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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

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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 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 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 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 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

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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

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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 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

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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

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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

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