Sodium in PDB 7yu0: Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
Enzymatic activity of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
All present enzymatic activity of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant:
3.5.1.117;
Protein crystallography data
The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant, PDB code: 7yu0
was solved by
S.Negoro,
Y.Higuchi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.01 /
1.35
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.242,
144.345,
129.178,
90,
90,
90
|
R / Rfree (%)
|
11.1 /
13.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
(pdb code 7yu0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant, PDB code: 7yu0:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 7yu0
Go back to
Sodium Binding Sites List in 7yu0
Sodium binding site 1 out
of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1009
b:51.6
occ:1.00
|
OE2
|
A:GLU136
|
2.5
|
29.1
|
1.0
|
O
|
A:HOH1281
|
2.7
|
27.9
|
1.0
|
O
|
A:HOH1352
|
2.8
|
52.7
|
1.0
|
H
|
A:GLY133
|
3.0
|
19.0
|
1.0
|
CD
|
A:GLU136
|
3.4
|
34.4
|
1.0
|
HA3
|
A:GLY133
|
3.5
|
19.8
|
1.0
|
HB3
|
A:ARG131
|
3.5
|
21.8
|
1.0
|
H
|
A:THR132
|
3.6
|
18.0
|
1.0
|
N
|
A:GLY133
|
3.6
|
18.6
|
1.0
|
OE1
|
A:GLU136
|
3.7
|
41.6
|
1.0
|
CA
|
A:GLY133
|
4.0
|
20.0
|
1.0
|
HA2
|
A:GLY133
|
4.2
|
19.7
|
1.0
|
HD2
|
A:ARG131
|
4.2
|
34.0
|
1.0
|
HA
|
A:ARG131
|
4.3
|
18.8
|
1.0
|
HG2
|
A:ARG131
|
4.3
|
26.4
|
1.0
|
N
|
A:THR132
|
4.3
|
18.1
|
1.0
|
CB
|
A:ARG131
|
4.4
|
21.7
|
1.0
|
O
|
B:HOH608
|
4.6
|
47.5
|
1.0
|
C
|
A:THR132
|
4.7
|
18.5
|
1.0
|
CG
|
A:ARG131
|
4.7
|
26.4
|
1.0
|
HD2
|
B:PHE30
|
4.7
|
78.1
|
1.0
|
CA
|
A:ARG131
|
4.7
|
18.8
|
1.0
|
HB2
|
B:PHE30
|
4.8
|
67.3
|
1.0
|
CD
|
A:ARG131
|
4.8
|
34.3
|
1.0
|
CD2
|
B:PHE30
|
4.8
|
79.9
|
1.0
|
CG
|
A:GLU136
|
4.8
|
30.9
|
1.0
|
HB3
|
B:PHE30
|
4.8
|
68.5
|
1.0
|
O
|
A:HOH1189
|
4.9
|
32.3
|
1.0
|
HD3
|
A:ARG131
|
4.9
|
34.4
|
1.0
|
C
|
A:ARG131
|
4.9
|
18.0
|
1.0
|
HG3
|
A:GLU136
|
5.0
|
30.3
|
1.0
|
|
Sodium binding site 2 out
of 3 in 7yu0
Go back to
Sodium Binding Sites List in 7yu0
Sodium binding site 2 out
of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na408
b:38.7
occ:1.00
|
O
|
B:HOH704
|
2.2
|
39.9
|
1.0
|
O
|
B:HOH754
|
2.3
|
30.9
|
1.0
|
O
|
B:THR315
|
2.5
|
21.1
|
1.0
|
O
|
B:HOH628
|
2.5
|
20.2
|
1.0
|
O
|
B:HOH805
|
2.6
|
47.7
|
1.0
|
C
|
B:THR315
|
3.5
|
17.8
|
1.0
|
HB
|
B:THR315
|
3.7
|
19.0
|
1.0
|
HA
|
B:THR315
|
3.7
|
17.0
|
1.0
|
HB2
|
B:ASP316
|
3.8
|
21.9
|
1.0
|
O
|
B:HOH690
|
3.9
|
26.1
|
1.0
|
O
|
B:HOH786
|
4.0
|
19.8
|
1.0
|
HB1
|
B:ALA79
|
4.0
|
22.1
|
1.0
|
CA
|
B:THR315
|
4.1
|
16.9
|
1.0
|
HB3
|
B:ALA79
|
4.2
|
22.6
|
1.0
|
O
|
B:GLY80
|
4.3
|
17.6
|
1.0
|
CB
|
B:THR315
|
4.4
|
18.8
|
1.0
|
HG3
|
B:GLU317
|
4.4
|
21.3
|
1.0
|
O
|
B:HOH543
|
4.4
|
18.8
|
1.0
|
CB
|
B:ALA79
|
4.5
|
22.6
|
1.0
|
HG2
|
B:GLU317
|
4.6
|
21.5
|
1.0
|
N
|
B:ASP316
|
4.6
|
17.6
|
1.0
|
CB
|
B:ASP316
|
4.6
|
21.9
|
1.0
|
O
|
B:ASP316
|
4.7
|
23.9
|
1.0
|
C
|
B:ASP316
|
4.8
|
19.1
|
1.0
|
HB2
|
B:ALA79
|
4.9
|
22.1
|
1.0
|
HB3
|
B:ASP316
|
4.9
|
21.4
|
1.0
|
CA
|
B:ASP316
|
4.9
|
19.2
|
1.0
|
HA
|
B:ALA81
|
5.0
|
15.5
|
1.0
|
CG
|
B:GLU317
|
5.0
|
21.7
|
1.0
|
|
Sodium binding site 3 out
of 3 in 7yu0
Go back to
Sodium Binding Sites List in 7yu0
Sodium binding site 3 out
of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na409
b:50.9
occ:1.00
|
OE1
|
B:GLU136
|
2.5
|
30.9
|
1.0
|
O
|
B:HOH696
|
2.7
|
35.5
|
1.0
|
O
|
B:HOH778
|
3.0
|
48.7
|
1.0
|
H
|
B:GLY133
|
3.0
|
20.5
|
1.0
|
CD
|
B:GLU136
|
3.3
|
37.5
|
1.0
|
OE2
|
B:GLU136
|
3.5
|
43.7
|
1.0
|
HA3
|
B:GLY133
|
3.5
|
21.0
|
1.0
|
HB3
|
B:ARG131
|
3.6
|
24.6
|
1.0
|
HD1
|
A:PHE30
|
3.6
|
62.0
|
1.0
|
H
|
B:THR132
|
3.7
|
19.7
|
1.0
|
N
|
B:GLY133
|
3.7
|
20.4
|
1.0
|
HE1
|
A:PHE30
|
3.9
|
67.7
|
1.0
|
CD1
|
A:PHE30
|
3.9
|
63.4
|
1.0
|
CE1
|
A:PHE30
|
4.0
|
68.8
|
1.0
|
HG2
|
B:ARG131
|
4.1
|
27.3
|
1.0
|
CA
|
B:GLY133
|
4.1
|
21.1
|
1.0
|
HD2
|
B:ARG131
|
4.1
|
35.6
|
1.0
|
HA
|
B:ARG131
|
4.3
|
21.0
|
1.0
|
HA2
|
B:GLY133
|
4.3
|
20.8
|
1.0
|
O
|
A:HOH1332
|
4.4
|
51.4
|
1.0
|
CB
|
B:ARG131
|
4.4
|
24.4
|
1.0
|
N
|
B:THR132
|
4.4
|
19.5
|
1.0
|
O
|
A:HOH1169
|
4.4
|
44.8
|
1.0
|
CG
|
B:ARG131
|
4.5
|
26.6
|
1.0
|
O
|
B:HOH776
|
4.5
|
45.8
|
1.0
|
HB3
|
A:PHE30
|
4.6
|
51.1
|
1.0
|
CD
|
B:ARG131
|
4.7
|
36.7
|
1.0
|
CG
|
A:PHE30
|
4.7
|
56.4
|
1.0
|
HD3
|
B:ARG131
|
4.7
|
36.9
|
1.0
|
CG
|
B:GLU136
|
4.7
|
32.8
|
1.0
|
CA
|
B:ARG131
|
4.7
|
21.0
|
1.0
|
C
|
B:THR132
|
4.8
|
20.0
|
1.0
|
O
|
B:HOH560
|
4.9
|
37.6
|
1.0
|
HG3
|
B:GLU136
|
4.9
|
32.2
|
1.0
|
CZ
|
A:PHE30
|
4.9
|
71.3
|
1.0
|
C
|
B:ARG131
|
5.0
|
20.1
|
1.0
|
|
Reference:
S.Negoro,
N.Shibata,
D.I.Kato,
Y.Tanaka,
K.Yasuhira,
K.Nagai,
S.Oshima,
Y.Furuno,
R.Yokoyama,
K.Miyazaki,
M.Takeo,
K.Hengphasatporn,
Y.Shigeta,
Y.H.Lee,
Y.Higuchi.
X-Ray Crystallographic and Mutational Analysis of the Nylc Precursor: Catalytic Mechanism of Autocleavage and Substrate Hydrolysis of Nylon Hydrolase. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 36799721
DOI: 10.1111/FEBS.16755
Page generated: Fri Apr 7 17:24:27 2023
|