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Nickel in PDB 1fwa: Klebsiella Aerogenes Urease, C319A Variant at pH 7.5

Enzymatic activity of Klebsiella Aerogenes Urease, C319A Variant at pH 7.5

All present enzymatic activity of Klebsiella Aerogenes Urease, C319A Variant at pH 7.5:
3.5.1.5;

Protein crystallography data

The structure of Klebsiella Aerogenes Urease, C319A Variant at pH 7.5, PDB code: 1fwa 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 (%) 16.9 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Klebsiella Aerogenes Urease, C319A Variant at pH 7.5 (pdb code 1fwa). 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, C319A Variant at pH 7.5, PDB code: 1fwa:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1fwa

Go back to Nickel Binding Sites List in 1fwa
Nickel binding site 1 out of 2 in the Klebsiella Aerogenes Urease, C319A Variant at pH 7.5


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, C319A Variant at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni574

b:17.0
occ:0.87
OQ1 C:KCX217 2.0 13.7 1.0
O C:HOH1228 2.1 20.0 0.9
O1 C:CO3999 2.1 26.9 0.0
O C:HOH1229 2.2 20.0 0.8
ND1 C:HIS246 2.2 11.2 1.0
NE2 C:HIS272 2.3 4.7 1.0
O2 C:CO3999 2.3 27.1 0.0
C C:CO3999 2.6 28.7 0.0
CX C:KCX217 3.1 11.9 1.0
CE1 C:HIS246 3.1 14.3 1.0
CD2 C:HIS272 3.1 10.2 1.0
CG C:HIS246 3.2 12.2 1.0
O C:GLY277 3.3 12.8 1.0
CE1 C:HIS272 3.3 7.0 1.0
OQ2 C:KCX217 3.4 9.6 1.0
NE2 C:HIS219 3.6 15.7 1.0
O C:HOH1230 3.7 20.0 1.1
CB C:HIS246 3.7 10.2 1.0
NI C:NI575 3.7 17.0 0.9
O C:HOH1144 3.8 28.7 1.0
O3 C:CO3999 3.9 23.6 0.0
CD2 C:HIS219 4.1 13.1 1.0
NE2 C:HIS246 4.2 16.7 1.0
NZ C:KCX217 4.2 13.8 1.0
C C:GLY277 4.3 12.2 1.0
CD2 C:HIS246 4.3 14.6 1.0
CG C:HIS272 4.3 10.5 1.0
CE1 C:HIS134 4.3 6.5 1.0
ND1 C:HIS272 4.4 11.9 1.0
NE2 C:HIS134 4.4 8.1 1.0
CE1 C:HIS219 4.5 15.2 1.0
OD2 C:ASP360 4.6 17.7 1.0
CE C:KCX217 4.7 11.9 1.0
CA C:HIS246 4.8 13.7 1.0
CA C:GLY278 4.9 6.6 1.0
N C:GLY278 5.0 9.6 1.0

Nickel binding site 2 out of 2 in 1fwa

Go back to Nickel Binding Sites List in 1fwa
Nickel binding site 2 out of 2 in the Klebsiella Aerogenes Urease, C319A Variant at pH 7.5


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, C319A Variant at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni575

b:17.0
occ:0.91
O1 C:CO3999 2.0 26.9 0.0
O C:HOH1228 2.1 20.0 0.9
OQ2 C:KCX217 2.1 9.6 1.0
NE2 C:HIS136 2.1 11.5 1.0
O C:HOH1230 2.2 20.0 1.1
OD1 C:ASP360 2.2 14.1 1.0
NE2 C:HIS134 2.3 8.1 1.0
O3 C:CO3999 2.3 23.6 0.0
C C:CO3999 2.3 28.7 0.0
CG C:ASP360 3.1 12.1 1.0
CD2 C:HIS136 3.1 7.7 1.0
CX C:KCX217 3.1 11.9 1.0
CE1 C:HIS136 3.1 7.5 1.0
CD2 C:HIS134 3.2 8.4 1.0
CE1 C:HIS134 3.3 6.5 1.0
O C:HOH1229 3.4 20.0 0.8
O2 C:CO3999 3.5 27.1 0.0
OD2 C:ASP360 3.5 17.7 1.0
OQ1 C:KCX217 3.5 13.7 1.0
NI C:NI574 3.7 17.0 0.9
CG2 C:THR169 4.0 5.4 1.0
NZ C:KCX217 4.2 13.8 1.0
ND1 C:HIS136 4.2 8.4 1.0
CG C:HIS136 4.3 7.2 1.0
CG C:HIS134 4.3 9.8 1.0
O C:HOH1144 4.3 28.7 1.0
CB C:ASP360 4.3 7.5 1.0
O C:ALA363 4.3 10.6 1.0
ND1 C:HIS134 4.4 10.7 1.0
O C:ALA167 4.5 8.2 1.0
CB C:ALA363 4.6 10.6 1.0
CA C:ASP360 4.6 9.5 1.0
O C:HOH1222 4.9 47.1 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: Wed Dec 16 01:11:49 2020

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