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:
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
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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
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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 Sites List in 8oz5
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 Sites List in 8oz5
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
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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
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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: Fri Jul 19 11:07:55 2024
|