Potassium in PDB 4jay: Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
Enzymatic activity of Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
All present enzymatic activity of Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+:
1.1.1.158;
Protein crystallography data
The structure of Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+, PDB code: 4jay
was solved by
M.W.Chen,
B.Lohkamp,
R.Schnell,
J.Lescar,
G.Schneider,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.33 /
2.23
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
153.700,
154.350,
64.470,
90.00,
102.26,
90.00
|
R / Rfree (%)
|
22.3 /
25.8
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
(pdb code 4jay). 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 P. Aeruginosa Murb in Complex with Nadp+, PDB code: 4jay:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 4jay
Go back to
Potassium Binding Sites List in 4jay
Potassium binding site 1 out
of 4 in the Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
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 P. Aeruginosa Murb in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1004
b:20.0
occ:1.00
|
OE2
|
A:GLU335
|
2.3
|
34.8
|
1.0
|
O
|
A:SER239
|
2.7
|
19.1
|
1.0
|
OD1
|
A:ASN57
|
2.7
|
17.1
|
1.0
|
O
|
A:ALA237
|
2.7
|
16.2
|
1.0
|
O7N
|
A:NAP1002
|
3.0
|
15.4
|
1.0
|
CD
|
A:GLU335
|
3.2
|
32.9
|
1.0
|
C
|
A:SER239
|
3.7
|
19.2
|
1.0
|
N
|
A:SER239
|
3.8
|
19.2
|
1.0
|
C1'
|
A:FAD1001
|
3.8
|
13.0
|
1.0
|
CG
|
A:GLU335
|
3.8
|
33.0
|
1.0
|
CG
|
A:ASN57
|
3.8
|
17.4
|
1.0
|
C7N
|
A:NAP1002
|
3.9
|
15.0
|
1.0
|
C
|
A:ALA237
|
3.9
|
18.6
|
1.0
|
N7N
|
A:NAP1002
|
4.0
|
13.9
|
1.0
|
C
|
A:GLY238
|
4.1
|
19.9
|
1.0
|
CB
|
A:GLU335
|
4.2
|
31.5
|
1.0
|
OE1
|
A:GLU335
|
4.2
|
33.9
|
1.0
|
N10
|
A:FAD1001
|
4.2
|
12.0
|
1.0
|
CA
|
A:SER239
|
4.2
|
19.3
|
1.0
|
CA
|
A:GLY238
|
4.4
|
18.9
|
1.0
|
CG
|
A:PRO336
|
4.5
|
31.0
|
1.0
|
CB
|
A:SER239
|
4.5
|
19.0
|
1.0
|
NE2
|
A:GLN127
|
4.6
|
21.1
|
1.0
|
N
|
A:GLY238
|
4.6
|
19.3
|
1.0
|
C9A
|
A:FAD1001
|
4.6
|
11.4
|
1.0
|
ND2
|
A:ASN57
|
4.7
|
17.9
|
1.0
|
CD
|
A:PRO336
|
4.7
|
28.7
|
1.0
|
CB
|
A:ASN57
|
4.7
|
16.7
|
1.0
|
C10
|
A:FAD1001
|
4.7
|
11.5
|
1.0
|
C9
|
A:FAD1001
|
4.8
|
11.4
|
1.0
|
O
|
A:GLY238
|
4.8
|
21.6
|
1.0
|
N
|
A:PRO336
|
4.8
|
29.1
|
1.0
|
N
|
A:PHE240
|
4.9
|
19.3
|
1.0
|
N1
|
A:FAD1001
|
4.9
|
11.3
|
1.0
|
CB
|
A:ALA237
|
4.9
|
19.2
|
1.0
|
O
|
A:SER56
|
4.9
|
13.1
|
1.0
|
|
Potassium binding site 2 out
of 4 in 4jay
Go back to
Potassium Binding Sites List in 4jay
Potassium binding site 2 out
of 4 in the Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
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 P. Aeruginosa Murb in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K401
b:16.3
occ:1.00
|
OE2
|
B:GLU335
|
2.4
|
36.8
|
1.0
|
OD1
|
B:ASN57
|
2.7
|
22.1
|
1.0
|
O
|
B:ALA237
|
2.7
|
18.8
|
1.0
|
O
|
B:SER239
|
2.9
|
22.1
|
1.0
|
O7N
|
B:NAP403
|
3.0
|
15.8
|
1.0
|
CD
|
B:GLU335
|
3.3
|
35.6
|
1.0
|
C1'
|
B:FAD402
|
3.5
|
15.3
|
1.0
|
CG
|
B:ASN57
|
3.8
|
21.1
|
1.0
|
N
|
B:SER239
|
3.9
|
21.6
|
1.0
|
C
|
B:SER239
|
3.9
|
22.1
|
1.0
|
CG
|
B:GLU335
|
3.9
|
36.0
|
1.0
|
C
|
B:ALA237
|
3.9
|
19.9
|
1.0
|
C7N
|
B:NAP403
|
3.9
|
15.5
|
1.0
|
N10
|
B:FAD402
|
3.9
|
15.7
|
1.0
|
N7N
|
B:NAP403
|
4.1
|
14.1
|
1.0
|
C
|
B:GLY238
|
4.2
|
21.8
|
1.0
|
OE1
|
B:GLU335
|
4.2
|
40.6
|
1.0
|
CB
|
B:GLU335
|
4.3
|
34.1
|
1.0
|
CA
|
B:SER239
|
4.3
|
21.5
|
1.0
|
CA
|
B:GLY238
|
4.4
|
20.7
|
1.0
|
C9A
|
B:FAD402
|
4.5
|
16.6
|
1.0
|
NE2
|
B:GLN127
|
4.5
|
28.3
|
1.0
|
C10
|
B:FAD402
|
4.5
|
15.0
|
1.0
|
CG
|
B:PRO336
|
4.6
|
30.3
|
1.0
|
C9
|
B:FAD402
|
4.6
|
16.7
|
1.0
|
CB
|
B:SER239
|
4.6
|
22.2
|
1.0
|
N
|
B:GLY238
|
4.6
|
20.2
|
1.0
|
CB
|
B:ASN57
|
4.6
|
19.7
|
1.0
|
ND2
|
B:ASN57
|
4.7
|
22.0
|
1.0
|
N1
|
B:FAD402
|
4.7
|
14.3
|
1.0
|
O
|
B:SER56
|
4.8
|
16.3
|
1.0
|
CD
|
B:PRO336
|
4.8
|
29.3
|
1.0
|
C2'
|
B:FAD402
|
4.8
|
14.6
|
1.0
|
CB
|
B:ALA237
|
4.9
|
19.9
|
1.0
|
O
|
B:GLY238
|
4.9
|
23.5
|
1.0
|
CA
|
B:ASN57
|
4.9
|
19.5
|
1.0
|
N
|
B:PRO336
|
4.9
|
30.4
|
1.0
|
CA
|
B:ALA237
|
5.0
|
19.9
|
1.0
|
|
Potassium binding site 3 out
of 4 in 4jay
Go back to
Potassium Binding Sites List in 4jay
Potassium binding site 3 out
of 4 in the Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
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 P. Aeruginosa Murb in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K401
b:19.7
occ:1.00
|
OE2
|
C:GLU335
|
2.3
|
30.3
|
1.0
|
OD1
|
C:ASN57
|
2.7
|
22.4
|
1.0
|
O
|
C:SER239
|
2.7
|
16.5
|
1.0
|
O
|
C:ALA237
|
2.8
|
18.4
|
1.0
|
O7N
|
C:NAP403
|
3.1
|
22.8
|
1.0
|
CD
|
C:GLU335
|
3.2
|
29.8
|
1.0
|
C1'
|
C:FAD402
|
3.7
|
16.3
|
1.0
|
CG
|
C:GLU335
|
3.7
|
29.3
|
1.0
|
C
|
C:SER239
|
3.8
|
17.6
|
1.0
|
CG
|
C:ASN57
|
3.8
|
22.0
|
1.0
|
N
|
C:SER239
|
3.8
|
18.7
|
1.0
|
C
|
C:ALA237
|
4.0
|
19.7
|
1.0
|
C7N
|
C:NAP403
|
4.0
|
20.6
|
1.0
|
N7N
|
C:NAP403
|
4.0
|
17.3
|
1.0
|
CB
|
C:GLU335
|
4.1
|
28.4
|
1.0
|
OE1
|
C:GLU335
|
4.1
|
30.2
|
1.0
|
N10
|
C:FAD402
|
4.2
|
16.2
|
1.0
|
C
|
C:GLY238
|
4.2
|
19.1
|
1.0
|
CA
|
C:SER239
|
4.3
|
18.3
|
1.0
|
CG
|
C:PRO336
|
4.4
|
29.0
|
1.0
|
CA
|
C:GLY238
|
4.5
|
19.3
|
1.0
|
NE2
|
C:GLN127
|
4.5
|
28.0
|
1.0
|
CB
|
C:SER239
|
4.6
|
18.7
|
1.0
|
ND2
|
C:ASN57
|
4.6
|
21.8
|
1.0
|
CD
|
C:PRO336
|
4.6
|
28.6
|
1.0
|
C9A
|
C:FAD402
|
4.7
|
16.0
|
1.0
|
N
|
C:GLY238
|
4.7
|
19.6
|
1.0
|
CB
|
C:ASN57
|
4.7
|
20.4
|
1.0
|
N
|
C:PRO336
|
4.7
|
29.0
|
1.0
|
C10
|
C:FAD402
|
4.7
|
15.7
|
1.0
|
C9
|
C:FAD402
|
4.8
|
15.9
|
1.0
|
CB
|
C:ALA237
|
4.9
|
20.9
|
1.0
|
O
|
C:GLY238
|
4.9
|
19.9
|
1.0
|
N
|
C:PHE240
|
4.9
|
18.0
|
1.0
|
N1
|
C:FAD402
|
4.9
|
14.4
|
1.0
|
O
|
C:SER56
|
4.9
|
16.7
|
1.0
|
C
|
C:GLU335
|
4.9
|
28.1
|
1.0
|
C2'
|
C:FAD402
|
5.0
|
15.1
|
1.0
|
CA
|
C:ASN57
|
5.0
|
20.3
|
1.0
|
|
Potassium binding site 4 out
of 4 in 4jay
Go back to
Potassium Binding Sites List in 4jay
Potassium binding site 4 out
of 4 in the Crystal Structure of P. Aeruginosa Murb in Complex with Nadp+
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 P. Aeruginosa Murb in Complex with Nadp+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K401
b:19.9
occ:1.00
|
OE2
|
D:GLU335
|
2.3
|
44.8
|
1.0
|
OD1
|
D:ASN57
|
2.6
|
25.4
|
1.0
|
O
|
D:ALA237
|
2.7
|
16.9
|
1.0
|
O
|
D:SER239
|
2.8
|
18.7
|
1.0
|
O7N
|
D:NAP403
|
3.1
|
15.5
|
1.0
|
CD
|
D:GLU335
|
3.2
|
44.0
|
1.0
|
C1'
|
D:FAD402
|
3.6
|
14.1
|
1.0
|
CG
|
D:ASN57
|
3.7
|
23.4
|
1.0
|
CG
|
D:GLU335
|
3.8
|
38.0
|
1.0
|
C
|
D:SER239
|
3.8
|
19.2
|
1.0
|
N
|
D:SER239
|
3.8
|
18.3
|
1.0
|
C
|
D:ALA237
|
3.9
|
17.7
|
1.0
|
C7N
|
D:NAP403
|
4.0
|
17.4
|
1.0
|
N10
|
D:FAD402
|
4.1
|
14.1
|
1.0
|
N7N
|
D:NAP403
|
4.1
|
16.9
|
1.0
|
CB
|
D:GLU335
|
4.1
|
33.0
|
1.0
|
OE1
|
D:GLU335
|
4.2
|
46.1
|
1.0
|
C
|
D:GLY238
|
4.2
|
18.7
|
1.0
|
CA
|
D:SER239
|
4.3
|
19.0
|
1.0
|
CA
|
D:GLY238
|
4.4
|
18.1
|
1.0
|
CG
|
D:PRO336
|
4.4
|
25.0
|
1.0
|
NE2
|
D:GLN127
|
4.6
|
32.2
|
1.0
|
C9A
|
D:FAD402
|
4.6
|
14.5
|
1.0
|
ND2
|
D:ASN57
|
4.6
|
23.5
|
1.0
|
CB
|
D:SER239
|
4.6
|
20.2
|
1.0
|
CB
|
D:ASN57
|
4.6
|
21.1
|
1.0
|
N
|
D:GLY238
|
4.6
|
17.8
|
1.0
|
C10
|
D:FAD402
|
4.7
|
14.0
|
1.0
|
C9
|
D:FAD402
|
4.7
|
15.3
|
1.0
|
CD
|
D:PRO336
|
4.7
|
24.6
|
1.0
|
N
|
D:PRO336
|
4.7
|
26.3
|
1.0
|
N1
|
D:FAD402
|
4.8
|
13.1
|
1.0
|
O
|
D:SER56
|
4.9
|
16.7
|
1.0
|
CB
|
D:ALA237
|
4.9
|
18.4
|
1.0
|
O
|
D:GLY238
|
4.9
|
22.7
|
1.0
|
CA
|
D:ASN57
|
4.9
|
20.3
|
1.0
|
N
|
D:PHE240
|
4.9
|
19.0
|
1.0
|
C2'
|
D:FAD402
|
4.9
|
13.9
|
1.0
|
C
|
D:GLU335
|
5.0
|
27.5
|
1.0
|
|
Reference:
M.W.Chen,
B.Lohkamp,
R.Schnell,
J.Lescar,
G.Schneider.
Substrate Channel Flexibility in Pseudomonas Aeruginosa Murb Accommodates Two Distinct Substrates. Plos One V. 8 66936 2013.
ISSN: ESSN 1932-6203
PubMed: 23805286
DOI: 10.1371/JOURNAL.PONE.0066936
Page generated: Mon Aug 12 11:04:50 2024
|