Potassium in PDB 8r56: Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
Protein crystallography data
The structure of Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz), PDB code: 8r56
was solved by
M.Sharma,
G.J.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
62.55 /
2.45
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.524,
194.726,
117.654,
90,
92.29,
90
|
R / Rfree (%)
|
21.2 /
24.4
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
(pdb code 8r56). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz), PDB code: 8r56:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8r56
Go back to
Potassium Binding Sites List in 8r56
Potassium binding site 1 out
of 4 in the Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
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 GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K702
b:48.2
occ:1.00
|
O
|
A:ASP473
|
2.4
|
17.4
|
1.0
|
O
|
A:GLY155
|
2.6
|
24.8
|
1.0
|
O
|
A:HOH859
|
2.7
|
14.4
|
1.0
|
OD1
|
A:ASP482
|
2.8
|
26.8
|
1.0
|
O
|
A:HOH959
|
2.8
|
14.0
|
1.0
|
OD2
|
A:ASP482
|
3.4
|
24.4
|
1.0
|
CG
|
A:ASP482
|
3.4
|
24.6
|
1.0
|
C
|
A:ASP473
|
3.6
|
20.7
|
1.0
|
C
|
A:GLY155
|
3.7
|
23.4
|
1.0
|
CG
|
A:PRO154
|
3.8
|
21.7
|
1.0
|
CB
|
A:ASP473
|
4.3
|
18.6
|
1.0
|
O
|
A:HOH929
|
4.3
|
21.7
|
1.0
|
CA
|
A:VAL156
|
4.4
|
24.8
|
1.0
|
N
|
A:VAL156
|
4.4
|
25.5
|
1.0
|
CA
|
A:GLN474
|
4.4
|
18.1
|
1.0
|
N
|
A:GLN474
|
4.4
|
20.1
|
1.0
|
O
|
A:HOH843
|
4.5
|
14.9
|
1.0
|
CA
|
A:ASP473
|
4.5
|
19.4
|
1.0
|
N
|
A:GLY155
|
4.5
|
20.8
|
1.0
|
CB
|
A:PRO154
|
4.6
|
21.1
|
1.0
|
CD
|
A:ARG158
|
4.6
|
21.4
|
1.0
|
CA
|
A:GLY155
|
4.7
|
22.5
|
1.0
|
O
|
A:HOH853
|
4.8
|
16.2
|
1.0
|
C
|
A:GLN474
|
4.8
|
19.5
|
1.0
|
OG1
|
A:THR510
|
4.8
|
19.8
|
1.0
|
N
|
A:SER475
|
4.8
|
20.0
|
1.0
|
CB
|
A:ASP482
|
4.9
|
22.6
|
1.0
|
CD
|
A:PRO154
|
4.9
|
20.4
|
1.0
|
O
|
A:HOH931
|
4.9
|
24.6
|
1.0
|
C
|
A:PRO154
|
4.9
|
21.2
|
1.0
|
CG2
|
A:VAL156
|
4.9
|
25.6
|
1.0
|
N
|
A:ASP473
|
5.0
|
21.5
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8r56
Go back to
Potassium Binding Sites List in 8r56
Potassium binding site 2 out
of 4 in the Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
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 GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K702
b:44.4
occ:1.00
|
O
|
B:ASP473
|
2.4
|
25.8
|
1.0
|
O
|
B:GLY155
|
2.6
|
24.5
|
1.0
|
OD1
|
B:ASP482
|
2.6
|
23.8
|
1.0
|
CG
|
B:ASP482
|
3.3
|
25.1
|
1.0
|
OD2
|
B:ASP482
|
3.4
|
27.7
|
1.0
|
C
|
B:ASP473
|
3.5
|
25.2
|
1.0
|
CG
|
B:PRO154
|
3.7
|
18.7
|
1.0
|
C
|
B:GLY155
|
3.8
|
22.6
|
1.0
|
O
|
B:HOH864
|
4.3
|
22.9
|
1.0
|
CA
|
B:GLN474
|
4.3
|
23.1
|
1.0
|
CB
|
B:ASP473
|
4.4
|
22.4
|
1.0
|
N
|
B:GLN474
|
4.4
|
24.3
|
1.0
|
CA
|
B:VAL156
|
4.5
|
24.2
|
1.0
|
CB
|
B:PRO154
|
4.5
|
18.3
|
1.0
|
N
|
B:VAL156
|
4.5
|
23.0
|
1.0
|
CA
|
B:ASP473
|
4.5
|
25.3
|
1.0
|
CD
|
B:ARG158
|
4.5
|
26.4
|
1.0
|
N
|
B:GLY155
|
4.6
|
20.2
|
1.0
|
C
|
B:GLN474
|
4.7
|
22.3
|
1.0
|
N
|
B:SER475
|
4.8
|
22.3
|
1.0
|
CB
|
B:ASP482
|
4.8
|
22.9
|
1.0
|
CA
|
B:GLY155
|
4.8
|
20.6
|
1.0
|
CD
|
B:PRO154
|
4.9
|
19.5
|
1.0
|
C
|
B:PRO154
|
4.9
|
20.1
|
1.0
|
CG
|
B:ARG158
|
5.0
|
28.6
|
1.0
|
OG1
|
B:THR510
|
5.0
|
27.8
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8r56
Go back to
Potassium Binding Sites List in 8r56
Potassium binding site 3 out
of 4 in the Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
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 GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K702
b:33.3
occ:1.00
|
O
|
C:GLY155
|
2.4
|
24.0
|
1.0
|
O
|
C:ASP473
|
2.5
|
19.8
|
1.0
|
O
|
C:HOH920
|
2.5
|
22.3
|
1.0
|
OD1
|
C:ASP482
|
2.6
|
22.2
|
1.0
|
CG
|
C:ASP482
|
3.4
|
20.6
|
1.0
|
OD2
|
C:ASP482
|
3.5
|
19.7
|
1.0
|
CG
|
C:PRO154
|
3.6
|
21.7
|
1.0
|
C
|
C:GLY155
|
3.6
|
23.7
|
1.0
|
C
|
C:ASP473
|
3.7
|
18.2
|
1.0
|
CB
|
C:PRO154
|
4.3
|
22.1
|
1.0
|
CD
|
C:ARG158
|
4.3
|
18.4
|
1.0
|
N
|
C:GLY155
|
4.4
|
22.1
|
1.0
|
N
|
C:VAL156
|
4.5
|
24.0
|
1.0
|
CA
|
C:GLN474
|
4.5
|
19.1
|
1.0
|
CA
|
C:VAL156
|
4.5
|
22.3
|
1.0
|
N
|
C:GLN474
|
4.5
|
19.6
|
1.0
|
CB
|
C:ASP473
|
4.6
|
20.0
|
1.0
|
O
|
C:HOH867
|
4.6
|
14.0
|
1.0
|
CA
|
C:GLY155
|
4.7
|
22.0
|
1.0
|
C
|
C:PRO154
|
4.7
|
20.1
|
1.0
|
CA
|
C:ASP473
|
4.7
|
19.9
|
1.0
|
CD
|
C:PRO154
|
4.7
|
22.0
|
1.0
|
O
|
C:HOH912
|
4.8
|
16.8
|
1.0
|
CG
|
C:ARG158
|
4.8
|
18.8
|
1.0
|
CB
|
C:ASP482
|
4.8
|
21.7
|
1.0
|
O
|
C:HOH858
|
4.8
|
24.4
|
1.0
|
O
|
C:HOH821
|
4.8
|
7.7
|
1.0
|
C
|
C:GLN474
|
4.9
|
21.5
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8r56
Go back to
Potassium Binding Sites List in 8r56
Potassium binding site 4 out
of 4 in the Crystal Structure of GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz)
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 GH31 Family Sulfoquinovosidase Bmsqase in Covalent Complex with Sq-Aziridine (Sqz) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K702
b:44.5
occ:1.00
|
OD1
|
D:ASP482
|
2.4
|
28.5
|
1.0
|
O
|
D:ASP473
|
2.4
|
34.4
|
1.0
|
O
|
D:GLY155
|
2.6
|
23.4
|
1.0
|
O
|
D:HOH851
|
3.0
|
26.6
|
1.0
|
CG
|
D:ASP482
|
3.1
|
23.3
|
1.0
|
OD2
|
D:ASP482
|
3.2
|
22.8
|
1.0
|
C
|
D:ASP473
|
3.6
|
30.2
|
1.0
|
CG
|
D:PRO154
|
3.7
|
22.1
|
1.0
|
C
|
D:GLY155
|
3.8
|
24.5
|
1.0
|
CD
|
D:ARG158
|
4.2
|
24.6
|
1.0
|
CA
|
D:GLN474
|
4.3
|
28.5
|
1.0
|
N
|
D:GLN474
|
4.4
|
31.2
|
1.0
|
CB
|
D:PRO154
|
4.4
|
22.9
|
1.0
|
CB
|
D:ASP482
|
4.5
|
22.8
|
1.0
|
CA
|
D:VAL156
|
4.6
|
24.6
|
1.0
|
N
|
D:VAL156
|
4.6
|
25.0
|
1.0
|
O
|
D:HOH866
|
4.6
|
25.1
|
1.0
|
CB
|
D:ASP473
|
4.6
|
28.6
|
1.0
|
N
|
D:GLY155
|
4.6
|
22.4
|
1.0
|
CA
|
D:ASP473
|
4.7
|
28.7
|
1.0
|
C
|
D:GLN474
|
4.7
|
27.4
|
1.0
|
CG
|
D:ARG158
|
4.7
|
25.2
|
1.0
|
N
|
D:SER475
|
4.8
|
25.5
|
1.0
|
CA
|
D:GLY155
|
4.9
|
24.6
|
1.0
|
C
|
D:PRO154
|
4.9
|
22.8
|
1.0
|
O
|
D:HOH828
|
4.9
|
16.2
|
1.0
|
CD
|
D:PRO154
|
5.0
|
22.0
|
1.0
|
|
Reference:
Z.Li,
I.Pickles,
M.Sharma,
B.Melling,
J.Codee,
L.Pallasdies,
S.Williams,
H.Overkleeft,
G.J.Davies.
Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes. Angew.Chem.Int.Ed.Engl. 01358 2024.
ISSN: ESSN 1521-3773
PubMed: 38647177
DOI: 10.1002/ANIE.202401358
Page generated: Tue Aug 13 00:39:49 2024
|