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Nickel in PDB 1a5n: K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel

Enzymatic activity of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel

All present enzymatic activity of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel:
3.5.1.5;

Protein crystallography data

The structure of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel, PDB code: 1a5n was solved by M.A.Pearson, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
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 (%) 16.7 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel (pdb code 1a5n). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel, PDB code: 1a5n:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1a5n

Go back to Nickel Binding Sites List in 1a5n
Nickel binding site 1 out of 2 in the K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni574

b:17.0
occ:0.42
O1 C:FMT999 1.5 44.8 1.0
C C:FMT999 2.5 34.6 1.0
NE2 C:HIS272 2.5 15.5 1.0
ND1 C:HIS246 2.5 30.0 1.0
O2 C:FMT999 2.8 32.6 1.0
NI C:NI575 3.0 17.0 0.9
CD2 C:HIS272 3.4 14.4 1.0
NE2 C:HIS219 3.4 37.9 1.0
O C:HOH1147 3.4 25.4 1.0
CE1 C:HIS246 3.4 31.8 1.0
CG C:HIS246 3.5 27.3 1.0
CE1 C:HIS272 3.6 12.4 1.0
CE1 C:HIS134 3.6 10.1 1.0
CD2 C:HIS219 3.7 28.0 1.0
NE2 C:HIS134 3.7 8.7 1.0
CB C:HIS246 3.8 21.8 1.0
O C:GLY277 4.1 20.4 1.0
O C:HOH1141 4.3 41.8 1.0
CD2 C:PHE271 4.4 8.4 1.0
OD2 C:ASP360 4.5 9.1 1.0
CE1 C:HIS219 4.5 34.8 1.0
NE2 C:HIS246 4.5 28.5 1.0
CG C:HIS272 4.6 15.2 1.0
CD2 C:HIS246 4.6 26.8 1.0
CB C:PHE271 4.6 10.1 1.0
ND1 C:HIS272 4.6 17.9 1.0
OD1 C:ASP360 4.7 14.4 1.0
CG C:PHE271 4.9 7.6 1.0
ND1 C:HIS134 4.9 16.5 1.0
CG C:HIS219 4.9 27.7 1.0
NE2 C:HIS136 4.9 6.4 1.0
CG C:ASP360 5.0 8.4 1.0

Nickel binding site 2 out of 2 in 1a5n

Go back to Nickel Binding Sites List in 1a5n
Nickel binding site 2 out of 2 in the K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni575

b:17.0
occ:0.92
O C:HOH1147 1.9 25.4 1.0
OD1 C:ASP360 2.0 14.4 1.0
O2 C:FMT999 2.2 32.6 1.0
NE2 C:HIS136 2.3 6.4 1.0
NE2 C:HIS134 2.3 8.7 1.0
CG C:ASP360 2.8 8.4 1.0
NI C:NI574 3.0 17.0 0.4
OD2 C:ASP360 3.0 9.1 1.0
C C:FMT999 3.2 34.6 1.0
CE1 C:HIS134 3.2 10.1 1.0
CE1 C:HIS136 3.2 7.9 1.0
CD2 C:HIS136 3.3 10.1 1.0
CD2 C:HIS134 3.3 10.6 1.0
O1 C:FMT999 3.5 44.8 1.0
O C:HOH1141 4.0 41.8 1.0
O C:ALA363 4.1 21.7 1.0
CB C:ASP360 4.2 5.4 1.0
ND1 C:HIS134 4.3 16.5 1.0
ND1 C:HIS136 4.3 7.2 1.0
CG C:HIS134 4.4 12.1 1.0
CG2 C:THR169 4.4 6.3 1.0
CG C:HIS136 4.4 8.6 1.0
CB C:ALA363 4.4 17.0 1.0
CA C:ASP360 4.6 8.2 1.0
O C:ALA167 4.7 10.7 1.0
NE2 C:HIS272 4.7 15.5 1.0
NE2 C:HIS219 4.7 37.9 1.0
CD2 C:HIS272 4.8 14.4 1.0

Reference:

M.A.Pearson, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger. Chemical Rescue of Klebsiella Aerogenes Urease Variants Lacking the Carbamylated-Lysine Nickel Ligand. Biochemistry V. 37 6214 1998.
ISSN: ISSN 0006-2960
PubMed: 9558361
DOI: 10.1021/BI980021U
Page generated: Wed Dec 16 01:11:29 2020

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