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Nickel in PDB 1ubp: Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution

Enzymatic activity of Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution

All present enzymatic activity of Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution, PDB code: 1ubp 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) 14.00 / 1.65
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.343, 131.343, 190.013, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution (pdb code 1ubp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution, PDB code: 1ubp:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ubp

Go back to Nickel Binding Sites List in 1ubp
Nickel binding site 1 out of 2 in the Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution


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 Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni701

b:14.4
occ:1.00
OQ1 C:KCX220 2.1 12.8 1.0
NE2 C:HIS275 2.2 12.0 1.0
ND1 C:HIS249 2.2 14.2 1.0
O1 C:BME600 2.3 21.4 1.0
S2 C:BME600 2.4 14.3 1.0
CX C:KCX220 3.0 15.5 1.0
CE1 C:HIS249 3.1 13.6 1.0
CD2 C:HIS275 3.1 12.6 1.0
NI C:NI702 3.1 12.3 1.0
CE1 C:HIS275 3.2 13.7 1.0
C1 C:BME600 3.2 18.5 1.0
CG C:HIS249 3.3 15.2 1.0
OQ2 C:KCX220 3.3 11.8 1.0
C2 C:BME600 3.4 16.5 1.0
CB C:HIS249 3.7 11.3 1.0
NE2 C:HIS222 3.7 12.0 1.0
CE1 C:HIS137 3.8 14.3 1.0
O C:GLY280 3.8 17.0 1.0
OD2 C:ASP363 3.9 14.5 1.0
NE2 C:HIS137 3.9 12.9 1.0
CD2 C:HIS222 4.1 11.7 1.0
NE2 C:HIS249 4.2 14.4 1.0
CG C:HIS275 4.2 13.5 1.0
ND1 C:HIS275 4.3 14.4 1.0
CD2 C:HIS249 4.3 15.3 1.0
NZ C:KCX220 4.4 12.7 1.0
OD1 C:ASP363 4.4 13.8 1.0
CG C:ASP363 4.6 15.5 1.0
CE1 C:HIS222 4.8 11.9 1.0
C C:GLY280 4.8 15.1 1.0
CE C:KCX220 4.9 12.5 1.0
CA C:HIS249 5.0 10.1 1.0

Nickel binding site 2 out of 2 in 1ubp

Go back to Nickel Binding Sites List in 1ubp
Nickel binding site 2 out of 2 in the Crystal Structure of Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution


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 Urease From Bacillus Pasteurii Inhibited with Beta-Mercaptoethanol at 1.65 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni702

b:12.3
occ:1.00
OQ2 C:KCX220 2.1 11.8 1.0
NE2 C:HIS139 2.1 9.9 1.0
NE2 C:HIS137 2.1 12.9 1.0
OD1 C:ASP363 2.1 13.8 1.0
S2 C:BME600 2.3 14.3 1.0
CE1 C:HIS139 2.9 16.6 1.0
CX C:KCX220 3.0 15.5 1.0
CG C:ASP363 3.0 15.5 1.0
CD2 C:HIS137 3.1 15.2 1.0
CE1 C:HIS137 3.1 14.3 1.0
NI C:NI701 3.1 14.4 1.0
OQ1 C:KCX220 3.2 12.8 1.0
CD2 C:HIS139 3.2 12.6 1.0
C2 C:BME600 3.3 16.5 1.0
OD2 C:ASP363 3.3 14.5 1.0
O1 C:BME600 4.0 21.4 1.0
CG2 C:THR172 4.1 10.6 1.0
ND1 C:HIS139 4.1 11.4 1.0
ND1 C:HIS137 4.2 12.9 1.0
CB C:ALA366 4.2 11.6 1.0
CG C:HIS137 4.2 11.0 1.0
CG C:HIS139 4.3 10.2 1.0
NZ C:KCX220 4.3 12.7 1.0
C1 C:BME600 4.3 18.5 1.0
CB C:ASP363 4.3 12.6 1.0
CA C:ASP363 4.6 12.1 1.0
NE2 C:HIS275 4.6 12.0 1.0
O C:ALA170 4.6 13.7 1.0
CD2 C:HIS275 4.7 12.6 1.0
N C:THR172 4.8 11.5 1.0

Reference:

S.Benini, W.R.Rypniewski, K.S.Wilson, S.Ciurli, S.Mangani. The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol From X-Ray Data at 1.65-A Resolution J.Biol.Inorg.Chem. V. 3 268 1998.
ISSN: ISSN 0949-8257
DOI: 10.1007/S007750050231
Page generated: Thu Oct 29 06:15:53 2020
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