Potassium in PDB 4ki8: Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Protein crystallography data
The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8
was solved by
X.Fei,
D.Yang,
N.Laronde-Leblanc,
G.H.Lorimer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.17 /
2.72
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
235.222,
141.655,
156.693,
90.00,
113.84,
90.00
|
R / Rfree (%)
|
16.6 /
20.3
|
Other elements in 4ki8:
The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
(pdb code 4ki8). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the
Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Potassium binding site 1 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 1 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:58.1
occ:1.00
|
O1A
|
A:ADP601
|
2.5
|
60.9
|
1.0
|
O
|
A:THR30
|
2.6
|
35.3
|
1.0
|
O
|
A:HOH768
|
2.6
|
47.4
|
1.0
|
O
|
A:HOH770
|
2.6
|
61.2
|
1.0
|
O
|
A:LYS51
|
2.7
|
31.9
|
1.0
|
O
|
A:HOH720
|
2.8
|
95.1
|
1.0
|
O
|
A:HOH742
|
2.8
|
91.5
|
1.0
|
PA
|
A:ADP601
|
3.7
|
51.8
|
1.0
|
C
|
A:LYS51
|
3.8
|
32.1
|
1.0
|
C
|
A:THR30
|
3.8
|
37.1
|
1.0
|
O
|
A:HOH771
|
3.9
|
66.6
|
1.0
|
O
|
A:GLY32
|
4.1
|
42.1
|
1.0
|
O2A
|
A:ADP601
|
4.1
|
39.7
|
1.0
|
ND2
|
A:ASN153
|
4.2
|
86.2
|
1.0
|
N
|
A:GLY32
|
4.2
|
35.0
|
1.0
|
CB
|
A:LYS51
|
4.3
|
30.8
|
1.0
|
OD1
|
A:ASN153
|
4.4
|
87.0
|
1.0
|
CB
|
A:THR30
|
4.5
|
32.8
|
1.0
|
OG1
|
A:THR30
|
4.6
|
31.4
|
1.0
|
CA
|
A:LYS51
|
4.6
|
38.1
|
1.0
|
CA
|
A:LEU31
|
4.6
|
27.4
|
1.0
|
N
|
A:ASP52
|
4.6
|
27.8
|
1.0
|
CA
|
A:ASP52
|
4.6
|
25.7
|
1.0
|
N
|
A:LEU31
|
4.6
|
41.5
|
1.0
|
CA
|
A:THR30
|
4.7
|
23.0
|
1.0
|
CG
|
A:ASN153
|
4.7
|
76.9
|
1.0
|
C
|
A:LEU31
|
4.7
|
34.5
|
1.0
|
O5'
|
A:ADP601
|
4.8
|
55.7
|
1.0
|
O3A
|
A:ADP601
|
4.8
|
75.2
|
1.0
|
C
|
A:GLY32
|
4.9
|
39.2
|
1.0
|
N
|
A:GLY53
|
4.9
|
37.5
|
1.0
|
|
Potassium binding site 2 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 2 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K603
b:62.2
occ:1.00
|
O1A
|
B:ADP601
|
2.5
|
62.7
|
1.0
|
O
|
B:LYS51
|
2.6
|
43.4
|
1.0
|
O
|
B:HOH782
|
2.7
|
48.5
|
1.0
|
O
|
B:HOH783
|
2.7
|
60.5
|
0.9
|
O
|
B:THR30
|
2.7
|
35.3
|
1.0
|
O
|
B:HOH784
|
3.1
|
62.0
|
1.0
|
PA
|
B:ADP601
|
3.5
|
43.0
|
1.0
|
C
|
B:LYS51
|
3.7
|
32.0
|
1.0
|
O
|
B:HOH758
|
3.8
|
51.2
|
1.0
|
C
|
B:THR30
|
3.9
|
37.7
|
1.0
|
O2A
|
B:ADP601
|
3.9
|
30.3
|
1.0
|
O3A
|
B:ADP601
|
4.2
|
0.6
|
1.0
|
O
|
B:HOH761
|
4.2
|
63.4
|
1.0
|
OG1
|
B:THR30
|
4.2
|
32.5
|
1.0
|
CA
|
B:ASP52
|
4.2
|
27.2
|
1.0
|
CB
|
B:THR30
|
4.3
|
36.9
|
1.0
|
N
|
B:ASP52
|
4.4
|
27.8
|
1.0
|
ND2
|
B:ASN153
|
4.4
|
67.3
|
1.0
|
N
|
B:GLY53
|
4.4
|
29.1
|
1.0
|
CB
|
B:LYS51
|
4.6
|
29.2
|
1.0
|
N
|
B:GLY32
|
4.6
|
35.8
|
1.0
|
O
|
B:GLY32
|
4.6
|
38.2
|
1.0
|
CA
|
B:THR30
|
4.7
|
31.8
|
1.0
|
CA
|
B:LYS51
|
4.7
|
28.5
|
1.0
|
N
|
B:LEU31
|
4.8
|
38.5
|
1.0
|
CA
|
B:LEU31
|
4.8
|
23.6
|
1.0
|
O5'
|
B:ADP601
|
4.9
|
46.3
|
1.0
|
O
|
B:HOH728
|
4.9
|
66.5
|
1.0
|
C
|
B:ASP52
|
4.9
|
33.5
|
1.0
|
|
Potassium binding site 3 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 3 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K603
b:79.3
occ:1.00
|
O
|
C:THR30
|
2.7
|
37.1
|
1.0
|
O
|
C:HOH766
|
2.7
|
54.8
|
1.0
|
O
|
C:HOH721
|
2.9
|
42.8
|
0.6
|
O2A
|
C:ADP601
|
2.9
|
60.6
|
1.0
|
O
|
C:LYS51
|
3.0
|
48.2
|
1.0
|
O
|
C:HOH767
|
3.1
|
68.2
|
1.0
|
O
|
C:GLY32
|
3.6
|
55.4
|
1.0
|
C
|
C:THR30
|
3.9
|
31.6
|
1.0
|
PA
|
C:ADP601
|
4.1
|
48.9
|
1.0
|
C
|
C:LYS51
|
4.1
|
36.1
|
1.0
|
O1A
|
C:ADP601
|
4.4
|
43.7
|
1.0
|
CB
|
C:LYS51
|
4.4
|
32.0
|
1.0
|
N
|
C:GLY32
|
4.4
|
34.1
|
1.0
|
CB
|
C:THR30
|
4.5
|
31.9
|
1.0
|
OD1
|
C:ASN153
|
4.6
|
88.3
|
1.0
|
C
|
C:GLY32
|
4.6
|
40.2
|
1.0
|
OG1
|
C:THR30
|
4.7
|
36.4
|
1.0
|
CA
|
C:THR30
|
4.7
|
29.1
|
1.0
|
N
|
C:LEU31
|
4.8
|
32.3
|
1.0
|
CA
|
C:LEU31
|
4.8
|
27.5
|
1.0
|
C
|
C:LEU31
|
4.8
|
34.9
|
1.0
|
CA
|
C:LYS51
|
4.9
|
38.9
|
1.0
|
CG
|
C:ASN153
|
5.0
|
80.4
|
1.0
|
O5'
|
C:ADP601
|
5.0
|
64.6
|
1.0
|
N
|
C:ASP52
|
5.0
|
30.3
|
1.0
|
|
Potassium binding site 4 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 4 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K603
b:64.8
occ:1.00
|
O
|
D:HOH767
|
2.5
|
52.2
|
0.9
|
O1A
|
D:ADP601
|
2.5
|
70.5
|
1.0
|
O
|
D:HOH766
|
2.6
|
54.6
|
1.0
|
O
|
D:LYS51
|
2.6
|
46.5
|
1.0
|
O
|
D:HOH768
|
2.6
|
66.3
|
1.0
|
O
|
D:THR30
|
2.7
|
40.2
|
1.0
|
O
|
D:HOH783
|
3.1
|
69.2
|
0.9
|
ND2
|
D:ASN153
|
3.4
|
0.4
|
1.0
|
O
|
D:HOH716
|
3.4
|
74.9
|
1.0
|
C
|
D:LYS51
|
3.6
|
35.7
|
1.0
|
PA
|
D:ADP601
|
3.8
|
54.7
|
1.0
|
C
|
D:THR30
|
3.8
|
38.1
|
1.0
|
CB
|
D:LYS51
|
4.1
|
38.0
|
1.0
|
O2A
|
D:ADP601
|
4.2
|
36.1
|
1.0
|
CA
|
D:ASP52
|
4.3
|
29.5
|
1.0
|
N
|
D:ASP52
|
4.4
|
29.7
|
1.0
|
CB
|
D:THR30
|
4.4
|
28.6
|
1.0
|
N
|
D:GLY32
|
4.5
|
43.8
|
1.0
|
CA
|
D:LYS51
|
4.5
|
33.1
|
1.0
|
OG1
|
D:THR30
|
4.6
|
39.6
|
1.0
|
CG
|
D:ASN153
|
4.6
|
0.7
|
1.0
|
CA
|
D:THR30
|
4.7
|
30.1
|
1.0
|
CA
|
D:LEU31
|
4.7
|
39.6
|
1.0
|
N
|
D:LEU31
|
4.7
|
48.4
|
1.0
|
O5'
|
D:ADP601
|
4.8
|
42.2
|
1.0
|
N
|
D:GLY53
|
4.8
|
31.6
|
1.0
|
O
|
D:GLY32
|
4.8
|
57.7
|
1.0
|
O3A
|
D:ADP601
|
4.9
|
80.7
|
1.0
|
C
|
D:LEU31
|
4.9
|
41.5
|
1.0
|
|
Potassium binding site 5 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 5 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K603
b:89.4
occ:1.00
|
O
|
E:THR30
|
2.6
|
48.7
|
1.0
|
O
|
E:HOH714
|
2.8
|
87.5
|
1.0
|
O1A
|
E:ADP601
|
2.9
|
60.0
|
1.0
|
O
|
E:HOH712
|
3.0
|
0.5
|
1.0
|
O
|
E:HOH713
|
3.0
|
89.5
|
1.0
|
O
|
E:GLY32
|
3.1
|
62.0
|
1.0
|
O
|
E:HOH746
|
3.4
|
63.1
|
1.0
|
O
|
E:HOH747
|
3.7
|
80.6
|
1.0
|
C
|
E:THR30
|
3.8
|
47.2
|
1.0
|
N
|
E:GLY32
|
4.0
|
41.4
|
1.0
|
O
|
E:LYS51
|
4.0
|
52.5
|
1.0
|
C
|
E:GLY32
|
4.1
|
50.9
|
1.0
|
PA
|
E:ADP601
|
4.2
|
57.8
|
1.0
|
OD1
|
E:ASN153
|
4.3
|
93.7
|
1.0
|
C
|
E:LEU31
|
4.4
|
49.9
|
1.0
|
CA
|
E:GLY32
|
4.6
|
47.2
|
1.0
|
O2A
|
E:ADP601
|
4.6
|
64.2
|
1.0
|
CA
|
E:LEU31
|
4.7
|
49.2
|
1.0
|
CB
|
E:THR30
|
4.7
|
42.6
|
1.0
|
N
|
E:LEU31
|
4.7
|
51.8
|
1.0
|
CA
|
E:THR30
|
4.8
|
39.9
|
1.0
|
OG1
|
E:THR30
|
4.8
|
44.7
|
1.0
|
|
Potassium binding site 6 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 6 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K603
b:60.9
occ:1.00
|
O
|
F:HOH745
|
2.5
|
85.8
|
1.0
|
O
|
F:HOH743
|
2.6
|
47.4
|
1.0
|
O
|
F:THR30
|
2.6
|
37.5
|
1.0
|
O
|
F:HOH744
|
2.6
|
55.6
|
1.0
|
O
|
F:LYS51
|
2.7
|
53.4
|
1.0
|
O1A
|
F:ADP601
|
2.7
|
51.6
|
1.0
|
PA
|
F:ADP601
|
3.7
|
51.5
|
1.0
|
C
|
F:THR30
|
3.8
|
35.4
|
1.0
|
C
|
F:LYS51
|
3.8
|
32.6
|
1.0
|
O2A
|
F:ADP601
|
3.9
|
38.1
|
1.0
|
O
|
F:HOH708
|
3.9
|
71.2
|
1.0
|
O
|
F:GLY32
|
4.3
|
50.0
|
1.0
|
O3A
|
F:ADP601
|
4.3
|
74.4
|
1.0
|
CB
|
F:THR30
|
4.4
|
30.6
|
1.0
|
CB
|
F:LYS51
|
4.4
|
27.7
|
1.0
|
N
|
F:GLY32
|
4.4
|
37.5
|
1.0
|
OG1
|
F:THR30
|
4.4
|
39.0
|
1.0
|
CA
|
F:ASP52
|
4.6
|
38.2
|
1.0
|
N
|
F:ASP52
|
4.6
|
32.7
|
1.0
|
CA
|
F:THR30
|
4.6
|
26.8
|
1.0
|
OD1
|
F:ASN153
|
4.6
|
0.7
|
1.0
|
CG
|
F:ASN153
|
4.7
|
0.6
|
1.0
|
CA
|
F:LYS51
|
4.7
|
35.0
|
1.0
|
N
|
F:LEU31
|
4.7
|
31.2
|
1.0
|
CA
|
F:LEU31
|
4.7
|
34.5
|
1.0
|
ND2
|
F:ASN153
|
4.8
|
0.9
|
1.0
|
C
|
F:LEU31
|
4.8
|
41.4
|
1.0
|
N
|
F:GLY53
|
4.8
|
37.6
|
1.0
|
|
Potassium binding site 7 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 7 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K605
b:0.7
occ:1.00
|
O
|
F:HOH759
|
2.8
|
85.1
|
1.0
|
OE1
|
F:GLU483
|
2.8
|
0.1
|
1.0
|
OE2
|
F:GLU460
|
3.2
|
73.5
|
1.0
|
O
|
G:HOH785
|
3.3
|
86.4
|
1.0
|
O
|
G:HOH768
|
3.5
|
69.8
|
1.0
|
CD
|
F:GLU460
|
3.8
|
69.1
|
1.0
|
OE1
|
F:GLU460
|
4.0
|
70.8
|
1.0
|
CD
|
F:GLU483
|
4.1
|
0.5
|
1.0
|
OE2
|
F:GLU483
|
4.8
|
99.2
|
1.0
|
CG
|
F:GLU460
|
5.0
|
55.2
|
1.0
|
|
Potassium binding site 8 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 8 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K603
b:65.6
occ:1.00
|
O1A
|
G:ADP601
|
2.5
|
64.1
|
1.0
|
O
|
G:HOH766
|
2.6
|
57.3
|
1.0
|
O
|
G:HOH762
|
2.6
|
51.1
|
1.0
|
O
|
G:THR30
|
2.7
|
34.0
|
1.0
|
O
|
G:LYS51
|
2.7
|
42.5
|
1.0
|
O
|
G:HOH765
|
2.7
|
77.5
|
1.0
|
O
|
G:HOH763
|
2.9
|
66.3
|
1.0
|
PA
|
G:ADP601
|
3.7
|
47.5
|
1.0
|
O
|
G:HOH779
|
3.8
|
71.5
|
1.0
|
C
|
G:LYS51
|
3.8
|
38.0
|
1.0
|
C
|
G:THR30
|
3.8
|
41.9
|
1.0
|
O2A
|
G:ADP601
|
4.1
|
42.2
|
1.0
|
CB
|
G:THR30
|
4.3
|
31.6
|
1.0
|
OG1
|
G:THR30
|
4.3
|
27.9
|
1.0
|
CA
|
G:ASP52
|
4.4
|
29.6
|
1.0
|
N
|
G:GLY53
|
4.4
|
30.5
|
1.0
|
OD1
|
G:ASN153
|
4.5
|
77.4
|
1.0
|
N
|
G:ASP52
|
4.5
|
32.4
|
1.0
|
CB
|
G:LYS51
|
4.6
|
29.9
|
1.0
|
O3A
|
G:ADP601
|
4.7
|
94.7
|
1.0
|
CA
|
G:THR30
|
4.7
|
25.9
|
1.0
|
N
|
G:LEU31
|
4.7
|
31.1
|
1.0
|
CA
|
G:LEU31
|
4.7
|
31.9
|
1.0
|
O
|
G:HOH733
|
4.8
|
54.2
|
1.0
|
N
|
G:GLY32
|
4.8
|
34.5
|
1.0
|
O
|
G:GLY32
|
4.8
|
45.2
|
1.0
|
CA
|
G:LYS51
|
4.8
|
42.5
|
1.0
|
O5'
|
G:ADP601
|
4.9
|
60.0
|
1.0
|
O
|
G:HOH772
|
4.9
|
57.7
|
1.0
|
C
|
G:ASP52
|
5.0
|
37.3
|
1.0
|
|
Potassium binding site 9 out
of 9 in 4ki8
Go back to
Potassium Binding Sites List in 4ki8
Potassium binding site 9 out
of 9 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K608
b:0.6
occ:1.00
|
OE2
|
G:GLU460
|
3.4
|
85.0
|
1.0
|
OE1
|
G:GLU483
|
3.4
|
0.5
|
1.0
|
O
|
G:HOH775
|
3.5
|
84.9
|
1.0
|
O
|
A:HOH739
|
3.5
|
89.7
|
1.0
|
OE2
|
G:GLU483
|
3.8
|
0.6
|
1.0
|
OD2
|
A:ASP115
|
3.9
|
63.6
|
1.0
|
ND2
|
A:ASN433
|
4.0
|
53.9
|
1.0
|
CD
|
G:GLU483
|
4.0
|
1.0
|
1.0
|
CD
|
G:GLU460
|
4.2
|
79.5
|
1.0
|
OE1
|
G:GLU460
|
4.3
|
82.2
|
1.0
|
CG
|
A:ASN433
|
4.9
|
64.4
|
1.0
|
CG
|
A:ASP115
|
4.9
|
56.4
|
1.0
|
|
Reference:
X.Fei,
D.Yang,
N.Laronde-Leblanc,
G.H.Lorimer.
Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State at 2.7 A Resolution. Proc.Natl.Acad.Sci.Usa V. 110 E2958 2013.
ISSN: ISSN 0027-8424
PubMed: 23861496
DOI: 10.1073/PNAS.1311996110
Page generated: Mon Aug 12 11:11:49 2024
|