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Nickel in PDB 9gv8: N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol

Enzymatic activity of N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol

All present enzymatic activity of N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol:
3.5.1.81;

Protein crystallography data

The structure of N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol, PDB code: 9gv8 was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.91 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.422, 101.422, 124.94, 90, 90, 120
R / Rfree (%) 22.6 / 26.9

Nickel Binding Sites:

The binding sites of Nickel atom in the N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol (pdb code 9gv8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol, PDB code: 9gv8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 9gv8

Go back to Nickel Binding Sites List in 9gv8
Nickel binding site 1 out of 2 in the N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni509

b:118.4
occ:1.00
NE2 A:HIS64 2.1 68.5 1.0
NE2 A:HIS62 2.2 81.0 1.0
O3 A:SO4505 2.3 73.8 1.0
SG A:CYS91 2.5 68.1 1.0
CE1 A:HIS64 2.9 66.9 1.0
CD2 A:HIS62 3.1 71.6 1.0
CD2 A:HIS64 3.2 68.3 1.0
OD1 A:ASP362 3.2 74.6 1.0
CE1 A:HIS62 3.2 75.7 1.0
S A:SO4505 3.4 60.6 1.0
NI A:NI510 3.5 72.6 1.0
O2 A:SO4505 3.7 58.4 1.0
CG A:ASP362 3.7 74.1 1.0
OD2 A:ASP362 3.7 75.3 1.0
O4 A:SO4505 3.8 69.7 1.0
CB A:CYS91 3.9 63.9 1.0
ND1 A:HIS64 4.1 64.9 1.0
CD2 A:HIS246 4.2 69.2 1.0
CG A:HIS64 4.2 63.3 1.0
CG A:HIS62 4.2 66.9 1.0
ND1 A:HIS62 4.3 68.6 1.0
CB A:ASN90 4.4 56.8 1.0
NE2 A:HIS246 4.5 73.7 1.0
O1 A:SO4505 4.7 71.5 1.0
C A:ASN90 4.9 59.0 1.0
CB A:ASP362 4.9 72.7 1.0
N A:CYS91 4.9 56.7 1.0

Nickel binding site 2 out of 2 in 9gv8

Go back to Nickel Binding Sites List in 9gv8
Nickel binding site 2 out of 2 in the N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of N-Acyl-D-Amino-Acid Deacylase (D-Acylase) From Klebsiella Pneumoniae in the Absence of Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni510

b:72.6
occ:1.00
O4 A:SO4505 2.0 69.7 1.0
NE2 A:HIS246 2.1 73.7 1.0
ND1 A:HIS216 2.1 82.4 1.0
SG A:CYS91 2.4 68.1 1.0
CE1 A:HIS216 2.9 79.8 1.0
CD2 A:HIS246 3.0 69.2 1.0
S A:SO4505 3.1 60.6 1.0
CG A:HIS216 3.2 83.4 1.0
CE1 A:HIS246 3.2 79.1 1.0
O3 A:SO4505 3.4 73.8 1.0
CB A:CYS91 3.5 63.9 1.0
NI A:NI509 3.5 118.4 1.0
CB A:HIS216 3.6 73.9 1.0
O2 A:SO4505 3.7 58.4 1.0
NE2 A:HIS216 4.0 85.1 1.0
CD2 A:HIS216 4.2 84.4 1.0
CG A:HIS246 4.2 70.5 1.0
ND1 A:HIS246 4.2 72.5 1.0
O1 A:SO4505 4.3 71.5 1.0
NE2 A:HIS62 4.4 81.0 1.0
OH A:TYR188 4.4 65.3 1.0
CE1 A:HIS62 4.5 75.7 1.0
CA A:CYS91 4.6 61.6 1.0
CA A:HIS216 4.7 71.2 1.0
CE2 A:TYR188 4.8 66.8 1.0

Reference:

S.Martinez-Rodriguez, J.A.Gavira. Revisiting D-Acylases For D-Amino Acid Production. Microb Biotechnol V. 18 70179 2025.
ISSN: ISSN 1751-7915
PubMed: 40491232
DOI: 10.1111/1751-7915.70179
Page generated: Mon Aug 18 22:37:13 2025

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