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Nickel in PDB 1ie7: Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure

Enzymatic activity of Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure

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

Protein crystallography data

The structure of Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure, PDB code: 1ie7 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) 11.99 / 1.85
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.489, 131.489, 189.489, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 21

Nickel Binding Sites:

The binding sites of Nickel atom in the Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure (pdb code 1ie7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure, PDB code: 1ie7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ie7

Go back to Nickel Binding Sites List in 1ie7
Nickel binding site 1 out of 2 in the Phosphate 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 Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni600

b:36.6
occ:1.00
O1 C:PO4901 1.9 33.6 0.7
NE2 C:HIS275 2.0 35.3 1.0
ND1 C:HIS249 2.0 31.2 1.0
OQ1 C:KCX220 2.1 35.6 1.0
O2 C:PO4901 2.4 35.0 0.7
P C:PO4901 2.5 41.5 0.7
CE1 C:HIS249 3.0 33.8 1.0
CE1 C:HIS275 3.0 35.6 1.0
CD2 C:HIS275 3.0 35.2 1.0
CX C:KCX220 3.0 40.2 1.0
CG C:HIS249 3.1 32.0 1.0
OQ2 C:KCX220 3.3 34.0 1.0
CB C:HIS249 3.4 23.6 1.0
O4 C:PO4901 3.5 39.6 0.7
NI C:NI601 3.5 34.9 1.0
O C:GLY280 3.6 38.5 1.0
NE2 C:HIS222 3.6 27.0 1.0
O3 C:PO4901 3.7 38.7 0.7
CD2 C:HIS222 3.8 26.1 1.0
CE1 C:HIS137 3.9 31.9 1.0
NE2 C:HIS137 4.0 28.9 1.0
NE2 C:HIS249 4.1 35.1 1.0
ND1 C:HIS275 4.1 34.3 1.0
CG C:HIS275 4.2 35.4 1.0
CD2 C:HIS249 4.2 28.6 1.0
OD2 C:ASP363 4.4 43.9 1.0
NZ C:KCX220 4.4 29.9 1.0
O C:HOH1362 4.6 59.7 1.0
C C:GLY280 4.6 39.2 1.0
CE1 C:HIS222 4.6 24.6 1.0
CE C:KCX220 4.7 30.6 1.0
CA C:HIS249 4.7 25.3 1.0
CG C:HIS222 5.0 24.6 1.0
CD2 C:PHE274 5.0 28.7 1.0

Nickel binding site 2 out of 2 in 1ie7

Go back to Nickel Binding Sites List in 1ie7
Nickel binding site 2 out of 2 in the Phosphate 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 Phosphate Inhibited Bacillus Pasteurii Urease Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:34.9
occ:1.00
O1 C:PO4901 2.0 33.6 0.7
OQ2 C:KCX220 2.0 34.0 1.0
NE2 C:HIS137 2.1 28.9 1.0
NE2 C:HIS139 2.2 23.9 1.0
OD1 C:ASP363 2.2 33.7 1.0
O3 C:PO4901 2.4 38.7 0.7
P C:PO4901 2.6 41.5 0.7
CE1 C:HIS139 2.9 26.9 1.0
CD2 C:HIS137 3.0 34.9 1.0
CX C:KCX220 3.0 40.2 1.0
CG C:ASP363 3.1 38.3 1.0
CE1 C:HIS137 3.2 31.9 1.0
OD2 C:ASP363 3.2 43.9 1.0
OQ1 C:KCX220 3.3 35.6 1.0
CD2 C:HIS139 3.3 23.4 1.0
NI C:NI600 3.5 36.6 1.0
O4 C:PO4901 3.7 39.6 0.7
O2 C:PO4901 3.8 35.0 0.7
CG2 C:THR172 3.9 25.4 1.0
ND1 C:HIS139 4.2 25.0 1.0
CG C:HIS137 4.2 29.5 1.0
O C:ALA366 4.2 48.4 1.0
NZ C:KCX220 4.2 29.9 1.0
ND1 C:HIS137 4.3 33.0 1.0
CG C:HIS139 4.4 25.3 1.0
CB C:ASP363 4.4 30.9 1.0
O C:ALA170 4.5 24.6 1.0
CB C:ALA366 4.5 38.9 1.0
CA C:ASP363 4.7 29.2 1.0
NE2 C:HIS275 4.7 35.3 1.0
N C:THR172 4.7 23.8 1.0
CD2 C:HIS275 4.8 35.2 1.0

Reference:

S.Benini, W.R.Rypniewski, K.S.Wilson, S.Ciurli, S.Mangani. Structure-Based Rationalization of Urease Inhibition By Phosphate: Novel Insights Into the Enzyme Mechanism. J.Biol.Inorg.Chem. V. 6 778 2001.
ISSN: ISSN 0949-8257
PubMed: 11713685
DOI: 10.1007/S007750100254
Page generated: Fri Sep 25 07:54:57 2020
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