Potassium in PDB 8pmk: Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Other elements in 8pmk:
The structure of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
(pdb code 8pmk). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound, PDB code: 8pmk:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 1 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K605
b:103.1
occ:1.00
|
O
|
A:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
A:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
A:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
A:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
A:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
A:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
A:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
A:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
A:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
A:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
A:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
A:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
A:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
A:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
A:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
A:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
A:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
A:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
A:FE602
|
4.1
|
120.9
|
1.0
|
N
|
A:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
A:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
A:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
A:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
A:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
A:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
A:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
A:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
A:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
A:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
A:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
A:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
A:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
A:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
A:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
A:GLY221
|
5.0
|
90.3
|
1.0
|
|
Potassium binding site 2 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 2 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K605
b:103.1
occ:1.00
|
O
|
B:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
B:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
B:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
B:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
B:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
B:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
B:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
B:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
B:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
B:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
B:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
B:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
B:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
B:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
B:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
B:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
B:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
B:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
B:FE602
|
4.1
|
120.9
|
1.0
|
N
|
B:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
B:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
B:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
B:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
B:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
B:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
B:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
B:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
B:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
B:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
B:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
B:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
B:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
B:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
B:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
B:GLY221
|
5.0
|
90.3
|
1.0
|
|
Potassium binding site 3 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 3 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K605
b:103.1
occ:1.00
|
O
|
C:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
C:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
C:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
C:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
C:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
C:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
C:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
C:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
C:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
C:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
C:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
C:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
C:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
C:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
C:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
C:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
C:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
C:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
C:FE602
|
4.1
|
120.9
|
1.0
|
N
|
C:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
C:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
C:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
C:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
C:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
C:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
C:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
C:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
C:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
C:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
C:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
C:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
C:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
C:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
C:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
C:GLY221
|
5.0
|
90.3
|
1.0
|
|
Potassium binding site 4 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 4 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K605
b:103.1
occ:1.00
|
O
|
D:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
D:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
D:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
D:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
D:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
D:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
D:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
D:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
D:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
D:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
D:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
D:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
D:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
D:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
D:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
D:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
D:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
D:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
D:FE602
|
4.1
|
120.9
|
1.0
|
N
|
D:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
D:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
D:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
D:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
D:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
D:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
D:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
D:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
D:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
D:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
D:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
D:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
D:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
D:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
D:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
D:GLY221
|
5.0
|
90.3
|
1.0
|
|
Potassium binding site 5 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 5 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K605
b:103.1
occ:1.00
|
O
|
E:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
E:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
E:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
E:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
E:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
E:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
E:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
E:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
E:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
E:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
E:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
E:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
E:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
E:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
E:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
E:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
E:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
E:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
E:FE602
|
4.1
|
120.9
|
1.0
|
N
|
E:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
E:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
E:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
E:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
E:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
E:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
E:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
E:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
E:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
E:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
E:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
E:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
E:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
E:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
E:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
E:GLY221
|
5.0
|
90.3
|
1.0
|
|
Potassium binding site 6 out
of 6 in 8pmk
Go back to
Potassium Binding Sites List in 8pmk
Potassium binding site 6 out
of 6 in the Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Cryo-Em Structure of Active Phthaloyl-Coa Decarboxylase (Pcd) Complex with Prfmn Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K605
b:103.1
occ:1.00
|
O
|
F:ALA222
|
2.4
|
94.5
|
1.0
|
O9
|
F:BYN601
|
2.6
|
103.2
|
1.0
|
O
|
F:ALA220
|
2.6
|
91.3
|
1.0
|
O
|
F:ILE167
|
2.6
|
83.4
|
1.0
|
OE2
|
F:GLU235
|
2.7
|
99.0
|
1.0
|
O
|
F:VAL219
|
2.8
|
88.6
|
1.0
|
C
|
F:ALA220
|
3.3
|
81.9
|
1.0
|
C
|
F:ALA222
|
3.4
|
88.6
|
1.0
|
O7
|
F:BYN601
|
3.5
|
94.0
|
1.0
|
N
|
F:ALA222
|
3.5
|
87.2
|
1.0
|
P1
|
F:BYN601
|
3.6
|
90.5
|
1.0
|
CA
|
F:ALA220
|
3.8
|
70.0
|
1.0
|
C
|
F:ILE167
|
3.8
|
79.5
|
1.0
|
CA
|
F:ALA222
|
3.8
|
83.9
|
1.0
|
C
|
F:VAL219
|
3.9
|
82.9
|
1.0
|
CA
|
F:GLY168
|
4.0
|
78.4
|
1.0
|
CD
|
F:GLU235
|
4.0
|
95.6
|
1.0
|
CB
|
F:ALA222
|
4.0
|
81.3
|
1.0
|
FE
|
F:FE602
|
4.1
|
120.9
|
1.0
|
N
|
F:GLY221
|
4.2
|
77.5
|
1.0
|
O10
|
F:BYN601
|
4.2
|
80.2
|
1.0
|
C
|
F:GLY221
|
4.2
|
86.2
|
1.0
|
N
|
F:ALA220
|
4.3
|
79.5
|
1.0
|
N
|
F:GLY168
|
4.4
|
82.3
|
1.0
|
C20
|
F:BYN601
|
4.5
|
90.3
|
1.0
|
N
|
F:GLY223
|
4.5
|
85.0
|
1.0
|
CA
|
F:GLY221
|
4.6
|
79.1
|
1.0
|
OE1
|
F:GLU235
|
4.8
|
96.3
|
1.0
|
O8
|
F:BYN601
|
4.8
|
93.3
|
1.0
|
C22
|
F:BYN601
|
4.8
|
91.5
|
1.0
|
CE1
|
F:HIS166
|
4.8
|
79.3
|
1.0
|
CG
|
F:GLU235
|
4.9
|
86.9
|
1.0
|
ND1
|
F:HIS166
|
4.9
|
77.5
|
1.0
|
CA
|
F:GLY223
|
5.0
|
89.1
|
1.0
|
O
|
F:GLY221
|
5.0
|
90.3
|
1.0
|
|
Reference:
K.Kayastha,
U.Ermler.
Active Pcd Complex with Prfmn Bound To Be Published.
Page generated: Tue Aug 13 00:25:08 2024
|