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:
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
|