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Nickel in PDB 1krb: Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants

Enzymatic activity of Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants

All present enzymatic activity of Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants, PDB code: 1krb was solved by E.Jabri, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
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 (%) 17.9 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants (pdb code 1krb). 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 Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants, PDB code: 1krb:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1krb

Go back to Nickel Binding Sites List in 1krb
Nickel binding site 1 out of 2 in the Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants


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 Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni574

b:17.3
occ:1.00
OQ2 C:KCX217 2.1 7.7 1.0
ND1 C:HIS246 2.1 9.9 1.0
NE2 C:HIS272 2.4 5.8 1.0
CE1 C:HIS246 2.8 10.0 1.0
O C:HOH577 3.0 27.0 1.0
CX C:KCX217 3.1 7.7 1.0
CG C:HIS246 3.2 9.9 1.0
CE1 C:HIS272 3.3 5.9 1.0
CD2 C:HIS272 3.3 5.9 1.0
OQ1 C:KCX217 3.4 7.6 1.0
O C:GLY277 3.4 8.1 1.0
NI C:NI575 3.5 17.7 1.0
O C:HOH704 3.8 16.5 1.0
CB C:HIS246 3.8 9.8 1.0
NE2 C:HIS246 4.0 10.0 1.0
CD2 C:HIS246 4.2 10.0 1.0
NZ C:KCX217 4.3 7.6 1.0
CE1 C:HIS134 4.3 4.1 1.0
NE2 C:HIS134 4.4 4.1 1.0
ND1 C:HIS272 4.4 6.0 1.0
CG C:HIS272 4.4 6.1 1.0
C C:GLY277 4.5 8.2 1.0
OD2 C:ASP360 4.6 5.7 1.0
CE1 C:HIS320 4.8 20.7 1.0
O C:ALA167 4.8 6.4 1.0
CE C:KCX217 4.8 7.3 1.0
CA C:HIS246 5.0 9.6 1.0

Nickel binding site 2 out of 2 in 1krb

Go back to Nickel Binding Sites List in 1krb
Nickel binding site 2 out of 2 in the Crystal Structure of Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants


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 Klebsiella Aerogenes Urease, Its Apoenzyme and Two Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni575

b:17.7
occ:1.00
O C:HOH577 2.0 27.0 1.0
OQ1 C:KCX217 2.1 7.6 1.0
NE2 C:HIS136 2.2 5.3 1.0
NE2 C:HIS134 2.2 4.1 1.0
OD1 C:ASP360 2.3 5.8 1.0
CX C:KCX217 3.1 7.7 1.0
CG C:ASP360 3.1 5.6 1.0
CE1 C:HIS136 3.1 5.3 1.0
CD2 C:HIS134 3.1 4.1 1.0
CD2 C:HIS136 3.2 5.2 1.0
CE1 C:HIS134 3.2 4.1 1.0
OD2 C:ASP360 3.4 5.7 1.0
OQ2 C:KCX217 3.5 7.7 1.0
NI C:NI574 3.5 17.3 1.0
NZ C:KCX217 4.2 7.6 1.0
CG2 C:THR169 4.3 7.5 1.0
ND1 C:HIS136 4.3 5.2 1.0
ND1 C:HIS134 4.3 4.2 1.0
CG C:HIS134 4.3 4.2 1.0
O C:ALA363 4.3 4.8 1.0
CG C:HIS136 4.3 5.2 1.0
CB C:ASP360 4.4 5.3 1.0
CB C:ALA363 4.5 4.6 1.0
O C:ALA167 4.6 6.4 1.0
O C:HOH704 4.6 16.5 1.0
CA C:ASP360 4.6 5.2 1.0
NE2 C:HIS272 4.8 5.8 1.0
CD2 C:HIS272 4.9 5.9 1.0
OG1 C:THR169 5.0 7.6 1.0
N C:THR169 5.0 7.4 1.0

Reference:

E.Jabri, P.A.Karplus. Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants. Biochemistry V. 35 10616 1996.
ISSN: ISSN 0006-2960
PubMed: 8718850
DOI: 10.1021/BI960424Z
Page generated: Fri Sep 25 07:56:38 2020
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