ILE366 2.5 56.6 1.0
OE2 F:GLU346 2.7 60.5 1.0
CB F:THR342 3.4 66.8 1.0
C F:ILE366 3.6 56.6 1.0
CD F:GLU346 3.7 60.5 1.0
CE1 F:HIS365 4.2 54.3 1.0
OE1 F:GLU346 4.3 60.5 1.0
CG2 F:THR342 4.3 66.8 1.0
N F:ILE366 4.3 56.6 1.0
CA F:ILE366 4.3 56.6 1.0
CB F:ILE366 4.4 56.6 1.0
OD1 F:ASN339 4.4 70.0 1.0
C F:THR342 4.4 66.8 1.0
ND1 F:HIS365 4.4 54.3 1.0
CA F:THR342 4.5 66.8 1.0
O F:THR342 4.6 66.8 1.0
N F:PRO367 4.6 57.6 1.0
O F:ALA338 4.6 70.3 1.0
CA F:PRO367 4.7 57.6 1.0
CG F:GLU346 4.7 60.5 1.0
N F:SER343 4.8 64.4 1.0
C F:PRO367 4.8 57.6 1.0
CA F:ASN339 5.0 70.0 1.0
CG2 F:ILE366 5.0 56.6 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: Thu Jul 10 06:25:28 2025

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