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Nickel in PDB 1s3t: Borate Inhibited Bacillus Pasteurii Urease Crystal Structure

Enzymatic activity of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure

All present enzymatic activity of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure:
3.5.1.5;

Protein crystallography data

The structure of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure, PDB code: 1s3t 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) 24.77 / 2.10
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.906, 130.906, 189.366, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 20.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Borate Inhibited Bacillus Pasteurii Urease Crystal Structure (pdb code 1s3t). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Borate Inhibited Bacillus Pasteurii Urease Crystal Structure, PDB code: 1s3t:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1s3t

Go back to Nickel Binding Sites List in 1s3t
Nickel binding site 1 out of 2 in the Borate Inhibited Bacillus Pasteurii Urease Crystal Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni600

b:21.8
occ:1.00
O C:HOH604 2.0 23.5 1.0
OQ1 C:KCX220 2.0 18.8 1.0
NE2 C:HIS275 2.1 19.3 1.0
ND1 C:HIS249 2.1 18.7 1.0
O2 C:BO3602 2.2 23.1 1.0
B C:BO3602 2.9 24.2 1.0
CE1 C:HIS275 3.0 20.4 1.0
CE1 C:HIS249 3.0 20.2 1.0
CD2 C:HIS275 3.1 19.7 1.0
CX C:KCX220 3.1 19.8 1.0
CG C:HIS249 3.2 19.7 1.0
O C:GLY280 3.4 25.0 1.0
OQ2 C:KCX220 3.4 19.2 1.0
CB C:HIS249 3.5 18.5 1.0
O1 C:BO3602 3.5 23.8 1.0
O3 C:BO3602 3.6 26.0 1.0
NE2 C:HIS222 3.6 18.5 1.0
NI C:NI601 3.6 20.9 1.0
CD2 C:HIS222 3.9 18.1 1.0
CE1 C:HIS137 3.9 17.3 1.0
ND1 C:HIS275 4.1 19.3 1.0
NE2 C:HIS137 4.1 15.7 1.0
NE2 C:HIS249 4.2 20.5 1.0
CG C:HIS275 4.2 20.2 1.0
NZ C:KCX220 4.3 18.3 1.0
CD2 C:HIS249 4.3 20.1 1.0
OD2 C:ASP363 4.3 20.6 1.0
C C:GLY280 4.3 24.4 1.0
O2 C:SO4603 4.5 40.0 1.0
CE1 C:HIS222 4.6 17.6 1.0
CE C:KCX220 4.7 19.1 1.0
CA C:HIS249 4.8 18.5 1.0
OD1 C:ASP363 5.0 20.2 1.0

Nickel binding site 2 out of 2 in 1s3t

Go back to Nickel Binding Sites List in 1s3t
Nickel binding site 2 out of 2 in the Borate Inhibited Bacillus Pasteurii Urease Crystal Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:20.9
occ:1.00
OQ2 C:KCX220 2.1 19.2 1.0
NE2 C:HIS137 2.1 15.7 1.0
O1 C:BO3602 2.1 23.8 1.0
NE2 C:HIS139 2.2 15.2 1.0
O C:HOH604 2.2 23.5 1.0
OD1 C:ASP363 2.2 20.2 1.0
B C:BO3602 3.0 24.2 1.0
CE1 C:HIS139 3.0 16.1 1.0
CX C:KCX220 3.0 19.8 1.0
CD2 C:HIS137 3.0 16.7 1.0
CE1 C:HIS137 3.1 17.3 1.0
CG C:ASP363 3.1 19.3 1.0
CD2 C:HIS139 3.3 15.4 1.0
OQ1 C:KCX220 3.3 18.8 1.0
OD2 C:ASP363 3.3 20.6 1.0
NI C:NI600 3.6 21.8 1.0
O2 C:BO3602 3.7 23.1 1.0
O3 C:BO3602 3.7 26.0 1.0
CB C:ALA366 4.1 21.2 1.0
CG2 C:THR172 4.1 17.4 1.0
NZ C:KCX220 4.1 18.3 1.0
ND1 C:HIS137 4.2 15.8 1.0
CG C:HIS137 4.2 16.3 1.0
ND1 C:HIS139 4.2 16.9 1.0
CG C:HIS139 4.3 15.8 1.0
O C:ALA170 4.3 17.4 1.0
CB C:ASP363 4.4 18.1 1.0
CA C:ASP363 4.6 18.1 1.0
NE2 C:HIS275 4.8 19.3 1.0
CD2 C:HIS275 4.9 19.7 1.0
N C:THR172 4.9 17.0 1.0

Reference:

S.Benini, W.R.Rypniewski, K.S.Wilson, S.Mangani, S.Ciurli. Molecular Details of Urease Inhibition By Boric Acid: Insights Into the Catalytic Mechanism. J.Am.Chem.Soc. V. 126 3714 2004.
ISSN: ISSN 0002-7863
PubMed: 15038715
DOI: 10.1021/JA049618P
Page generated: Fri Sep 25 08:01:09 2020
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