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Nickel in PDB 1fwf: Klebsiella Aerogenes Urease, C319D Variant

Enzymatic activity of Klebsiella Aerogenes Urease, C319D Variant

All present enzymatic activity of Klebsiella Aerogenes Urease, C319D Variant:
3.5.1.5;

Protein crystallography data

The structure of Klebsiella Aerogenes Urease, C319D Variant, PDB code: 1fwf was solved by M.A.Pearson, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 170.800, 170.800, 170.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Klebsiella Aerogenes Urease, C319D Variant (pdb code 1fwf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Klebsiella Aerogenes Urease, C319D Variant, PDB code: 1fwf:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1fwf

Go back to Nickel Binding Sites List in 1fwf
Nickel binding site 1 out of 2 in the Klebsiella Aerogenes Urease, C319D Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Klebsiella Aerogenes Urease, C319D Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni574

b:17.0
occ:0.67
O C:HOH807 1.9 20.0 0.7
OQ1 C:KCX217 2.1 24.6 1.0
ND1 C:HIS246 2.2 18.0 1.0
NE2 C:HIS272 2.4 18.3 1.0
O C:HOH808 2.6 20.0 0.7
CE1 C:HIS246 3.0 19.0 1.0
CX C:KCX217 3.0 21.1 1.0
CG C:HIS246 3.2 14.4 1.0
CD2 C:HIS272 3.2 22.2 1.0
OQ2 C:KCX217 3.3 23.6 1.0
O C:GLY277 3.4 24.3 1.0
CE1 C:HIS272 3.5 22.6 1.0
O C:HOH719 3.5 44.4 1.0
O C:HOH809 3.5 20.0 0.6
NI C:NI575 3.5 17.0 0.6
NE2 C:HIS219 3.6 16.6 1.0
CB C:HIS246 3.6 12.9 1.0
CD2 C:HIS219 3.8 13.3 1.0
NE2 C:HIS246 4.1 21.9 1.0
CD2 C:HIS246 4.2 16.4 1.0
NZ C:KCX217 4.3 17.4 1.0
NE2 C:HIS134 4.3 22.4 1.0
OD2 C:ASP360 4.3 22.4 1.0
CE1 C:HIS134 4.3 24.0 1.0
CG C:HIS272 4.4 24.0 1.0
ND1 C:HIS272 4.5 26.2 1.0
C C:GLY277 4.5 24.2 1.0
CE1 C:HIS219 4.7 15.4 1.0
CE C:KCX217 4.8 12.8 1.0
CA C:HIS246 4.8 14.3 1.0
OD1 C:ASP360 4.9 20.5 1.0
CB C:PHE271 5.0 14.7 1.0
CD2 C:PHE271 5.0 17.3 1.0

Nickel binding site 2 out of 2 in 1fwf

Go back to Nickel Binding Sites List in 1fwf
Nickel binding site 2 out of 2 in the Klebsiella Aerogenes Urease, C319D Variant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Klebsiella Aerogenes Urease, C319D Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni575

b:17.0
occ:0.64
O C:HOH807 1.9 20.0 0.7
OQ2 C:KCX217 2.1 23.6 1.0
OD1 C:ASP360 2.1 20.5 1.0
NE2 C:HIS136 2.2 9.8 1.0
NE2 C:HIS134 2.3 22.4 1.0
O C:HOH809 2.5 20.0 0.6
CG C:ASP360 2.9 20.1 1.0
CD2 C:HIS136 3.1 4.6 1.0
CE1 C:HIS136 3.1 9.6 1.0
CX C:KCX217 3.1 21.1 1.0
CD2 C:HIS134 3.2 21.4 1.0
OD2 C:ASP360 3.2 22.4 1.0
CE1 C:HIS134 3.3 24.0 1.0
NI C:NI574 3.5 17.0 0.7
OQ1 C:KCX217 3.6 24.6 1.0
O C:HOH808 3.7 20.0 0.7
O C:HOH719 3.9 44.4 1.0
CG2 C:THR169 4.0 6.9 1.0
CB C:ASP360 4.2 15.1 1.0
ND1 C:HIS136 4.2 8.4 1.0
NZ C:KCX217 4.2 17.4 1.0
CG C:HIS136 4.3 7.2 1.0
CG C:HIS134 4.3 20.7 1.0
ND1 C:HIS134 4.4 24.2 1.0
O C:ALA363 4.5 24.6 1.0
CB C:ALA363 4.5 16.4 1.0
CA C:ASP360 4.5 12.2 1.0
O C:ALA167 4.5 10.9 1.0

Reference:

M.A.Pearson, L.O.Michel, R.P.Hausinger, P.A.Karplus. Structures of CYS319 Variants and Acetohydroxamate-Inhibited Klebsiella Aerogenes Urease. Biochemistry V. 36 8164 1997.
ISSN: ISSN 0006-2960
PubMed: 9201965
DOI: 10.1021/BI970514J
Page generated: Fri Sep 25 07:53:15 2020
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