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Calcium in PDB 8p02: Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, Benzoyl-Coa

Other elements in 8p02:

The structure of Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa (pdb code 8p02). 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 Product, Benzoyl-Coa, PDB code: 8p02:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 1 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:92.4
occ:1.00
 OG1 A:THR342 2.5 88.0 1.0
O A:ILE366 2.6 74.5 1.0
OE2 A:GLU346 2.8 79.9 1.0
CB A:THR342 3.5 88.0 1.0
C A:ILE366 3.8 74.5 1.0
CD A:GLU346 3.9 79.9 1.0
C A:THR342 4.2 88.0 1.0
OD1 A:ASN339 4.3 92.8 1.0
OE1 A:GLU346 4.4 79.9 1.0
O A:THR342 4.4 88.0 1.0
CE1 A:HIS365 4.5 72.2 1.0
CA A:THR342 4.5 88.0 1.0
O A:ALA338 4.5 93.5 1.0
CB A:ILE366 4.5 74.5 1.0
CA A:ILE366 4.5 74.5 1.0
N A:SER343 4.5 85.9 1.0
N A:ILE366 4.6 74.5 1.0
CG2 A:THR342 4.6 88.0 1.0
ND1 A:HIS365 4.7 72.2 1.0
N A:PRO367 4.7 78.0 1.0
CA A:PRO367 4.8 78.0 1.0
CA A:ASN339 4.8 92.8 1.0
OG A:SER343 4.9 85.9 1.0
C A:PRO367 4.9 78.0 1.0
CG A:GLU346 5.0 79.9 1.0
CA A:SER343 5.0 85.9 1.0

Calcium binding site 2 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 2 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:94.8
occ:1.00
 OG1 B:THR342 2.5 88.6 1.0
O B:ILE366 2.6 74.6 1.0
OE2 B:GLU346 2.8 79.7 1.0
CB B:THR342 3.5 88.6 1.0
C B:ILE366 3.8 74.6 1.0
CD B:GLU346 3.9 79.7 1.0
C B:THR342 4.2 88.6 1.0
OD1 B:ASN339 4.3 93.5 1.0
OE1 B:GLU346 4.4 79.7 1.0
O B:THR342 4.4 88.6 1.0
CE1 B:HIS365 4.5 72.8 1.0
CA B:THR342 4.5 88.6 1.0
O B:ALA338 4.5 94.4 1.0
CB B:ILE366 4.5 74.6 1.0
CA B:ILE366 4.5 74.6 1.0
N B:SER343 4.5 86.8 1.0
N B:ILE366 4.6 74.6 1.0
CG2 B:THR342 4.6 88.6 1.0
ND1 B:HIS365 4.7 72.8 1.0
N B:PRO367 4.7 77.4 1.0
CA B:PRO367 4.8 77.4 1.0
CA B:ASN339 4.8 93.5 1.0
OG B:SER343 4.9 86.8 1.0
C B:PRO367 4.9 77.4 1.0
CG B:GLU346 5.0 79.7 1.0
CA B:SER343 5.0 86.8 1.0

Calcium binding site 3 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 3 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:95.4
occ:1.00
 OG1 C:THR342 2.5 88.8 1.0
O C:ILE366 2.6 74.5 1.0
OE2 C:GLU346 2.8 79.9 1.0
CB C:THR342 3.5 88.8 1.0
C C:ILE366 3.8 74.5 1.0
CD C:GLU346 3.9 79.9 1.0
C C:THR342 4.2 88.8 1.0
OD1 C:ASN339 4.3 93.5 1.0
OE1 C:GLU346 4.4 79.9 1.0
O C:THR342 4.4 88.8 1.0
CE1 C:HIS365 4.5 72.8 1.0
CA C:THR342 4.5 88.8 1.0
O C:ALA338 4.5 94.5 1.0
CB C:ILE366 4.5 74.5 1.0
CA C:ILE366 4.5 74.5 1.0
N C:SER343 4.5 86.8 1.0
N C:ILE366 4.6 74.5 1.0
CG2 C:THR342 4.6 88.8 1.0
ND1 C:HIS365 4.7 72.8 1.0
N C:PRO367 4.7 77.3 1.0
CA C:PRO367 4.8 77.3 1.0
CA C:ASN339 4.8 93.5 1.0
OG C:SER343 4.9 86.8 1.0
C C:PRO367 4.9 77.3 1.0
CG C:GLU346 5.0 79.9 1.0
CA C:SER343 5.0 86.8 1.0

Calcium binding site 4 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 4 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca605

b:92.6
occ:1.00
 OG1 D:THR342 2.5 88.0 1.0
O D:ILE366 2.6 74.2 1.0
OE2 D:GLU346 2.8 79.8 1.0
CB D:THR342 3.5 88.0 1.0
C D:ILE366 3.8 74.2 1.0
CD D:GLU346 3.9 79.8 1.0
C D:THR342 4.2 88.0 1.0
OD1 D:ASN339 4.3 92.9 1.0
OE1 D:GLU346 4.4 79.8 1.0
O D:THR342 4.4 88.0 1.0
CE1 D:HIS365 4.5 71.9 1.0
CA D:THR342 4.5 88.0 1.0
O D:ALA338 4.5 93.5 1.0
CB D:ILE366 4.5 74.2 1.0
CA D:ILE366 4.5 74.2 1.0
N D:SER343 4.5 85.8 1.0
N D:ILE366 4.6 74.2 1.0
CG2 D:THR342 4.6 88.0 1.0
ND1 D:HIS365 4.7 71.9 1.0
N D:PRO367 4.7 77.8 1.0
CA D:PRO367 4.8 77.8 1.0
CA D:ASN339 4.8 92.9 1.0
OG D:SER343 4.9 85.8 1.0
C D:PRO367 4.9 77.8 1.0
CG D:GLU346 5.0 79.8 1.0
CA D:SER343 5.0 85.8 1.0

Calcium binding site 5 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 5 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca605

b:93.0
occ:1.00
 OG1 E:THR342 2.5 87.8 1.0
O E:ILE366 2.6 73.5 1.0
OE2 E:GLU346 2.8 79.5 1.0
CB E:THR342 3.5 87.8 1.0
C E:ILE366 3.8 73.5 1.0
CD E:GLU346 3.9 79.5 1.0
C E:THR342 4.2 87.8 1.0
OD1 E:ASN339 4.3 92.8 1.0
OE1 E:GLU346 4.4 79.5 1.0
O E:THR342 4.4 87.8 1.0
CE1 E:HIS365 4.5 72.0 1.0
CA E:THR342 4.5 87.8 1.0
O E:ALA338 4.5 93.4 1.0
CB E:ILE366 4.5 73.5 1.0
CA E:ILE366 4.5 73.5 1.0
N E:SER343 4.5 85.7 1.0
N E:ILE366 4.6 73.5 1.0
CG2 E:THR342 4.6 87.8 1.0
ND1 E:HIS365 4.7 72.0 1.0
N E:PRO367 4.7 77.0 1.0
CA E:PRO367 4.8 77.0 1.0
CA E:ASN339 4.8 92.8 1.0
OG E:SER343 4.9 85.7 1.0
C E:PRO367 4.9 77.0 1.0
CG E:GLU346 5.0 79.5 1.0
CA E:SER343 5.0 85.7 1.0

Calcium binding site 6 out of 6 in 8p02

Go back to Calcium Binding Sites List in 8p02
Calcium binding site 6 out of 6 in the Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, 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 Product, Benzoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca605

b:92.9
occ:1.00
 OG1 F:THR342 2.5 88.0 1.0
O F:ILE366 2.6 73.5 1.0
OE2 F:GLU346 2.8 79.6 1.0
CB F:THR342 3.5 88.0 1.0
C F:ILE366 3.8 73.5 1.0
CD F:GLU346 3.9 79.6 1.0
C F:THR342 4.2 88.0 1.0
OD1 F:ASN339 4.3 92.8 1.0
OE1 F:GLU346 4.4 79.6 1.0
O F:THR342 4.4 88.0 1.0
CE1 F:HIS365 4.5 71.9 1.0
CA F:THR342 4.5 88.0 1.0
O F:ALA338 4.5 93.1 1.0
CB F:ILE366 4.5 73.5 1.0
CA F:ILE366 4.5 73.5 1.0
N F:SER343 4.5 86.1 1.0
N F:ILE366 4.6 73.5 1.0
CG2 F:THR342 4.6 88.0 1.0
ND1 F:HIS365 4.7 71.9 1.0
N F:PRO367 4.7 76.9 1.0
CA F:PRO367 4.8 76.9 1.0
CA F:ASN339 4.8 92.8 1.0
OG F:SER343 4.9 86.1 1.0
C F:PRO367 4.9 76.9 1.0
CG F:GLU346 5.0 79.6 1.0
CA F:SER343 5.0 86.1 1.0

Reference:

K.Kayastha, U.Ermler. Cryo-Em Structure of Phthaloyl-Coa Decarboxylase (Pcd) Bound with Product, Benzoyl-Coa To Be Published.
Page generated: Fri Jul 19 11:07:54 2024

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