Potassium in PDB 8bv3: Bacillus Subtilis Dnaa Domain III Structure
Protein crystallography data
The structure of Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3
was solved by
S.Pintar,
J.A.Hubbard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
74.40 /
2.38
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.578,
81.578,
223.196,
90,
90,
120
|
R / Rfree (%)
|
19.1 /
23.9
|
Other elements in 8bv3:
The structure of Bacillus Subtilis Dnaa Domain III Structure also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Bacillus Subtilis Dnaa Domain III Structure
(pdb code 8bv3). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the
Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Potassium binding site 1 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 1 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K302
b:48.0
occ:1.00
|
NH2
|
A:ARG157
|
3.2
|
59.4
|
1.0
|
NE
|
A:ARG157
|
3.3
|
64.0
|
1.0
|
CZ
|
A:ARG157
|
3.7
|
58.2
|
1.0
|
N
|
A:GLU124
|
3.7
|
45.4
|
1.0
|
CA
|
A:GLU124
|
3.8
|
52.1
|
1.0
|
C
|
A:GLN123
|
3.9
|
41.5
|
1.0
|
CG
|
A:GLU155
|
4.0
|
85.3
|
1.0
|
CB
|
A:PHE127
|
4.1
|
46.6
|
1.0
|
O
|
A:GLN123
|
4.1
|
39.3
|
1.0
|
CD2
|
A:LEU158
|
4.2
|
56.0
|
1.0
|
CB
|
A:GLU155
|
4.2
|
82.8
|
1.0
|
CB
|
A:LEU158
|
4.4
|
50.9
|
1.0
|
CB
|
A:GLN123
|
4.4
|
48.6
|
1.0
|
CG
|
A:PHE127
|
4.4
|
53.6
|
1.0
|
CD
|
A:ARG157
|
4.4
|
69.1
|
1.0
|
CB
|
A:GLU124
|
4.5
|
53.9
|
1.0
|
CG
|
A:ARG157
|
4.6
|
69.0
|
1.0
|
CD1
|
A:PHE127
|
4.6
|
60.7
|
1.0
|
CA
|
A:GLN123
|
4.8
|
45.9
|
1.0
|
CG
|
A:LEU158
|
4.8
|
49.4
|
1.0
|
CG
|
A:GLU124
|
4.8
|
60.6
|
1.0
|
C
|
A:GLU124
|
5.0
|
47.6
|
1.0
|
|
Potassium binding site 2 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 2 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K302
b:72.2
occ:1.00
|
OE1
|
B:GLU196
|
3.6
|
54.6
|
1.0
|
N
|
B:ALA232
|
3.6
|
47.6
|
1.0
|
CB
|
B:GLU196
|
3.7
|
50.6
|
1.0
|
CB
|
B:ASN231
|
4.0
|
55.0
|
1.0
|
CA
|
B:ASN231
|
4.0
|
49.6
|
1.0
|
CB
|
B:PRO194
|
4.1
|
39.2
|
1.0
|
CB
|
B:ALA232
|
4.1
|
55.5
|
1.0
|
CG
|
B:GLU196
|
4.2
|
56.8
|
1.0
|
C
|
B:ASN231
|
4.3
|
48.2
|
1.0
|
CD
|
B:GLU196
|
4.3
|
58.3
|
1.0
|
CG2
|
B:VAL197
|
4.3
|
37.7
|
1.0
|
CG
|
B:PRO194
|
4.3
|
40.5
|
1.0
|
CA
|
B:ALA232
|
4.5
|
56.6
|
1.0
|
CA
|
B:GLU196
|
4.8
|
47.8
|
1.0
|
N
|
B:VAL197
|
4.9
|
40.7
|
1.0
|
|
Potassium binding site 3 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 3 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K303
b:64.5
occ:1.00
|
OG1
|
B:THR122
|
3.3
|
35.4
|
1.0
|
CB
|
B:LYS119
|
3.6
|
53.7
|
1.0
|
CA
|
B:LYS119
|
3.7
|
53.6
|
1.0
|
N
|
B:THR122
|
3.7
|
39.3
|
1.0
|
C
|
B:LYS119
|
3.8
|
51.8
|
1.0
|
CB
|
B:GLN121
|
3.8
|
61.1
|
1.0
|
N
|
B:GLN121
|
4.0
|
51.5
|
1.0
|
CD1
|
B:ILE87
|
4.1
|
51.4
|
1.0
|
O
|
B:LYS119
|
4.1
|
49.6
|
1.0
|
CB
|
B:THR122
|
4.1
|
39.6
|
1.0
|
N
|
B:GLU120
|
4.2
|
53.4
|
1.0
|
CA
|
B:GLN121
|
4.3
|
53.8
|
1.0
|
CG
|
B:LYS119
|
4.3
|
55.7
|
1.0
|
OE1
|
B:GLN121
|
4.4
|
81.0
|
1.0
|
C
|
B:GLN121
|
4.5
|
41.9
|
1.0
|
CD
|
B:LYS119
|
4.5
|
62.1
|
1.0
|
CA
|
B:THR122
|
4.6
|
42.2
|
1.0
|
CG
|
B:GLN121
|
4.7
|
71.8
|
1.0
|
CG1
|
B:ILE87
|
4.8
|
45.6
|
1.0
|
C
|
B:GLU120
|
4.8
|
49.8
|
1.0
|
CD
|
B:GLN121
|
5.0
|
81.1
|
1.0
|
CG2
|
B:THR83
|
5.0
|
33.1
|
1.0
|
|
Potassium binding site 4 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 4 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K302
b:34.2
occ:1.00
|
NH2
|
C:ARG157
|
3.2
|
49.2
|
1.0
|
NE
|
C:ARG157
|
3.3
|
50.4
|
1.0
|
CZ
|
C:ARG157
|
3.7
|
52.1
|
1.0
|
CA
|
C:GLU124
|
3.9
|
34.4
|
1.0
|
N
|
C:GLU124
|
3.9
|
34.1
|
1.0
|
C
|
C:GLN123
|
4.0
|
31.3
|
1.0
|
O
|
C:GLN123
|
4.0
|
31.4
|
1.0
|
CB
|
C:PHE127
|
4.0
|
31.4
|
1.0
|
CB
|
C:GLU155
|
4.1
|
53.9
|
1.0
|
CG
|
C:GLU155
|
4.2
|
56.7
|
1.0
|
CB
|
C:GLN123
|
4.3
|
34.7
|
1.0
|
CG
|
C:PHE127
|
4.3
|
31.6
|
1.0
|
CD
|
C:ARG157
|
4.5
|
48.9
|
1.0
|
CB
|
C:LEU158
|
4.5
|
37.4
|
1.0
|
CG
|
C:ARG157
|
4.5
|
47.1
|
1.0
|
CD2
|
C:LEU158
|
4.5
|
39.4
|
1.0
|
CB
|
C:GLU124
|
4.6
|
39.0
|
1.0
|
CD1
|
C:PHE127
|
4.6
|
30.0
|
1.0
|
CG
|
C:GLU124
|
4.7
|
45.0
|
1.0
|
CA
|
C:GLN123
|
4.8
|
33.2
|
1.0
|
OE1
|
C:GLN123
|
4.8
|
49.4
|
1.0
|
CD2
|
C:PHE127
|
4.9
|
35.7
|
1.0
|
CG
|
C:LEU158
|
5.0
|
39.0
|
1.0
|
NH1
|
C:ARG157
|
5.0
|
47.7
|
1.0
|
|
Potassium binding site 5 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 5 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K303
b:55.6
occ:1.00
|
OG1
|
C:THR122
|
3.4
|
35.4
|
1.0
|
CB
|
C:GLN121
|
3.6
|
50.7
|
1.0
|
N
|
C:THR122
|
3.7
|
41.5
|
1.0
|
N
|
C:GLN121
|
3.8
|
45.3
|
1.0
|
C
|
C:LYS119
|
3.8
|
45.0
|
1.0
|
CA
|
C:LYS119
|
3.8
|
46.7
|
1.0
|
CB
|
C:LYS119
|
3.9
|
50.3
|
1.0
|
O
|
C:LYS119
|
4.0
|
46.0
|
1.0
|
CA
|
C:GLN121
|
4.1
|
47.5
|
1.0
|
N
|
C:GLU120
|
4.1
|
50.0
|
1.0
|
CB
|
C:THR122
|
4.2
|
36.4
|
1.0
|
CD1
|
C:ILE87
|
4.2
|
46.4
|
1.0
|
OE1
|
C:GLN121
|
4.2
|
69.8
|
1.0
|
CD
|
C:LYS119
|
4.3
|
61.7
|
1.0
|
C
|
C:GLN121
|
4.4
|
46.7
|
1.0
|
CA
|
C:THR122
|
4.6
|
36.5
|
1.0
|
CG
|
C:LYS119
|
4.7
|
54.0
|
1.0
|
C
|
C:GLU120
|
4.7
|
46.0
|
1.0
|
CG
|
C:GLN121
|
4.9
|
59.2
|
1.0
|
CD
|
C:GLN121
|
5.0
|
68.8
|
1.0
|
|
Potassium binding site 6 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 6 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K304
b:67.2
occ:1.00
|
O
|
C:ALA38
|
3.6
|
37.9
|
1.0
|
O
|
C:HOH413
|
3.7
|
37.1
|
1.0
|
O
|
C:HOH422
|
3.8
|
35.5
|
1.0
|
C
|
C:LYS39
|
4.2
|
41.1
|
1.0
|
CA
|
C:LYS39
|
4.3
|
39.5
|
1.0
|
C
|
C:ALA38
|
4.3
|
37.2
|
1.0
|
N
|
C:ALA40
|
4.4
|
36.7
|
1.0
|
CB
|
C:ASN42
|
4.4
|
31.5
|
1.0
|
NZ
|
B:LYS11
|
4.4
|
88.2
|
1.0
|
C
|
C:ALA40
|
4.5
|
38.7
|
1.0
|
O
|
C:LYS39
|
4.5
|
40.8
|
1.0
|
N
|
C:LYS39
|
4.6
|
38.5
|
1.0
|
O
|
C:ALA40
|
4.6
|
48.2
|
1.0
|
N
|
C:ASN42
|
4.7
|
37.4
|
1.0
|
N
|
C:TYR41
|
4.8
|
36.3
|
1.0
|
CA
|
C:ALA40
|
5.0
|
35.7
|
1.0
|
CA
|
C:TYR41
|
5.0
|
31.6
|
1.0
|
C
|
C:TYR41
|
5.0
|
37.0
|
1.0
|
|
Potassium binding site 7 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 7 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K302
b:45.4
occ:1.00
|
NH2
|
D:ARG157
|
3.2
|
62.1
|
1.0
|
NE
|
D:ARG157
|
3.4
|
58.6
|
1.0
|
O
|
D:HOH401
|
3.5
|
30.0
|
1.0
|
CZ
|
D:ARG157
|
3.5
|
67.9
|
1.0
|
CA
|
D:GLU124
|
4.0
|
43.0
|
1.0
|
O
|
D:GLN123
|
4.1
|
42.3
|
1.0
|
C
|
D:GLN123
|
4.1
|
39.5
|
1.0
|
N
|
D:GLU124
|
4.1
|
42.0
|
1.0
|
CB
|
D:PHE127
|
4.2
|
38.3
|
1.0
|
CB
|
D:GLU155
|
4.2
|
68.6
|
1.0
|
CG
|
D:GLU155
|
4.3
|
78.0
|
1.0
|
CG
|
D:ARG157
|
4.3
|
49.7
|
1.0
|
CB
|
D:GLN123
|
4.3
|
46.1
|
1.0
|
NH1
|
D:ARG157
|
4.3
|
71.9
|
1.0
|
CG
|
D:PHE127
|
4.4
|
41.8
|
1.0
|
CD
|
D:ARG157
|
4.4
|
52.0
|
1.0
|
CG
|
D:GLU124
|
4.5
|
64.1
|
1.0
|
CD2
|
D:LEU158
|
4.5
|
43.3
|
1.0
|
CD1
|
D:PHE127
|
4.6
|
46.2
|
1.0
|
CB
|
D:LEU158
|
4.6
|
47.0
|
1.0
|
CB
|
D:GLU124
|
4.6
|
49.9
|
1.0
|
OE1
|
D:GLN123
|
4.7
|
57.3
|
1.0
|
CA
|
D:GLN123
|
4.9
|
41.5
|
1.0
|
|
Potassium binding site 8 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 8 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K303
b:73.3
occ:1.00
|
ND2
|
D:ASN208
|
3.4
|
37.9
|
1.0
|
OD2
|
E:ASP156
|
3.4
|
83.3
|
1.0
|
NH2
|
E:ARG159
|
3.8
|
98.7
|
1.0
|
CB
|
D:SER207
|
3.9
|
50.0
|
1.0
|
C
|
D:SER207
|
4.2
|
46.3
|
1.0
|
CA
|
D:SER207
|
4.3
|
49.3
|
1.0
|
CG
|
E:ASP156
|
4.3
|
78.1
|
1.0
|
O
|
D:SER207
|
4.4
|
48.5
|
1.0
|
CG
|
D:ASN208
|
4.5
|
39.7
|
1.0
|
N
|
D:ASN208
|
4.6
|
45.5
|
1.0
|
CB
|
D:ASN208
|
4.7
|
41.6
|
1.0
|
CB
|
E:ASP156
|
4.9
|
68.5
|
1.0
|
CB
|
D:VAL50
|
4.9
|
38.5
|
1.0
|
OG
|
D:SER207
|
4.9
|
43.4
|
1.0
|
|
Potassium binding site 9 out
of 9 in 8bv3
Go back to
Potassium Binding Sites List in 8bv3
Potassium binding site 9 out
of 9 in the Bacillus Subtilis Dnaa Domain III Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K302
b:47.5
occ:1.00
|
NH2
|
E:ARG157
|
3.1
|
61.5
|
1.0
|
NE
|
E:ARG157
|
3.4
|
63.9
|
1.0
|
CZ
|
E:ARG157
|
3.7
|
65.3
|
1.0
|
N
|
E:GLU124
|
3.9
|
47.3
|
1.0
|
CA
|
E:GLU124
|
3.9
|
45.2
|
1.0
|
CB
|
E:PHE127
|
4.1
|
36.5
|
1.0
|
C
|
E:GLN123
|
4.1
|
46.1
|
1.0
|
CB
|
E:GLU155
|
4.1
|
64.3
|
1.0
|
CB
|
E:GLN123
|
4.3
|
48.8
|
1.0
|
CG
|
E:GLU155
|
4.3
|
67.2
|
1.0
|
CG
|
E:PHE127
|
4.4
|
39.0
|
1.0
|
CD2
|
E:LEU158
|
4.4
|
43.8
|
1.0
|
O
|
E:GLN123
|
4.4
|
50.9
|
1.0
|
CB
|
E:LEU158
|
4.4
|
41.3
|
1.0
|
CB
|
E:GLU124
|
4.5
|
47.4
|
1.0
|
CG
|
E:ARG157
|
4.6
|
57.8
|
1.0
|
CD
|
E:ARG157
|
4.6
|
58.6
|
1.0
|
CD1
|
E:PHE127
|
4.6
|
38.3
|
1.0
|
CG
|
E:GLU124
|
4.7
|
53.7
|
1.0
|
CA
|
E:GLN123
|
4.8
|
48.5
|
1.0
|
OE1
|
E:GLN123
|
4.8
|
45.7
|
1.0
|
|
Reference:
S.Pintar,
A.Basle,
J.A.Hubbard.
Bacillus Subtilis Dnaa Domain III_IV Structure To Be Published.
Page generated: Mon Aug 12 22:08:07 2024
|