Potassium in PDB 9qdi: Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
Protein crystallography data
The structure of Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide, PDB code: 9qdi
was solved by
A.Martinez Gascuena,
M.A.Marquez-Monino,
A.Manzanares-Gomez,
M.Aguillo-Urarte,
B.Trastoy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.64 /
1.94
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.294,
99.435,
103.386,
74.16,
88.13,
82.44
|
|
R / Rfree (%)
|
17.1 /
21.3
|
Other elements in 9qdi:
The structure of Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
(pdb code 9qdi). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide, PDB code: 9qdi:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 1 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K501
b:26.5
occ:1.00
|
OD2
|
A:ASP177
|
2.2
|
31.3
|
1.0
|
|
O
|
A:CYS175
|
2.3
|
23.3
|
1.0
|
|
OE2
|
A:GLU275
|
2.3
|
27.5
|
1.0
|
|
O
|
A:ALA58
|
2.3
|
26.5
|
1.0
|
|
O
|
A:GLU172
|
2.3
|
33.7
|
1.0
|
|
O1
|
A:EDO504
|
2.4
|
39.5
|
1.0
|
|
H11
|
A:EDO504
|
2.8
|
51.3
|
1.0
|
|
C1
|
A:EDO504
|
3.1
|
42.8
|
1.0
|
|
HO1
|
A:EDO504
|
3.1
|
47.4
|
1.0
|
|
CD
|
A:GLU275
|
3.2
|
32.9
|
1.0
|
|
HO2
|
A:EDO504
|
3.2
|
41.9
|
1.0
|
|
CG
|
A:ASP177
|
3.4
|
35.1
|
1.0
|
|
C
|
A:GLU172
|
3.4
|
36.0
|
1.0
|
|
C
|
A:CYS175
|
3.5
|
29.6
|
1.0
|
|
C
|
A:ALA58
|
3.5
|
25.4
|
1.0
|
|
O2
|
A:EDO504
|
3.8
|
34.9
|
1.0
|
|
H12
|
A:EDO504
|
3.9
|
51.3
|
1.0
|
|
N
|
A:ASP177
|
3.9
|
23.0
|
1.0
|
|
OE1
|
A:GLU275
|
3.9
|
26.8
|
1.0
|
|
C2
|
A:EDO504
|
4.0
|
37.4
|
1.0
|
|
CA
|
A:GLU172
|
4.0
|
39.7
|
1.0
|
|
CG
|
A:GLU275
|
4.1
|
29.1
|
1.0
|
|
CA
|
A:ILE176
|
4.2
|
27.7
|
1.0
|
|
CA
|
A:ALA58
|
4.2
|
25.7
|
1.0
|
|
N
|
A:ILE176
|
4.3
|
29.0
|
1.0
|
|
CB
|
A:ASP177
|
4.3
|
23.4
|
1.0
|
|
OD1
|
A:ASP177
|
4.3
|
31.6
|
1.0
|
|
H21
|
A:EDO504
|
4.3
|
44.9
|
1.0
|
|
CB
|
A:ALA58
|
4.3
|
23.4
|
1.0
|
|
C
|
A:ILE176
|
4.4
|
25.2
|
1.0
|
|
O
|
A:GLY59
|
4.4
|
25.9
|
1.0
|
|
N
|
A:CYS175
|
4.5
|
34.0
|
1.0
|
|
CB
|
A:GLU172
|
4.5
|
34.1
|
1.0
|
|
N
|
A:GLU173
|
4.5
|
35.9
|
1.0
|
|
N
|
A:GLY59
|
4.6
|
24.3
|
1.0
|
|
CA
|
A:CYS175
|
4.6
|
28.6
|
1.0
|
|
CA
|
A:ASP177
|
4.7
|
26.4
|
1.0
|
|
CA
|
A:GLU173
|
4.7
|
37.5
|
1.0
|
|
C
|
A:GLU173
|
4.8
|
39.6
|
1.0
|
|
CA
|
A:GLY59
|
4.8
|
23.7
|
1.0
|
|
C
|
A:GLY59
|
4.8
|
29.8
|
1.0
|
|
H22
|
A:EDO504
|
4.8
|
44.9
|
1.0
|
|
Potassium binding site 2 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 2 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K501
b:31.9
occ:1.00
|
HO2
|
B:EDO504
|
2.0
|
48.4
|
1.0
|
|
O
|
B:CYS175
|
2.2
|
30.1
|
1.0
|
|
O
|
B:ALA58
|
2.2
|
28.2
|
1.0
|
|
OD2
|
B:ASP177
|
2.3
|
34.6
|
1.0
|
|
OE2
|
B:GLU275
|
2.3
|
29.8
|
1.0
|
|
O2
|
B:EDO504
|
2.3
|
40.3
|
1.0
|
|
O
|
B:GLU172
|
2.4
|
32.3
|
1.0
|
|
H22
|
B:EDO504
|
3.1
|
51.1
|
1.0
|
|
CD
|
B:GLU275
|
3.2
|
33.5
|
1.0
|
|
C2
|
B:EDO504
|
3.2
|
42.5
|
1.0
|
|
C
|
B:ALA58
|
3.4
|
29.6
|
1.0
|
|
CG
|
B:ASP177
|
3.5
|
37.0
|
1.0
|
|
C
|
B:CYS175
|
3.5
|
34.1
|
1.0
|
|
C
|
B:GLU172
|
3.5
|
49.7
|
1.0
|
|
O1
|
B:EDO504
|
3.8
|
39.5
|
1.0
|
|
OE1
|
B:GLU275
|
3.9
|
36.0
|
1.0
|
|
N
|
B:ASP177
|
3.9
|
24.9
|
1.0
|
|
C1
|
B:EDO504
|
4.0
|
44.5
|
1.0
|
|
CG
|
B:GLU275
|
4.0
|
27.2
|
1.0
|
|
H21
|
B:EDO504
|
4.0
|
51.1
|
1.0
|
|
CA
|
B:GLU172
|
4.1
|
47.4
|
1.0
|
|
CA
|
B:ALA58
|
4.1
|
27.9
|
1.0
|
|
H12
|
B:EDO504
|
4.2
|
53.4
|
1.0
|
|
CA
|
B:ILE176
|
4.2
|
29.8
|
1.0
|
|
CB
|
B:ALA58
|
4.2
|
35.4
|
1.0
|
|
N
|
B:ILE176
|
4.3
|
36.3
|
1.0
|
|
OD1
|
B:ASP177
|
4.3
|
36.6
|
1.0
|
|
CB
|
B:ASP177
|
4.3
|
29.8
|
1.0
|
|
N
|
B:CYS175
|
4.4
|
37.4
|
1.0
|
|
O
|
B:GLY59
|
4.5
|
32.0
|
1.0
|
|
N
|
B:GLY59
|
4.5
|
26.5
|
1.0
|
|
C
|
B:ILE176
|
4.5
|
25.4
|
1.0
|
|
N
|
B:GLU173
|
4.5
|
42.5
|
1.0
|
|
CA
|
B:CYS175
|
4.5
|
35.2
|
1.0
|
|
CB
|
B:GLU172
|
4.6
|
36.0
|
1.0
|
|
HO1
|
B:EDO504
|
4.6
|
47.4
|
1.0
|
|
CA
|
B:GLY59
|
4.7
|
29.1
|
1.0
|
|
CA
|
B:GLU173
|
4.8
|
40.2
|
1.0
|
|
CA
|
B:ASP177
|
4.8
|
26.3
|
1.0
|
|
C
|
B:GLU173
|
4.8
|
41.8
|
1.0
|
|
C
|
B:GLY59
|
4.8
|
32.1
|
1.0
|
|
H11
|
B:EDO504
|
4.9
|
53.4
|
1.0
|
|
Potassium binding site 3 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 3 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K501
b:28.8
occ:1.00
|
HO1
|
C:EDO504
|
2.1
|
45.6
|
1.0
|
|
O
|
C:CYS175
|
2.3
|
31.4
|
1.0
|
|
O1
|
C:EDO504
|
2.3
|
38.0
|
1.0
|
|
O
|
C:GLU172
|
2.3
|
35.7
|
1.0
|
|
O
|
C:ALA58
|
2.3
|
26.3
|
1.0
|
|
OE2
|
C:GLU275
|
2.3
|
29.8
|
1.0
|
|
OD2
|
C:ASP177
|
2.3
|
32.3
|
1.0
|
|
H11
|
C:EDO504
|
2.8
|
51.5
|
1.0
|
|
C1
|
C:EDO504
|
3.1
|
42.9
|
1.0
|
|
CD
|
C:GLU275
|
3.2
|
30.6
|
1.0
|
|
H
|
C:ASP177
|
3.3
|
27.8
|
1.0
|
|
C
|
C:GLU172
|
3.4
|
35.1
|
1.0
|
|
HA
|
C:ILE176
|
3.5
|
32.4
|
1.0
|
|
C
|
C:CYS175
|
3.5
|
32.6
|
1.0
|
|
C
|
C:ALA58
|
3.5
|
26.8
|
1.0
|
|
CG
|
C:ASP177
|
3.5
|
31.2
|
1.0
|
|
HB1
|
C:ALA58
|
3.7
|
36.5
|
1.0
|
|
HA
|
C:GLU172
|
3.7
|
52.9
|
1.0
|
|
HG3
|
C:GLU275
|
3.7
|
40.1
|
1.0
|
|
H12
|
C:EDO504
|
3.8
|
51.5
|
1.0
|
|
O2
|
C:EDO504
|
3.8
|
42.6
|
1.0
|
|
N
|
C:ASP177
|
3.9
|
23.2
|
1.0
|
|
HB2
|
C:GLU172
|
3.9
|
47.1
|
1.0
|
|
OE1
|
C:GLU275
|
3.9
|
28.8
|
1.0
|
|
HB2
|
C:ASP177
|
4.0
|
33.9
|
1.0
|
|
CG
|
C:GLU275
|
4.0
|
33.4
|
1.0
|
|
HA
|
C:ALA58
|
4.0
|
33.3
|
1.0
|
|
C2
|
C:EDO504
|
4.0
|
41.0
|
1.0
|
|
CA
|
C:GLU172
|
4.1
|
44.1
|
1.0
|
|
CA
|
C:ILE176
|
4.1
|
26.9
|
1.0
|
|
H
|
C:CYS175
|
4.2
|
41.9
|
1.0
|
|
CA
|
C:ALA58
|
4.2
|
27.7
|
1.0
|
|
HA2
|
C:GLY59
|
4.2
|
30.8
|
1.0
|
|
N
|
C:ILE176
|
4.2
|
30.1
|
1.0
|
|
CB
|
C:ASP177
|
4.3
|
28.3
|
1.0
|
|
HA
|
C:GLU173
|
4.3
|
41.8
|
1.0
|
|
HG2
|
C:GLU275
|
4.4
|
40.1
|
1.0
|
|
C
|
C:ILE176
|
4.4
|
27.0
|
1.0
|
|
CB
|
C:ALA58
|
4.4
|
30.4
|
1.0
|
|
OD1
|
C:ASP177
|
4.4
|
33.4
|
1.0
|
|
N
|
C:CYS175
|
4.4
|
35.0
|
1.0
|
|
O
|
C:GLY59
|
4.5
|
31.9
|
1.0
|
|
N
|
C:GLU173
|
4.5
|
39.9
|
1.0
|
|
N
|
C:GLY59
|
4.5
|
24.2
|
1.0
|
|
CB
|
C:GLU172
|
4.5
|
39.3
|
1.0
|
|
CA
|
C:CYS175
|
4.6
|
31.1
|
1.0
|
|
HO2
|
C:EDO504
|
4.6
|
51.1
|
1.0
|
|
H22
|
C:EDO504
|
4.6
|
49.1
|
1.0
|
|
CA
|
C:GLY59
|
4.7
|
25.7
|
1.0
|
|
H21
|
C:EDO504
|
4.7
|
49.1
|
1.0
|
|
CA
|
C:ASP177
|
4.7
|
23.2
|
1.0
|
|
CA
|
C:GLU173
|
4.7
|
34.8
|
1.0
|
|
C
|
C:GLY59
|
4.8
|
32.0
|
1.0
|
|
C
|
C:GLU173
|
4.8
|
40.1
|
1.0
|
|
HB3
|
C:ALA58
|
4.9
|
36.5
|
1.0
|
|
Potassium binding site 4 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 4 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K501
b:27.2
occ:1.00
|
O1
|
D:EDO504
|
2.0
|
37.1
|
1.0
|
|
OD2
|
D:ASP177
|
2.2
|
28.9
|
1.0
|
|
O
|
D:CYS175
|
2.2
|
26.1
|
1.0
|
|
O
|
D:GLU172
|
2.3
|
32.1
|
1.0
|
|
HO1
|
D:EDO504
|
2.3
|
44.6
|
1.0
|
|
O
|
D:ALA58
|
2.4
|
22.7
|
1.0
|
|
OE2
|
D:GLU275
|
2.4
|
29.0
|
1.0
|
|
CD
|
D:GLU275
|
3.2
|
36.4
|
1.0
|
|
C1
|
D:EDO504
|
3.3
|
35.3
|
1.0
|
|
CG
|
D:ASP177
|
3.4
|
34.6
|
1.0
|
|
C
|
D:GLU172
|
3.4
|
36.1
|
1.0
|
|
C
|
D:CYS175
|
3.4
|
34.5
|
1.0
|
|
H
|
D:ASP177
|
3.4
|
33.4
|
1.0
|
|
HA
|
D:ILE176
|
3.5
|
35.4
|
1.0
|
|
H21
|
D:EDO504
|
3.5
|
47.6
|
1.0
|
|
C
|
D:ALA58
|
3.5
|
30.3
|
1.0
|
|
HA
|
D:GLU172
|
3.6
|
43.4
|
1.0
|
|
HB1
|
D:ALA58
|
3.7
|
33.6
|
1.0
|
|
HG3
|
D:GLU275
|
3.7
|
35.1
|
1.0
|
|
C2
|
D:EDO504
|
3.8
|
39.6
|
1.0
|
|
H11
|
D:EDO504
|
3.8
|
42.3
|
1.0
|
|
O2
|
D:EDO504
|
3.8
|
41.7
|
1.0
|
|
HB2
|
D:GLU172
|
3.9
|
48.1
|
1.0
|
|
N
|
D:ASP177
|
3.9
|
27.8
|
1.0
|
|
HB2
|
D:ASP177
|
3.9
|
33.9
|
1.0
|
|
OE1
|
D:GLU275
|
4.0
|
29.7
|
1.0
|
|
H12
|
D:EDO504
|
4.0
|
42.3
|
1.0
|
|
CA
|
D:GLU172
|
4.0
|
36.2
|
1.0
|
|
HA
|
D:ALA58
|
4.0
|
35.0
|
1.0
|
|
CG
|
D:GLU275
|
4.1
|
29.2
|
1.0
|
|
H
|
D:CYS175
|
4.1
|
39.9
|
1.0
|
|
CA
|
D:ILE176
|
4.2
|
29.5
|
1.0
|
|
CB
|
D:ASP177
|
4.2
|
28.3
|
1.0
|
|
HA2
|
D:GLY59
|
4.2
|
30.3
|
1.0
|
|
N
|
D:ILE176
|
4.2
|
30.5
|
1.0
|
|
HO2
|
D:EDO504
|
4.2
|
50.1
|
1.0
|
|
CA
|
D:ALA58
|
4.2
|
29.1
|
1.0
|
|
OD1
|
D:ASP177
|
4.3
|
35.7
|
1.0
|
|
HA
|
D:GLU173
|
4.3
|
38.0
|
1.0
|
|
CB
|
D:ALA58
|
4.4
|
28.0
|
1.0
|
|
C
|
D:ILE176
|
4.4
|
29.8
|
1.0
|
|
N
|
D:GLU173
|
4.5
|
32.7
|
1.0
|
|
N
|
D:CYS175
|
4.5
|
33.3
|
1.0
|
|
O
|
D:GLY59
|
4.5
|
26.5
|
1.0
|
|
CB
|
D:GLU172
|
4.5
|
40.1
|
1.0
|
|
N
|
D:GLY59
|
4.5
|
23.7
|
1.0
|
|
CA
|
D:CYS175
|
4.6
|
29.9
|
1.0
|
|
HG2
|
D:GLU275
|
4.6
|
35.1
|
1.0
|
|
CA
|
D:GLY59
|
4.7
|
25.3
|
1.0
|
|
H22
|
D:EDO504
|
4.7
|
47.6
|
1.0
|
|
CA
|
D:ASP177
|
4.7
|
25.1
|
1.0
|
|
CA
|
D:GLU173
|
4.8
|
31.7
|
1.0
|
|
C
|
D:GLY59
|
4.8
|
25.6
|
1.0
|
|
C
|
D:GLU173
|
4.8
|
40.0
|
1.0
|
|
HB3
|
D:ALA58
|
5.0
|
33.6
|
1.0
|
|
Potassium binding site 5 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 5 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K501
b:28.6
occ:1.00
|
HO2
|
E:EDO504
|
1.8
|
20.0
|
1.0
|
|
OE2
|
E:GLU275
|
2.3
|
31.5
|
1.0
|
|
O
|
E:GLU172
|
2.3
|
33.4
|
1.0
|
|
O
|
E:CYS175
|
2.3
|
32.1
|
1.0
|
|
O
|
E:ALA58
|
2.3
|
28.5
|
1.0
|
|
OD2
|
E:ASP177
|
2.4
|
30.3
|
1.0
|
|
O2
|
E:EDO504
|
2.4
|
20.0
|
1.0
|
|
HO1
|
E:EDO504
|
2.6
|
20.0
|
1.0
|
|
O1
|
E:EDO504
|
3.0
|
20.0
|
1.0
|
|
CD
|
E:GLU275
|
3.2
|
36.7
|
1.0
|
|
H
|
E:ASP177
|
3.4
|
29.1
|
1.0
|
|
C
|
E:GLU172
|
3.4
|
38.7
|
1.0
|
|
C
|
E:ALA58
|
3.5
|
30.5
|
1.0
|
|
C
|
E:CYS175
|
3.5
|
31.1
|
1.0
|
|
HA
|
E:ILE176
|
3.5
|
35.8
|
1.0
|
|
CG
|
E:ASP177
|
3.5
|
28.3
|
1.0
|
|
C2
|
E:EDO504
|
3.6
|
20.0
|
1.0
|
|
HB1
|
E:ALA58
|
3.6
|
40.6
|
1.0
|
|
HA
|
E:GLU172
|
3.7
|
47.8
|
1.0
|
|
C1
|
E:EDO504
|
3.8
|
20.0
|
1.0
|
|
HG3
|
E:GLU275
|
3.8
|
47.2
|
1.0
|
|
OE1
|
E:GLU275
|
3.8
|
33.7
|
1.0
|
|
HB2
|
E:GLU172
|
3.9
|
46.0
|
1.0
|
|
HB2
|
E:ASP177
|
3.9
|
31.4
|
1.0
|
|
N
|
E:ASP177
|
3.9
|
24.3
|
1.0
|
|
H22
|
E:EDO504
|
4.0
|
20.0
|
1.0
|
|
HA
|
E:ALA58
|
4.0
|
34.2
|
1.0
|
|
CA
|
E:GLU172
|
4.1
|
39.8
|
1.0
|
|
CG
|
E:GLU275
|
4.1
|
39.3
|
1.0
|
|
CA
|
E:ALA58
|
4.2
|
28.5
|
1.0
|
|
CA
|
E:ILE176
|
4.2
|
29.8
|
1.0
|
|
HA
|
E:GLU173
|
4.2
|
40.9
|
1.0
|
|
CB
|
E:ASP177
|
4.2
|
26.1
|
1.0
|
|
H
|
E:CYS175
|
4.2
|
40.0
|
1.0
|
|
H21
|
E:EDO504
|
4.3
|
20.0
|
1.0
|
|
HA2
|
E:GLY59
|
4.3
|
30.6
|
1.0
|
|
N
|
E:ILE176
|
4.3
|
31.0
|
1.0
|
|
CB
|
E:ALA58
|
4.3
|
33.9
|
1.0
|
|
H12
|
E:EDO504
|
4.4
|
20.0
|
1.0
|
|
HG2
|
E:GLU275
|
4.4
|
47.2
|
1.0
|
|
OD1
|
E:ASP177
|
4.5
|
35.6
|
1.0
|
|
N
|
E:GLU173
|
4.5
|
37.2
|
1.0
|
|
C
|
E:ILE176
|
4.5
|
30.2
|
1.0
|
|
N
|
E:CYS175
|
4.5
|
33.3
|
1.0
|
|
O
|
E:GLY59
|
4.5
|
32.2
|
1.0
|
|
H11
|
E:EDO504
|
4.5
|
20.0
|
1.0
|
|
N
|
E:GLY59
|
4.5
|
27.2
|
1.0
|
|
CB
|
E:GLU172
|
4.5
|
38.3
|
1.0
|
|
CA
|
E:CYS175
|
4.6
|
32.8
|
1.0
|
|
CA
|
E:GLU173
|
4.7
|
34.1
|
1.0
|
|
HB3
|
E:ALA58
|
4.7
|
40.6
|
1.0
|
|
CA
|
E:GLY59
|
4.7
|
25.5
|
1.0
|
|
CA
|
E:ASP177
|
4.7
|
23.6
|
1.0
|
|
C
|
E:GLU173
|
4.8
|
36.2
|
1.0
|
|
C
|
E:GLY59
|
4.8
|
31.5
|
1.0
|
|
O
|
E:GLU173
|
5.0
|
44.1
|
1.0
|
|
Potassium binding site 6 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 6 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K501
b:28.4
occ:1.00
|
O
|
F:GLU172
|
2.2
|
32.2
|
1.0
|
|
OD2
|
F:ASP177
|
2.3
|
33.3
|
1.0
|
|
OE2
|
F:GLU275
|
2.3
|
29.5
|
1.0
|
|
O
|
F:CYS175
|
2.3
|
31.2
|
1.0
|
|
O2
|
F:EDO504
|
2.3
|
40.2
|
1.0
|
|
O
|
F:ALA58
|
2.4
|
29.4
|
1.0
|
|
HO2
|
F:EDO504
|
2.4
|
48.2
|
1.0
|
|
H21
|
F:EDO504
|
3.1
|
60.3
|
1.0
|
|
C2
|
F:EDO504
|
3.1
|
50.2
|
1.0
|
|
CD
|
F:GLU275
|
3.2
|
35.9
|
1.0
|
|
C
|
F:GLU172
|
3.4
|
36.5
|
1.0
|
|
H
|
F:ASP177
|
3.5
|
33.3
|
1.0
|
|
C
|
F:ALA58
|
3.5
|
30.7
|
1.0
|
|
CG
|
F:ASP177
|
3.5
|
38.4
|
1.0
|
|
H11
|
F:EDO504
|
3.5
|
50.6
|
1.0
|
|
HA
|
F:ILE176
|
3.5
|
38.5
|
1.0
|
|
C
|
F:CYS175
|
3.5
|
37.8
|
1.0
|
|
HB1
|
F:ALA58
|
3.6
|
36.5
|
1.0
|
|
HA
|
F:GLU172
|
3.6
|
44.6
|
1.0
|
|
C1
|
F:EDO504
|
3.7
|
42.2
|
1.0
|
|
O1
|
F:EDO504
|
3.7
|
53.8
|
1.0
|
|
HG3
|
F:GLU275
|
3.7
|
39.9
|
1.0
|
|
OE1
|
F:GLU275
|
3.9
|
32.8
|
1.0
|
|
HB2
|
F:GLU172
|
4.0
|
53.5
|
1.0
|
|
CA
|
F:GLU172
|
4.0
|
37.2
|
1.0
|
|
H22
|
F:EDO504
|
4.0
|
60.3
|
1.0
|
|
HA
|
F:ALA58
|
4.0
|
33.9
|
1.0
|
|
N
|
F:ASP177
|
4.0
|
27.7
|
1.0
|
|
CG
|
F:GLU275
|
4.0
|
33.2
|
1.0
|
|
HO1
|
F:EDO504
|
4.1
|
64.5
|
1.0
|
|
HB2
|
F:ASP177
|
4.1
|
33.2
|
1.0
|
|
CA
|
F:ALA58
|
4.2
|
28.2
|
1.0
|
|
CA
|
F:ILE176
|
4.2
|
32.1
|
1.0
|
|
H
|
F:CYS175
|
4.3
|
43.2
|
1.0
|
|
HA
|
F:GLU173
|
4.3
|
36.6
|
1.0
|
|
HA2
|
F:GLY59
|
4.3
|
34.0
|
1.0
|
|
N
|
F:ILE176
|
4.3
|
33.6
|
1.0
|
|
CB
|
F:ALA58
|
4.3
|
30.4
|
1.0
|
|
CB
|
F:ASP177
|
4.3
|
27.7
|
1.0
|
|
OD1
|
F:ASP177
|
4.4
|
34.5
|
1.0
|
|
O
|
F:GLY59
|
4.4
|
31.7
|
1.0
|
|
HG2
|
F:GLU275
|
4.4
|
39.9
|
1.0
|
|
N
|
F:GLU173
|
4.4
|
30.4
|
1.0
|
|
N
|
F:CYS175
|
4.5
|
36.0
|
1.0
|
|
N
|
F:GLY59
|
4.5
|
26.4
|
1.0
|
|
C
|
F:ILE176
|
4.5
|
34.2
|
1.0
|
|
CB
|
F:GLU172
|
4.5
|
44.6
|
1.0
|
|
CA
|
F:CYS175
|
4.6
|
33.9
|
1.0
|
|
H12
|
F:EDO504
|
4.6
|
50.6
|
1.0
|
|
CA
|
F:GLU173
|
4.7
|
30.5
|
1.0
|
|
CA
|
F:GLY59
|
4.7
|
28.3
|
1.0
|
|
C
|
F:GLU173
|
4.7
|
37.3
|
1.0
|
|
C
|
F:GLY59
|
4.8
|
30.4
|
1.0
|
|
HB3
|
F:ALA58
|
4.8
|
36.5
|
1.0
|
|
CA
|
F:ASP177
|
4.8
|
29.7
|
1.0
|
|
O
|
F:HOH655
|
5.0
|
28.6
|
1.0
|
|
HB2
|
F:ALA58
|
5.0
|
36.5
|
1.0
|
|
N
|
F:GLN174
|
5.0
|
39.9
|
1.0
|
|
Potassium binding site 7 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 7 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K502
b:42.1
occ:1.00
|
HO1
|
G:EDO505
|
2.1
|
61.4
|
1.0
|
|
OD1
|
G:ASP177
|
2.2
|
43.6
|
1.0
|
|
O
|
G:GLU172
|
2.2
|
53.5
|
1.0
|
|
O
|
G:CYS175
|
2.3
|
47.9
|
1.0
|
|
O1
|
G:EDO505
|
2.3
|
51.2
|
1.0
|
|
O
|
G:ALA58
|
2.3
|
40.8
|
1.0
|
|
OE1
|
G:GLU275
|
2.5
|
41.9
|
1.0
|
|
H
|
G:ASP177
|
3.1
|
47.7
|
1.0
|
|
HA
|
G:GLU172
|
3.2
|
71.8
|
1.0
|
|
C
|
G:GLU172
|
3.2
|
52.7
|
1.0
|
|
CG
|
G:ASP177
|
3.4
|
56.5
|
1.0
|
|
HB1
|
G:ALA58
|
3.4
|
54.1
|
1.0
|
|
HB3
|
G:GLU172
|
3.4
|
75.2
|
1.0
|
|
CD
|
G:GLU275
|
3.5
|
47.5
|
1.0
|
|
C
|
G:ALA58
|
3.5
|
39.8
|
1.0
|
|
O2
|
G:EDO505
|
3.5
|
62.3
|
1.0
|
|
C
|
G:CYS175
|
3.5
|
53.6
|
1.0
|
|
HA
|
G:ILE176
|
3.5
|
57.0
|
1.0
|
|
CA
|
G:GLU172
|
3.6
|
59.9
|
1.0
|
|
N
|
G:ASP177
|
3.7
|
39.8
|
1.0
|
|
C1
|
G:EDO505
|
3.7
|
48.6
|
1.0
|
|
HG3
|
G:GLU275
|
3.8
|
61.7
|
1.0
|
|
HB2
|
G:ASP177
|
3.9
|
52.2
|
1.0
|
|
HA
|
G:ALA58
|
3.9
|
55.8
|
1.0
|
|
HO2
|
G:EDO505
|
3.9
|
74.8
|
1.0
|
|
CB
|
G:GLU172
|
4.0
|
62.7
|
1.0
|
|
CA
|
G:ALA58
|
4.1
|
46.5
|
1.0
|
|
CB
|
G:ASP177
|
4.1
|
43.5
|
1.0
|
|
H11
|
G:EDO505
|
4.1
|
58.4
|
1.0
|
|
CB
|
G:ALA58
|
4.1
|
45.1
|
1.0
|
|
CA
|
G:ILE176
|
4.2
|
47.5
|
1.0
|
|
OE2
|
G:GLU275
|
4.2
|
46.5
|
1.0
|
|
CG
|
G:GLU275
|
4.2
|
51.4
|
1.0
|
|
H12
|
G:EDO505
|
4.3
|
58.4
|
1.0
|
|
N
|
G:ILE176
|
4.3
|
50.9
|
1.0
|
|
OD2
|
G:ASP177
|
4.3
|
50.8
|
1.0
|
|
C2
|
G:EDO505
|
4.3
|
49.7
|
1.0
|
|
HA2
|
G:GLY59
|
4.4
|
49.6
|
1.0
|
|
C
|
G:ILE176
|
4.4
|
47.6
|
1.0
|
|
N
|
G:GLU173
|
4.4
|
63.8
|
1.0
|
|
HB2
|
G:GLU172
|
4.4
|
75.2
|
1.0
|
|
H
|
G:CYS175
|
4.5
|
68.0
|
1.0
|
|
HA
|
G:GLU173
|
4.5
|
73.5
|
1.0
|
|
CA
|
G:ASP177
|
4.5
|
39.8
|
1.0
|
|
N
|
G:GLY59
|
4.6
|
45.5
|
1.0
|
|
HB3
|
G:ALA58
|
4.6
|
54.1
|
1.0
|
|
N
|
G:CYS175
|
4.6
|
56.6
|
1.0
|
|
CA
|
G:CYS175
|
4.6
|
57.0
|
1.0
|
|
O
|
G:GLY59
|
4.7
|
45.8
|
1.0
|
|
HG2
|
G:GLU275
|
4.8
|
61.7
|
1.0
|
|
CA
|
G:GLY59
|
4.8
|
41.3
|
1.0
|
|
CA
|
G:GLU173
|
4.8
|
61.2
|
1.0
|
|
H22
|
G:EDO505
|
4.9
|
59.7
|
1.0
|
|
HB2
|
G:ALA58
|
4.9
|
54.1
|
1.0
|
|
HB2
|
G:CYS175
|
4.9
|
71.2
|
1.0
|
|
N
|
G:GLU172
|
5.0
|
66.8
|
1.0
|
|
HB3
|
G:ASP177
|
5.0
|
52.2
|
1.0
|
|
Potassium binding site 8 out
of 8 in 9qdi
Go back to
Potassium Binding Sites List in 9qdi
Potassium binding site 8 out
of 8 in the Crystal Structure of BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide
 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 BF3526 Peptidase From Bacteroides Fragilis in Complex with A Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:K501
b:51.9
occ:1.00
|
HO1
|
H:EDO504
|
2.2
|
78.8
|
1.0
|
|
OD2
|
H:ASP177
|
2.3
|
60.7
|
1.0
|
|
H11
|
H:EDO504
|
2.3
|
82.4
|
1.0
|
|
O1
|
H:EDO504
|
2.3
|
65.7
|
1.0
|
|
O
|
H:ALA58
|
2.4
|
56.7
|
1.0
|
|
O
|
H:GLU172
|
2.5
|
68.6
|
1.0
|
|
OE2
|
H:GLU275
|
2.5
|
50.7
|
1.0
|
|
O
|
H:CYS175
|
2.5
|
65.9
|
1.0
|
|
C1
|
H:EDO504
|
2.7
|
68.7
|
1.0
|
|
HO2
|
H:EDO504
|
3.1
|
75.4
|
1.0
|
|
H12
|
H:EDO504
|
3.4
|
82.4
|
1.0
|
|
CG
|
H:ASP177
|
3.4
|
70.1
|
1.0
|
|
CD
|
H:GLU275
|
3.5
|
54.9
|
1.0
|
|
C
|
H:ALA58
|
3.5
|
48.1
|
1.0
|
|
C
|
H:GLU172
|
3.5
|
71.2
|
1.0
|
|
O2
|
H:EDO504
|
3.7
|
62.9
|
1.0
|
|
C
|
H:CYS175
|
3.7
|
71.0
|
1.0
|
|
C2
|
H:EDO504
|
3.8
|
67.6
|
1.0
|
|
N
|
H:ASP177
|
3.9
|
55.8
|
1.0
|
|
CB
|
H:ASP177
|
4.1
|
60.3
|
1.0
|
|
CA
|
H:ALA58
|
4.1
|
55.5
|
1.0
|
|
CA
|
H:GLU172
|
4.1
|
72.1
|
1.0
|
|
H22
|
H:EDO504
|
4.1
|
81.1
|
1.0
|
|
CB
|
H:ALA58
|
4.2
|
46.7
|
1.0
|
|
CG
|
H:GLU275
|
4.2
|
54.0
|
1.0
|
|
OE1
|
H:GLU275
|
4.3
|
53.3
|
1.0
|
|
CA
|
H:ILE176
|
4.3
|
61.6
|
1.0
|
|
O
|
H:GLY59
|
4.3
|
56.7
|
1.0
|
|
N
|
H:ILE176
|
4.4
|
69.2
|
1.0
|
|
C
|
H:ILE176
|
4.4
|
62.0
|
1.0
|
|
OD1
|
H:ASP177
|
4.4
|
63.3
|
1.0
|
|
CB
|
H:GLU172
|
4.5
|
73.8
|
1.0
|
|
H21
|
H:EDO504
|
4.5
|
81.1
|
1.0
|
|
N
|
H:GLY59
|
4.6
|
50.9
|
1.0
|
|
N
|
H:GLU173
|
4.6
|
71.7
|
1.0
|
|
N
|
H:CYS175
|
4.6
|
58.8
|
1.0
|
|
CA
|
H:ASP177
|
4.6
|
54.4
|
1.0
|
|
CA
|
H:CYS175
|
4.8
|
65.5
|
1.0
|
|
C
|
H:GLY59
|
4.8
|
56.8
|
1.0
|
|
CA
|
H:GLY59
|
4.8
|
47.0
|
1.0
|
|
CA
|
H:GLU173
|
4.9
|
75.5
|
1.0
|
|
C
|
H:GLU173
|
4.9
|
72.1
|
1.0
|
|
Reference:
M.A.Marquez-Monino,
A.Martinez Gascuena,
T.Azzam,
A.Persson,
A.Manzanares-Gomez,
M.Aguillo-Urarte,
T.T.Brown,
A.Montero,
R.Lood,
A.Naegali,
J.J.Du,
S.R.Connell,
D.E.Sastre,
E.J.Sundberg,
B.Trastoy.
Structural Insights Into Iga Recognition By M64 Peptidases To Be Published.
Page generated: Sat Aug 9 19:26:38 2025
|
