Nickel in PDB 9kho: Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
Enzymatic activity of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
All present enzymatic activity of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L):
3.1.1.81;
Protein crystallography data
The structure of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L), PDB code: 9kho
was solved by
Y.Chen,
X.H.Chu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.97 /
2.16
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.098,
149.83,
80.184,
90,
109.75,
90
|
R / Rfree (%)
|
18.4 /
22.5
|
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Nickel atom in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
(pdb code 9kho). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the
Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L), PDB code: 9kho:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 12 in 9kho
Go back to
Nickel Binding Sites List in 9kho
Nickel binding site 1 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni301
b:40.9
occ:1.00
|
NE2
|
A:HIS178
|
2.2
|
23.8
|
1.0
|
NE2
|
A:HIS102
|
2.4
|
26.4
|
1.0
|
OD2
|
A:ASP200
|
2.4
|
28.1
|
1.0
|
ND1
|
A:HIS104
|
2.4
|
24.2
|
1.0
|
O
|
A:HOH412
|
2.7
|
34.1
|
1.0
|
CE1
|
A:HIS178
|
3.0
|
27.9
|
1.0
|
CD2
|
A:HIS178
|
3.2
|
28.1
|
1.0
|
CD2
|
A:HIS102
|
3.3
|
21.1
|
1.0
|
CG
|
A:HIS104
|
3.4
|
26.0
|
1.0
|
NI
|
A:NI302
|
3.4
|
40.1
|
1.0
|
CE1
|
A:HIS104
|
3.4
|
26.2
|
1.0
|
CE1
|
A:HIS102
|
3.5
|
23.9
|
1.0
|
CG
|
A:ASP200
|
3.5
|
27.1
|
1.0
|
CB
|
A:HIS104
|
3.6
|
25.0
|
1.0
|
CB
|
A:ASP200
|
4.0
|
25.9
|
1.0
|
CD2
|
A:HIS107
|
4.2
|
26.8
|
1.0
|
ND1
|
A:HIS178
|
4.2
|
22.2
|
1.0
|
NE2
|
A:HIS107
|
4.2
|
24.9
|
1.0
|
CG
|
A:HIS178
|
4.3
|
27.1
|
1.0
|
OH
|
A:TYR203
|
4.3
|
39.2
|
1.0
|
OD1
|
A:ASP106
|
4.5
|
27.4
|
1.0
|
CG
|
A:HIS102
|
4.5
|
22.2
|
1.0
|
NE2
|
A:HIS104
|
4.5
|
27.5
|
1.0
|
CD2
|
A:HIS104
|
4.5
|
23.8
|
1.0
|
ND1
|
A:HIS102
|
4.5
|
24.1
|
1.0
|
OD1
|
A:ASP200
|
4.6
|
29.3
|
1.0
|
CE1
|
A:TYR203
|
5.0
|
32.6
|
1.0
|
|
Nickel binding site 2 out
of 12 in 9kho
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Nickel Binding Sites List in 9kho
Nickel binding site 2 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni302
b:40.1
occ:1.00
|
NE2
|
A:HIS107
|
2.3
|
24.9
|
1.0
|
OD2
|
A:ASP200
|
2.3
|
28.1
|
1.0
|
OD2
|
A:ASP106
|
2.3
|
26.2
|
1.0
|
NE2
|
A:HIS245
|
2.3
|
32.9
|
1.0
|
CD2
|
A:HIS107
|
3.0
|
26.8
|
1.0
|
CG
|
A:ASP200
|
3.1
|
27.1
|
1.0
|
CG
|
A:ASP106
|
3.1
|
31.3
|
1.0
|
OD1
|
A:ASP200
|
3.2
|
29.3
|
1.0
|
CD2
|
A:HIS245
|
3.3
|
35.2
|
1.0
|
OD1
|
A:ASP106
|
3.3
|
27.4
|
1.0
|
NI
|
A:NI301
|
3.4
|
40.9
|
1.0
|
CE1
|
A:HIS245
|
3.4
|
36.2
|
1.0
|
CE1
|
A:HIS107
|
3.4
|
24.8
|
1.0
|
O
|
A:HOH412
|
3.6
|
34.1
|
1.0
|
O
|
A:HOH441
|
4.1
|
30.8
|
1.0
|
CG
|
A:HIS107
|
4.2
|
20.9
|
1.0
|
NE2
|
A:HIS102
|
4.3
|
26.4
|
1.0
|
ND1
|
A:HIS107
|
4.4
|
19.9
|
1.0
|
CE1
|
A:HIS102
|
4.4
|
23.9
|
1.0
|
CG
|
A:HIS245
|
4.4
|
36.6
|
1.0
|
ND1
|
A:HIS245
|
4.4
|
35.5
|
1.0
|
CB
|
A:ASP106
|
4.5
|
24.6
|
1.0
|
CB
|
A:ASP200
|
4.5
|
25.9
|
1.0
|
CE1
|
A:TYR203
|
4.6
|
32.6
|
1.0
|
|
Nickel binding site 3 out
of 12 in 9kho
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Nickel Binding Sites List in 9kho
Nickel binding site 3 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:41.4
occ:1.00
|
NE2
|
B:HIS178
|
2.1
|
28.6
|
1.0
|
OD2
|
B:ASP200
|
2.4
|
29.1
|
1.0
|
NE2
|
B:HIS102
|
2.4
|
30.2
|
1.0
|
ND1
|
B:HIS104
|
2.5
|
26.2
|
1.0
|
CE1
|
B:HIS178
|
2.9
|
26.0
|
1.0
|
O
|
B:HOH512
|
3.0
|
42.9
|
1.0
|
CD2
|
B:HIS178
|
3.1
|
26.8
|
1.0
|
CD2
|
B:HIS102
|
3.2
|
28.0
|
1.0
|
NI
|
B:NI302
|
3.3
|
44.6
|
1.0
|
CG
|
B:HIS104
|
3.4
|
26.7
|
1.0
|
CG
|
B:ASP200
|
3.5
|
30.6
|
1.0
|
CE1
|
B:HIS102
|
3.5
|
28.4
|
1.0
|
CE1
|
B:HIS104
|
3.5
|
31.6
|
1.0
|
CB
|
B:HIS104
|
3.6
|
27.4
|
1.0
|
NE2
|
B:HIS107
|
4.0
|
30.5
|
1.0
|
CB
|
B:ASP200
|
4.0
|
26.4
|
1.0
|
ND1
|
B:HIS178
|
4.1
|
28.8
|
1.0
|
CD2
|
B:HIS107
|
4.1
|
33.4
|
1.0
|
CG
|
B:HIS178
|
4.2
|
25.9
|
1.0
|
OD1
|
B:ASP106
|
4.4
|
35.3
|
1.0
|
OH
|
B:TYR203
|
4.4
|
45.2
|
1.0
|
CG
|
B:HIS102
|
4.5
|
28.6
|
1.0
|
ND1
|
B:HIS102
|
4.5
|
28.0
|
1.0
|
OD1
|
B:ASP200
|
4.6
|
28.7
|
1.0
|
CD2
|
B:HIS104
|
4.6
|
25.2
|
1.0
|
NE2
|
B:HIS104
|
4.6
|
29.9
|
1.0
|
OD2
|
B:ASP106
|
4.8
|
36.2
|
1.0
|
CE1
|
B:TYR203
|
5.0
|
33.0
|
1.0
|
|
Nickel binding site 4 out
of 12 in 9kho
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Nickel Binding Sites List in 9kho
Nickel binding site 4 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni302
b:44.6
occ:1.00
|
NE2
|
B:HIS107
|
2.1
|
30.5
|
1.0
|
OD2
|
B:ASP106
|
2.1
|
36.2
|
1.0
|
NE2
|
B:HIS245
|
2.3
|
35.0
|
1.0
|
OD2
|
B:ASP200
|
2.3
|
29.1
|
1.0
|
O
|
B:HOH512
|
2.9
|
42.9
|
1.0
|
CG
|
B:ASP106
|
3.0
|
35.3
|
1.0
|
CD2
|
B:HIS107
|
3.0
|
33.4
|
1.0
|
CE1
|
B:HIS107
|
3.1
|
30.3
|
1.0
|
CG
|
B:ASP200
|
3.1
|
30.6
|
1.0
|
OD1
|
B:ASP200
|
3.2
|
28.7
|
1.0
|
CE1
|
B:HIS245
|
3.3
|
39.6
|
1.0
|
OD1
|
B:ASP106
|
3.3
|
35.3
|
1.0
|
CD2
|
B:HIS245
|
3.3
|
36.9
|
1.0
|
NI
|
B:NI301
|
3.3
|
41.4
|
1.0
|
O
|
B:HOH422
|
4.0
|
32.9
|
1.0
|
ND1
|
B:HIS107
|
4.2
|
26.3
|
1.0
|
CG
|
B:HIS107
|
4.2
|
30.5
|
1.0
|
NE2
|
B:HIS102
|
4.3
|
30.2
|
1.0
|
CB
|
B:ASP106
|
4.4
|
32.8
|
1.0
|
ND1
|
B:HIS245
|
4.4
|
39.5
|
1.0
|
CE1
|
B:HIS102
|
4.4
|
28.4
|
1.0
|
CG
|
B:HIS245
|
4.4
|
35.6
|
1.0
|
CB
|
B:ASP200
|
4.6
|
26.4
|
1.0
|
CE1
|
B:TYR203
|
4.7
|
33.0
|
1.0
|
NE2
|
B:HIS178
|
4.9
|
28.6
|
1.0
|
|
Nickel binding site 5 out
of 12 in 9kho
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Nickel Binding Sites List in 9kho
Nickel binding site 5 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni301
b:40.6
occ:1.00
|
NE2
|
C:HIS178
|
2.1
|
30.8
|
1.0
|
OD2
|
C:ASP200
|
2.3
|
25.8
|
1.0
|
ND1
|
C:HIS104
|
2.4
|
23.4
|
1.0
|
O
|
C:HOH401
|
2.4
|
35.7
|
1.0
|
NE2
|
C:HIS102
|
2.5
|
28.3
|
1.0
|
CE1
|
C:HIS178
|
3.0
|
29.8
|
1.0
|
CD2
|
C:HIS178
|
3.1
|
27.8
|
1.0
|
CE1
|
C:HIS104
|
3.3
|
24.4
|
1.0
|
CD2
|
C:HIS102
|
3.3
|
25.1
|
1.0
|
CG
|
C:HIS104
|
3.4
|
26.9
|
1.0
|
CG
|
C:ASP200
|
3.4
|
29.1
|
1.0
|
NI
|
C:NI302
|
3.4
|
40.6
|
1.0
|
CE1
|
C:HIS102
|
3.5
|
25.7
|
1.0
|
CB
|
C:HIS104
|
3.7
|
26.4
|
1.0
|
CB
|
C:ASP200
|
3.9
|
25.3
|
1.0
|
ND1
|
C:HIS178
|
4.2
|
29.5
|
1.0
|
NE2
|
C:HIS107
|
4.2
|
29.8
|
1.0
|
CD2
|
C:HIS107
|
4.2
|
27.7
|
1.0
|
CG
|
C:HIS178
|
4.2
|
23.4
|
1.0
|
NE2
|
C:HIS104
|
4.4
|
27.3
|
1.0
|
CD2
|
C:HIS104
|
4.5
|
25.5
|
1.0
|
OD1
|
C:ASP106
|
4.5
|
26.8
|
1.0
|
OD1
|
C:ASP200
|
4.5
|
30.1
|
1.0
|
CG
|
C:HIS102
|
4.5
|
23.3
|
1.0
|
ND1
|
C:HIS102
|
4.6
|
30.7
|
1.0
|
OH
|
C:TYR203
|
4.8
|
42.2
|
1.0
|
OD2
|
C:ASP106
|
5.0
|
33.5
|
1.0
|
|
Nickel binding site 6 out
of 12 in 9kho
Go back to
Nickel Binding Sites List in 9kho
Nickel binding site 6 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni302
b:40.6
occ:1.00
|
NE2
|
C:HIS245
|
2.2
|
32.5
|
1.0
|
OD2
|
C:ASP200
|
2.2
|
25.8
|
1.0
|
NE2
|
C:HIS107
|
2.2
|
29.8
|
1.0
|
OD2
|
C:ASP106
|
2.4
|
33.5
|
1.0
|
O
|
C:HOH401
|
2.5
|
35.7
|
1.0
|
CG
|
C:ASP200
|
3.0
|
29.1
|
1.0
|
OD1
|
C:ASP200
|
3.0
|
30.1
|
1.0
|
CD2
|
C:HIS107
|
3.1
|
27.7
|
1.0
|
CE1
|
C:HIS245
|
3.1
|
32.4
|
1.0
|
CD2
|
C:HIS245
|
3.2
|
32.4
|
1.0
|
CG
|
C:ASP106
|
3.3
|
31.5
|
1.0
|
CE1
|
C:HIS107
|
3.3
|
29.0
|
1.0
|
NI
|
C:NI301
|
3.4
|
40.6
|
1.0
|
OD1
|
C:ASP106
|
3.5
|
26.8
|
1.0
|
O
|
C:HOH406
|
3.8
|
31.2
|
1.0
|
ND1
|
C:HIS245
|
4.2
|
34.4
|
1.0
|
CG
|
C:HIS245
|
4.3
|
35.3
|
1.0
|
CG
|
C:HIS107
|
4.3
|
26.3
|
1.0
|
ND1
|
C:HIS107
|
4.4
|
29.2
|
1.0
|
NE2
|
C:HIS102
|
4.5
|
28.3
|
1.0
|
CB
|
C:ASP200
|
4.5
|
25.3
|
1.0
|
CE1
|
C:HIS102
|
4.5
|
25.7
|
1.0
|
CB
|
C:ASP106
|
4.6
|
29.2
|
1.0
|
CE1
|
C:TYR203
|
4.8
|
35.1
|
1.0
|
|
Nickel binding site 7 out
of 12 in 9kho
Go back to
Nickel Binding Sites List in 9kho
Nickel binding site 7 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni301
b:45.0
occ:1.00
|
NE2
|
D:HIS107
|
2.2
|
35.0
|
1.0
|
OD2
|
D:ASP106
|
2.3
|
34.8
|
1.0
|
NE2
|
D:HIS245
|
2.3
|
39.4
|
1.0
|
OD2
|
D:ASP200
|
2.4
|
33.9
|
1.0
|
CD2
|
D:HIS107
|
3.0
|
30.4
|
1.0
|
CG
|
D:ASP106
|
3.1
|
33.9
|
1.0
|
CG
|
D:ASP200
|
3.2
|
32.9
|
1.0
|
OD1
|
D:ASP200
|
3.2
|
35.4
|
1.0
|
CE1
|
D:HIS245
|
3.2
|
40.4
|
1.0
|
OD1
|
D:ASP106
|
3.2
|
34.0
|
1.0
|
CE1
|
D:HIS107
|
3.3
|
30.0
|
1.0
|
CD2
|
D:HIS245
|
3.4
|
38.6
|
1.0
|
O
|
D:HOH516
|
3.4
|
39.8
|
1.0
|
NI
|
D:NI302
|
3.5
|
42.1
|
1.0
|
CG
|
D:HIS107
|
4.3
|
29.7
|
1.0
|
ND1
|
D:HIS107
|
4.4
|
31.5
|
1.0
|
ND1
|
D:HIS245
|
4.4
|
43.2
|
1.0
|
NE2
|
D:HIS102
|
4.4
|
31.0
|
1.0
|
CE1
|
D:HIS102
|
4.4
|
31.1
|
1.0
|
CB
|
D:ASP106
|
4.5
|
33.6
|
1.0
|
CG
|
D:HIS245
|
4.5
|
40.7
|
1.0
|
CB
|
D:ASP200
|
4.7
|
26.7
|
1.0
|
CE1
|
D:TYR203
|
4.9
|
36.9
|
1.0
|
|
Nickel binding site 8 out
of 12 in 9kho
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Nickel Binding Sites List in 9kho
Nickel binding site 8 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni302
b:42.1
occ:1.00
|
CE1
|
D:HIS178
|
2.1
|
31.3
|
1.0
|
NE2
|
D:HIS102
|
2.3
|
31.0
|
1.0
|
ND1
|
D:HIS104
|
2.3
|
28.6
|
1.0
|
OD2
|
D:ASP200
|
2.4
|
33.9
|
1.0
|
NE2
|
D:HIS178
|
2.9
|
32.8
|
1.0
|
O
|
D:HOH516
|
3.0
|
39.8
|
1.0
|
ND1
|
D:HIS178
|
3.1
|
31.3
|
1.0
|
CD2
|
D:HIS102
|
3.2
|
28.1
|
1.0
|
CE1
|
D:HIS104
|
3.3
|
35.4
|
1.0
|
CG
|
D:HIS104
|
3.3
|
32.8
|
1.0
|
CE1
|
D:HIS102
|
3.4
|
31.1
|
1.0
|
NI
|
D:NI301
|
3.5
|
45.0
|
1.0
|
CG
|
D:ASP200
|
3.5
|
32.9
|
1.0
|
CB
|
D:HIS104
|
3.6
|
30.5
|
1.0
|
CB
|
D:ASP200
|
4.0
|
26.7
|
1.0
|
CD2
|
D:HIS178
|
4.2
|
33.6
|
1.0
|
CG
|
D:HIS178
|
4.3
|
28.8
|
1.0
|
NE2
|
D:HIS107
|
4.3
|
35.0
|
1.0
|
CD2
|
D:HIS107
|
4.3
|
30.4
|
1.0
|
NE2
|
D:HIS104
|
4.4
|
35.9
|
1.0
|
CD2
|
D:HIS104
|
4.4
|
31.9
|
1.0
|
CG
|
D:HIS102
|
4.4
|
33.1
|
1.0
|
ND1
|
D:HIS102
|
4.5
|
32.6
|
1.0
|
OD1
|
D:ASP106
|
4.5
|
34.0
|
1.0
|
OH
|
D:TYR203
|
4.5
|
40.1
|
1.0
|
OD1
|
D:ASP200
|
4.6
|
35.4
|
1.0
|
|
Nickel binding site 9 out
of 12 in 9kho
Go back to
Nickel Binding Sites List in 9kho
Nickel binding site 9 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni301
b:42.7
occ:1.00
|
NE2
|
E:HIS178
|
2.0
|
34.5
|
1.0
|
NE2
|
E:HIS102
|
2.3
|
28.8
|
1.0
|
ND1
|
E:HIS104
|
2.4
|
25.9
|
1.0
|
OD2
|
E:ASP200
|
2.4
|
29.4
|
1.0
|
O
|
E:HOH426
|
2.6
|
35.4
|
1.0
|
CE1
|
E:HIS178
|
3.0
|
30.9
|
1.0
|
CD2
|
E:HIS178
|
3.0
|
29.1
|
1.0
|
CD2
|
E:HIS102
|
3.1
|
25.9
|
1.0
|
CE1
|
E:HIS104
|
3.3
|
30.4
|
1.0
|
CG
|
E:HIS104
|
3.3
|
27.8
|
1.0
|
NI
|
E:NI302
|
3.4
|
42.8
|
1.0
|
CE1
|
E:HIS102
|
3.5
|
28.0
|
1.0
|
CG
|
E:ASP200
|
3.5
|
30.9
|
1.0
|
CB
|
E:HIS104
|
3.6
|
25.2
|
1.0
|
CB
|
E:ASP200
|
4.0
|
27.8
|
1.0
|
NE2
|
E:HIS107
|
4.1
|
28.8
|
1.0
|
ND1
|
E:HIS178
|
4.1
|
28.2
|
1.0
|
CG
|
E:HIS178
|
4.2
|
30.2
|
1.0
|
CD2
|
E:HIS107
|
4.2
|
27.7
|
1.0
|
OH
|
E:TYR203
|
4.3
|
44.7
|
1.0
|
CG
|
E:HIS102
|
4.3
|
28.1
|
1.0
|
NE2
|
E:HIS104
|
4.4
|
28.6
|
1.0
|
CD2
|
E:HIS104
|
4.5
|
24.9
|
1.0
|
OD1
|
E:ASP106
|
4.5
|
33.3
|
1.0
|
ND1
|
E:HIS102
|
4.5
|
28.8
|
1.0
|
OD1
|
E:ASP200
|
4.6
|
33.6
|
1.0
|
|
Nickel binding site 10 out
of 12 in 9kho
Go back to
Nickel Binding Sites List in 9kho
Nickel binding site 10 out
of 12 in the Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L)
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Crystal Structure of N-Acyl Homoserine Lactonase Ahlx Mutant M41(E77I/D177G/T243Y/H255L) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni302
b:42.8
occ:1.00
|
NE2
|
E:HIS107
|
2.2
|
28.8
|
1.0
|
OD2
|
E:ASP200
|
2.3
|
29.4
|
1.0
|
NE2
|
E:HIS245
|
2.3
|
42.0
|
1.0
|
OD2
|
E:ASP106
|
2.3
|
32.1
|
1.0
|
CG
|
E:ASP200
|
3.1
|
30.9
|
1.0
|
CD2
|
E:HIS107
|
3.1
|
27.7
|
1.0
|
OD1
|
E:ASP200
|
3.1
|
33.6
|
1.0
|
CG
|
E:ASP106
|
3.2
|
35.2
|
1.0
|
CE1
|
E:HIS245
|
3.2
|
41.1
|
1.0
|
CE1
|
E:HIS107
|
3.3
|
24.7
|
1.0
|
CD2
|
E:HIS245
|
3.3
|
41.5
|
1.0
|
OD1
|
E:ASP106
|
3.3
|
33.3
|
1.0
|
NI
|
E:NI301
|
3.4
|
42.7
|
1.0
|
O
|
E:HOH426
|
3.6
|
35.4
|
1.0
|
O
|
E:HOH444
|
4.1
|
31.6
|
1.0
|
NE2
|
E:HIS102
|
4.3
|
28.8
|
1.0
|
ND1
|
E:HIS245
|
4.3
|
40.2
|
1.0
|
CG
|
E:HIS107
|
4.3
|
28.1
|
1.0
|
ND1
|
E:HIS107
|
4.3
|
25.4
|
1.0
|
CG
|
E:HIS245
|
4.4
|
43.6
|
1.0
|
CE1
|
E:HIS102
|
4.4
|
28.0
|
1.0
|
CB
|
E:ASP200
|
4.5
|
27.8
|
1.0
|
CB
|
E:ASP106
|
4.6
|
31.8
|
1.0
|
CE1
|
E:TYR203
|
4.6
|
40.5
|
1.0
|
NE2
|
E:HIS178
|
5.0
|
34.5
|
1.0
|
|
Reference:
Y.Chen,
X.Xie,
J.Zhou,
L.Dai,
X.Chu,
P.Liu.
An Ahl-Lactonase Mutant Featuring A Unique "Tri-His" Motif Exhibits Enhanced Activity, Stability and Effectively Controls Plant Soft Rot. Int.J.Biol.Macromol. V. 308 42543 2025.
ISSN: ISSN 0141-8130
PubMed: 40157672
DOI: 10.1016/J.IJBIOMAC.2025.142543
Page generated: Mon Aug 18 22:39:07 2025
|