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Nickel in PDB 4ubp: Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution

Enzymatic activity of Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution

All present enzymatic activity of Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution:
3.5.1.5;

Protein crystallography data

The structure of Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution, PDB code: 4ubp was solved by S.Benini, W.R.Rypniewski, K.S.Wilson, S.Ciurli, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.73 / 1.55
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.880, 130.880, 189.000, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 19

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution (pdb code 4ubp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution, PDB code: 4ubp:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4ubp

Go back to Nickel Binding Sites List in 4ubp
Nickel binding site 1 out of 2 in the Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni798

b:22.1
occ:1.00
O C:HAE800 2.0 23.4 1.0
OQ2 C:KCX220 2.0 21.0 1.0
ND1 C:HIS249 2.0 21.3 1.0
NE2 C:HIS275 2.0 20.9 1.0
O2 C:HAE800 2.2 24.3 1.0
N C:HAE800 2.7 26.5 1.0
C2 C:HAE800 2.7 28.3 1.0
CE1 C:HIS249 2.9 22.6 1.0
CX C:KCX220 3.0 19.4 1.0
CE1 C:HIS275 3.0 21.7 1.0
CD2 C:HIS275 3.0 20.3 1.0
CG C:HIS249 3.0 20.7 1.0
OQ1 C:KCX220 3.3 19.2 1.0
O C:GLY280 3.4 23.5 1.0
CB C:HIS249 3.5 18.2 1.0
NI C:NI799 3.5 20.5 1.0
NE2 C:HIS222 3.6 21.1 1.0
CD2 C:HIS222 3.9 19.8 1.0
CE1 C:HIS137 4.1 20.0 1.0
NE2 C:HIS249 4.1 22.0 1.0
ND1 C:HIS275 4.1 20.6 1.0
CD2 C:HIS249 4.2 20.0 1.0
CG C:HIS275 4.2 20.2 1.0
NE2 C:HIS137 4.2 20.1 1.0
C1 C:HAE800 4.2 30.1 1.0
NZ C:KCX220 4.3 18.5 1.0
C C:GLY280 4.4 22.4 1.0
CE1 C:HIS222 4.6 21.0 1.0
CE C:KCX220 4.7 19.9 1.0
OD2 C:ASP363 4.8 26.3 1.0
CA C:HIS249 4.8 18.5 1.0
OD1 C:ASP363 4.9 20.9 1.0
O C:ALA170 4.9 20.6 1.0

Nickel binding site 2 out of 2 in 4ubp

Go back to Nickel Binding Sites List in 4ubp
Nickel binding site 2 out of 2 in the Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Bacillus Pasteurii Urease Inhibited with Acetohydroxamic Acid at 1.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni799

b:20.5
occ:1.00
NE2 C:HIS137 2.0 20.1 1.0
NE2 C:HIS139 2.0 16.6 1.0
O C:HAE800 2.0 23.4 1.0
OQ1 C:KCX220 2.0 19.2 1.0
OD1 C:ASP363 2.1 20.9 1.0
N C:HAE800 2.6 26.5 1.0
CE1 C:HIS139 2.9 17.7 1.0
CD2 C:HIS137 2.9 19.1 1.0
CX C:KCX220 3.0 19.4 1.0
CE1 C:HIS137 3.0 20.0 1.0
CG C:ASP363 3.0 21.7 1.0
CD2 C:HIS139 3.1 16.8 1.0
OQ2 C:KCX220 3.4 21.0 1.0
C2 C:HAE800 3.4 28.3 1.0
OD2 C:ASP363 3.5 26.3 1.0
NI C:NI798 3.5 22.1 1.0
O2 C:HAE800 3.8 24.3 1.0
CG2 C:THR172 3.9 19.4 1.0
CG C:HIS137 4.1 18.7 1.0
ND1 C:HIS139 4.1 17.2 1.0
ND1 C:HIS137 4.1 20.4 1.0
NZ C:KCX220 4.2 18.5 1.0
CB C:ALA366 4.2 19.2 1.0
CG C:HIS139 4.2 16.8 1.0
CB C:ASP363 4.3 20.5 1.0
C1 C:HAE800 4.5 30.1 1.0
CA C:ASP363 4.6 20.3 1.0
O C:ALA170 4.6 20.6 1.0
NE2 C:HIS275 4.6 20.9 1.0
CD2 C:HIS275 4.7 20.3 1.0
N C:THR172 4.9 18.2 1.0

Reference:

S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Ciurli, S.Mangani. The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion From X-Ray Data at 1.55 A Resolution. J.Biol.Inorg.Chem. V. 5 110 2000.
ISSN: ISSN 0949-8257
PubMed: 10766443
DOI: 10.1007/S007750050014
Page generated: Fri Sep 25 08:56:05 2020
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